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cloud-tool-conf-apr-2021
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| <?xml version="1.0" encoding="UTF-8"?> | |
| <toolbox tool_path="/cvmfs/cloud.galaxyproject.org/tools" tool_cache_data_dir="/cvmfs/cloud.galaxyproject.org/var/tool_cache"> | |
| <section id="virology" name="Virology" version=""> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/db536ad45f28/ivar_trim/ivar_trim.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>ivar_trim</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>db536ad45f28</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1</id> | |
| <version>1.2.2+galaxy1</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ee2beb764a7b/ivar_removereads/ivar_removereads.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>ivar_removereads</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ee2beb764a7b</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1</id> | |
| <version>1.2.2+galaxy1</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/2a3a00c1fa0a/snpeff_sars_cov_2/snpEff.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>snpeff_sars_cov_2</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>2a3a00c1fa0a</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19</id> | |
| <version>4.5covid19</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/78bbd17d0703/ivar_consensus/ivar_consensus.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>ivar_consensus</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>78bbd17d0703</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0</id> | |
| <version>1.2.2+galaxy0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/7fe36019c073/ivar_filtervariants/ivar_filtervariants.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>ivar_filtervariants</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>7fe36019c073</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0</id> | |
| <version>1.2.2+galaxy0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/2cf4a1cafc16/ivar_getmasked/ivar_getmasked.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>ivar_getmasked</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>2cf4a1cafc16</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0</id> | |
| <version>1.2.2+galaxy0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/f95f403841ad/ivar_variants/ivar_variants.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>ivar_variants</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>f95f403841ad</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0</id> | |
| <version>1.2.2+galaxy0</version> | |
| </tool> | |
| </section> | |
| <section id="vcf_bcf" name="VCF/BCF" version=""> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/d6dc477167f8/bcftools_consensus/bcftools_consensus.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_consensus</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>d6dc477167f8</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1</id> | |
| <version>1.10+galaxy1</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/672b6c02fbc7/bcftools_gtcheck/bcftools_gtcheck.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_gtcheck</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>672b6c02fbc7</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10</id> | |
| <version>1.10</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/365325116147/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_plugin_fixploidy</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>365325116147</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10</id> | |
| <version>1.10</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/fec517907949/bcftools_convert_to_vcf/bcftools_convert_to_vcf.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_convert_to_vcf</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>fec517907949</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10</id> | |
| <version>1.10</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/c077f71d351f/bcftools_norm/bcftools_norm.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_norm</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>c077f71d351f</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10</id> | |
| <version>1.10</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/ed4ea9de1791/bcftools_query_list_samples/bcftools_query_list_samples.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_query_list_samples</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ed4ea9de1791</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10</id> | |
| <version>1.10</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/dfef7a353ed0/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_plugin_missing2ref</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>dfef7a353ed0</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10</id> | |
| <version>1.10</version> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/01d6b7d6365e/bcftools_cnv/bcftools_cnv.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_cnv</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>01d6b7d6365e</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10</id> | |
| <version>1.10</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/8abfcd1a6949/bcftools_plugin_setgt/bcftools_plugin_setgt.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_plugin_setgt</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10</id> | |
| <version>1.10</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/4813f99d81b7/bcftools_plugin_counts/bcftools_plugin_counts.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_plugin_counts</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>4813f99d81b7</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1</id> | |
| <version>1.10+galaxy1</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/0dbff46d5a1b/bcftools_mpileup/bcftools_mpileup.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_mpileup</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10</id> | |
| <version>1.10</version> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bf235558f2cf/bcftools_plugin_mendelian/bcftools_plugin_mendelian.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_plugin_mendelian</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <id>toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10</id> | |
| <version>1.10</version> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/d40d4bf05718/bcftools_concat/bcftools_concat.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bcftools_concat</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <version>1.10</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/b8e9da766b0f/bcftools_convert_from_vcf/bcftools_convert_from_vcf.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10"> | |
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| <repository_name>bcftools_convert_from_vcf</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/776ad0b21536/bcftools_plugin_impute_info/bcftools_plugin_impute_info.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10"> | |
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| <repository_name>bcftools_plugin_impute_info</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <repository_name>bcftools_reheader</repository_name> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/bedtools/mapBed.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bedtools</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ce3c7f062223</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2</id> | |
| <version>2.30.0.2</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/bedtools/intersectBed.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bedtools</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ce3c7f062223</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0</id> | |
| <version>2.30.0</version> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/bedtools/maskFastaBed.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bedtools</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ce3c7f062223</installed_changeset_revision> | |
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| <version>2.30.0</version> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/bedtools/tagBed.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bedtools</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ce3c7f062223</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0</id> | |
| <version>2.30.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/bedtools/groupbyBed.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bedtools</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ce3c7f062223</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0</id> | |
| <version>2.30.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/bedtools/bedpeToBam.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bedtools</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ce3c7f062223</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0</id> | |
| <version>2.30.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/bedtools/spacingBed.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bedtools</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ce3c7f062223</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0</id> | |
| <version>2.30.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/bedtools/genomeCoverageBed.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bedtools</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ce3c7f062223</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0</id> | |
| <version>2.30.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/bedtools/fisherBed.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bedtools</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>ce3c7f062223</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0</id> | |
| <version>2.30.0</version> | |
| </tool> | |
| </section> | |
| <section id="collection_operations" name="Collection Operations" version=""> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/90981f86000f/collapse_collections/merge.xml" guid="toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>collapse_collections</repository_name> | |
| <repository_owner>nml</repository_owner> | |
| <installed_changeset_revision>90981f86000f</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0</id> | |
| <version>5.1.0</version> | |
| </tool> | |
| </section> | |
