| Previous changeset 0:cad28d7b49d2 (2016-05-27) |
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Commit message:
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit c4f56b2888e1aa876a7137e17330fe1ff057d38b |
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modified:
group_humann2_uniref_abundances_to_go.xml test-data/expected_cellular_component_abundance.txt test-data/humann2_gene_families.csv |
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added:
test-data/map_infogo1000_uniref50_02_22_2016_trimmed.txt |
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removed:
test-data/expected_biological_process_abundance.txt test-data/expected_molecular_function_abundances.txt test-data/go_02_22_2016.obo test-data/map_infogo1000_uniref50_02_22_2016.txt test-data/o_02_22_2016.obo tool_dependencies.xml |
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| diff -r cad28d7b49d2 -r fd2cf7c9d3ec group_humann2_uniref_abundances_to_go.xml --- a/group_humann2_uniref_abundances_to_go.xml Fri May 27 05:58:11 2016 -0400 +++ b/group_humann2_uniref_abundances_to_go.xml Fri Jun 14 11:12:44 2019 -0400 |
| [ |
| @@ -1,11 +1,11 @@ -<tool id="group_humann2_uniref_abundances_to_go" name="Group abundances" version="1.2.0"> +<tool id="group_humann2_uniref_abundances_to_go" name="Group abundances" version="1.2.3"> <description> of UniRef50 gene families obtained (HUMAnN2 output) to Gene Ontology (GO) slim terms</description> <requirements> <requirement type="package" version="1.9">numpy</requirement> - <requirement type="package" version="0.6.1">humann2</requirement> <requirement type="package" version="0.6.4">goatools</requirement> - <requirement type="package" version="1.2.0">group_humann2_uniref_abundances_to_go</requirement> + <requirement type="package" version="0.11.2">humann2</requirement> + <requirement type="package" version="1.3.0">group_humann2_uniref_abundances_to_go</requirement> </requirements> <stdio> @@ -19,26 +19,23 @@ level="fatal" description="PKG Error" /> </stdio> - - <version_command></version_command> - <command><![CDATA[ group_humann2_uniref_abundances_to_GO.sh - -i $humann2_gene_families_abundance - -m $molecular_function_abundance - -b $biological_process_abundance - -c $cellular_component_abundance + -i '$humann2_gene_families_abundance' + -m '$molecular_function_abundance' + -b '$biological_process_abundance' + -c '$cellular_component_abundance' - #if $gene_ontology.gene_ontology_test: - -a $gene_ontology.gene_ontology_file + #if $gene_ontology_file: + -a '$gene_ontology_file' #end if - #if $slim_gene_ontology.slim_gene_ontology_test: - -s $slim_gene_ontology.slim_gene_ontology_file + #if $slim_gene_ontology_file: + -s '$slim_gene_ontology_file' #end if - #if $uniref50_go.uniref50_go_test: - -u $uniref50_go.uniref50_go_file + #if $uniref50_go_file: + -u '$uniref50_go_file' #end if -g `which map_to_slim.py | xargs -n1 dirname` @@ -48,31 +45,11 @@ <inputs> <param name="humann2_gene_families_abundance" type="data" format="tabular,tsv,txt" label="HUMAnN2 output with UniRef50 gene family abundance" help="(-i)"/> - <conditional name="gene_ontology"> - <param name='gene_ontology_test' type='boolean' checked="false" truevalue='true' falsevalue='false' label="Use a custom Gene Ontology file?" help="By default, the used Gene Ontology is the core ontology downloaded on Gene - Ontology website"/> - <when value="true"> - <param name="gene_ontology_file" type="data" format="txt" label="Gene Ontology" help=""/> - </when> - <when value="false" /> - </conditional> + <param name="gene_ontology_file" optional="true" type="data" format="txt" label="Custom Gene Ontology (Optional)" help="By default, the used Gene Ontology is the core ontology downloaded on the Gene Ontology website"/> - <conditional name="slim_gene_ontology"> - <param name='slim_gene_ontology_test' type='boolean' checked="false" truevalue='true' falsevalue='false' label="Use a custom slim Gene Ontology file?" help="By default, the used slim Gene Ontology is the metagenomics slim developed by Jane Lomax and the InterPro group"/> - <when value="true"> - <param name="slim_gene_ontology_file" type="data" format="txt" label="Slim Gene Ontology" help=""/> - </when> - <when value="false" /> - </conditional> + <param name="slim_gene_ontology_file" optional="true" type="data" format="txt" label="Custom Slim Gene Ontology (Optional)" help="By default, the used slim Gene Ontology is the metagenomics slim developed by Jane Lomax and the InterPro group"/> - <conditional name="uniref50_go"> - <param name='uniref50_go_test' type='boolean' checked="false" truevalue='true' falsevalue='false' label="Use a custom correspondance between UniRef50 and precise GO?" help="By default, the used correspondance is the one - proposed in HUMAnN2"/> - <when value="true"> - <param name="uniref50_go_file" type="data" format="txt" label="Correspondance between UniRef50 and GO" help=""/> - </when> - <when value="false" /> - </conditional> + <param name="uniref50_go_file" optional="true" type="data" format="txt" label="Custom correspondance between UniRef50 and GO (Optional)" help="By default, the used correspondance is the one proposed in HUMAnN2"/> </inputs> <outputs> @@ -84,14 +61,8 @@ <tests> <test> <param name="humann2_gene_families_abundance" value="humann2_gene_families.csv"/> - <param