| <section id="collection_operations" name="Collection Operations" version=""> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>split_file_to_collection</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>6cbe2f30c2d7</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0</id> | |
| <version>0.5.0</version> | |
| </tool> | |
| </section> | |
| <section id="collection_operations" name="Collection Operations" version=""> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/d3c07d270a50/collection_element_identifiers/collection_element_identifiers.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>collection_element_identifiers</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>d3c07d270a50</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2</id> | |
| <version>0.0.2</version> | |
| </tool> | |
| </section> | |
| <section id="collection_operations" name="Collection Operations" version=""> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/071084070619/collection_column_join/collection_column_join.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>collection_column_join</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
| <installed_changeset_revision>071084070619</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3</id> | |
| <version>0.0.3</version> | |
| </tool> | |
| </section> | |
| <section id="deeptools" name="deepTools" version=""> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/514fa53b5efb/deeptools_compute_matrix/computeMatrix.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_compute_matrix</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>514fa53b5efb</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/a4dfb122e52b/deeptools_plot_heatmap/plotHeatmap.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_plot_heatmap</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>a4dfb122e52b</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1</id> | |
| <version>3.3.2.0.1</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/e821645ef8fc/deeptools_bam_compare/bamCompare.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_bam_compare</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>e821645ef8fc</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/62eb6d63f582/deeptools_bam_pe_fragmentsize/bamPEFragmentSize.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_bam_pe_fragmentsize</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>62eb6d63f582</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/26e7304d6737/deeptools_bigwig_compare/bigwigCompare.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_bigwig_compare</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>26e7304d6737</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/2bc10a9ca58b/deeptools_compute_gc_bias/computeGCBias.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_compute_gc_bias</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>2bc10a9ca58b</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/2c37ce318bc3/deeptools_correct_gc_bias/correctGCBias.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_correct_gc_bias</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>2c37ce318bc3</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/78f405266706/deeptools_multi_bam_summary/multiBamSummary.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_multi_bam_summary</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>78f405266706</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/3c9f0c486cca/deeptools_multi_bigwig_summary/multiBigwigSummary.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_multi_bigwig_summary</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>3c9f0c486cca</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/32e451def88c/deeptools_plot_correlation/plotCorrelation.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_plot_correlation</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>32e451def88c</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/56bce3c82278/deeptools_plot_coverage/plotCoverage.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_plot_coverage</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
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| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/e65d16fb2724/deeptools_plot_enrichment/plotEnrichment.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_plot_enrichment</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>e65d16fb2724</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/2da482e408b8/deeptools_plot_fingerprint/plotFingerprint.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_plot_fingerprint</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>2da482e408b8</installed_changeset_revision> | |
| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/69264da0ce77/deeptools_plot_pca/plotPCA.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_plot_pca</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
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| <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.3.2.0.0</id> | |
| <version>3.3.2.0.0</version> | |
| </tool> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/bb1e4f63e0e6/deeptools_bam_coverage/bamCoverage.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_bam_coverage</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
| <installed_changeset_revision>bb1e4f63e0e6</installed_changeset_revision> | |
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| <version>3.3.2.0.0</version> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/c361b12d207a/deeptools_plot_profile/plotProfiler.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.2.0.0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>deeptools_plot_profile</repository_name> | |
| <repository_owner>bgruening</repository_owner> | |
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| <section id="fastq_quality_control" name="FASTQ Quality Control" version=""> | |
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| <repository_name>fastp</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <repository_name>fastqc</repository_name> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/d94aff5ee623/trimmomatic/trimmomatic.xml" guid="toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"> | |
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| </section> | |
| <section id="get_data" name="Get Data" version=""> | |
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| <repository_name>sra_tools</repository_name> | |
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| <repository_name>sra_tools</repository_name> | |
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| <repository_name>sra_tools</repository_name> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/1c58de56d587/ncbi_acc_download/ncbi_acc_download.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0"> | |
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| <repository_name>ncbi_acc_download</repository_name> | |
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| </section> | |
| <section id="graph_display_data" name="Graph/Display Data" version=""> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/circos/tiles-from-interval.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/circos/tableviewer.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7"> | |
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| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <id>toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7</id> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/circos/text-from-interval.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <repository_name>circos</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <id>toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7</id> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/4542035c1075/jbrowse/jbrowse.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>jbrowse</repository_name> | |
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| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>jbrowse</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/73b8cb5bddcd/volcanoplot/volcanoplot.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>volcanoplot</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <section id="mapping" name="Mapping" version=""> | |
| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/minimap2/f54f5baedfdd/minimap2/minimap2.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4"> | |
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| <repository_name>minimap2</repository_name> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/09b2cdb7ace5/bowtie2/bowtie2_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bowtie2</repository_name> | |
| <repository_owner>devteam</repository_owner> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bwa/3fe632431b68/bwa/bwa.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bwa</repository_name> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bwa/3fe632431b68/bwa/bwa-mem.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1"> | |
| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>bwa</repository_name> | |
| <repository_owner>devteam</repository_owner> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bwameth/29bdbc353f20/bwameth/bwameth.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2"> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/devteam/lastz/e7f19d6a9af8/lastz/lastz.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2"> | |
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| <section id="multiple_alignments" name="Multiple Alignments" version=""> | |
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| <repository_name>snpeff</repository_name> | |
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| <tool file="toolshed.g2.bx.psu.edu/repos/iuc/snpsift/2e497a770bca/snpsift/snpSift_vcfCheck.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0"> | |
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| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>snpsift</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>snpsift</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
| <repository_name>snpsift</repository_name> | |
| <repository_owner>iuc</repository_owner> | |
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| </tool> | |
| </section> | |
| </toolbox> |
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