name='gene_ontology_test' value='true'/> - <param name="gene_ontology_file" value="go_02_22_2016.obo" /> - <param name='slim_gene_ontology_test' value="true"/> <param name="slim_gene_ontology_file" value="goslim_metagenomics_02_22_2016.obo" /> - <param name='uniref50_go_test' value="true"/> - <param name="uniref50_go_file" value="map_infogo1000_uniref50_02_22_2016.txt"/> - <output name="molecular_function_abundance" file="expected_molecular_function_abundances.txt"/> - <output name="biological_process_abundance" file="expected_biological_process_abundance.txt"/> + <param name="uniref50_go_file" value="map_infogo1000_uniref50_02_22_2016_trimmed.txt"/> <output name="cellular_component_abundance" file="expected_cellular_component_abundance.txt"/> </test> </tests> @@ -101,7 +72,7 @@ HUMAnN2 is a pipeline to profile the presence/absence and abundance of microbial pathways in community of microbiota sequencing data. One output is a file with UniRef50 gene family abundances. HUMAnN2 proposes a script to regroup Uniref50 to GO, but used GO terms are too precise to get a broad overview of the ontology content. -The tool described here contains scripts to group UniRef50 abundances obtained using main HUMANn2 script (Gene families) to GO slim terms. GO slim is a subset of the terms in the whole GO. For this tool, metagenomics GO slim terms developed by Jane Lomax and the InterPro group. +The tool described here contains scripts to group UniRef50 abundances obtained using main HUMAnN2 script (Gene families) to GO slim terms. GO slim is a subset of the terms in the whole GO. For this tool, metagenomics GO slim terms developed by Jane Lomax and the InterPro group. More information on `dedicated GitHub repository <https://github.com/ASaiM/group_humann2_uniref_abundances_to_GO>`_. @@ -123,4 +94,4 @@ <citation type="doi">10.5281/zenodo.31628</citation> <citation type="doi">10.1371/journal.pcbi.1002358</citation> </citations> -</tool> \ No newline at end of file +</tool> |
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| diff -r cad28d7b49d2 -r fd2cf7c9d3ec test-data/expected_biological_process_abundance.txt --- a/test-data/expected_biological_process_abundance.txt Fri May 27 05:58:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,47 +0,0 @@ -GO id GO name Abundance -GO:0000160 phosphorelay signal transduction system 1112.3915515778 -GO:0000746 conjugation 46.559859807600006 -GO:0000902 cell morphogenesis 1.8470267351 -GO:0002376 immune system process 23.700662623200003 -GO:0005975 carbohydrate metabolic process 2612.6970692966993 -GO:0006091 generation of precursor metabolites and energy 943.0642504650992 -GO:0006259 DNA metabolic process 2760.3666308885995 -GO:0006351 transcription, DNA-templated 0.0615114205 -GO:0006412 translation 3280.1516158372006 -GO:0006520 cellular amino acid metabolic process 3953.6382689974002 -GO:0006629 lipid metabolic process 1380.8390328801004 -GO:0006790 sulfur compound metabolic process 1012.3221601218003 -GO:0006807 nitrogen compound metabolic process 3915.4792502578994 -GO:0006810 transport 1101.0465624405 -GO:0006811 ion transport 1276.2633195375001 -GO:0006950 response to stress 954.8641672250999 -GO:0007154 cell communication 316.8910362473 -GO:0007165 signal transduction 45.3316263193 -GO:0008150 biological_process 2784.3062048235997 -GO:0009056 catabolic process 1728.292233976299 -GO:0009058 biosynthetic process 12048.508539055703 -GO:0009117 nucleotide metabolic process 2472.3435074350996 -GO:0009306 protein secretion 23.141466690899996 -GO:0009404 toxin metabolic process 9.095920561400002 -GO:0009405 pathogenesis 58.27509464559998 -GO:0015979 photosynthesis 44.73480409939999 -GO:0016032 viral process 0.7986287266 -GO:0016043 cellular component organization 1246.5641915709 -GO:0016049 cell growth 4.1997618312 -GO:0016070 RNA metabolic process 1855.2220049666994 -GO:0016310 phosphorylation 1372.0241480503992 -GO:0019538 protein metabolic process 672.0486860101004 -GO:0022900 electron transport chain 103.16706894990003 -GO:0030031 cell projection assembly 32.495419504000004 -GO:0032196 transposition 300.7048225378001 -GO:0042592 homeostatic process 306.4798266318999 -GO:0043934 sporulation 174.71346946979997 -GO:0044281 small molecule metabolic process 4445.203127840403 -GO:0045333 cellular respiration 5.518723520100001 -GO:0046034 ATP metabolic process 1002.5305430942991 -GO:0048870 cell motility 107.9960707376 -GO:0051186 cofactor metabolic process 2456.361318531299 -GO:0051301 cell division 864.5391215972995 -GO:0055114 oxidation-reduction process 215.51031499180004 -GO:0071554 cell wall organization or biogenesis 36.7500063207 -GO:0071941 nitrogen cycle metabolic process 56.684053508 |
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| diff -r cad28d7b49d2 -r fd2cf7c9d3ec test-data/expected_cellular_component_abundance.txt --- a/test-data/expected_cellular_component_abundance.txt Fri May 27 05:58:11 2016 -0400 +++ b/test-data/expected_cellular_component_abundance.txt Fri Jun 14 11:12:44 2019 -0400 |
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| @@ -1,25 +1,2 @@ GO id GO name Abundance -GO:0005575 cellular_component 4211.620011669099 -GO:0005618 cell wall 101.24244809220001 -GO:0005634 nucleus 86.82707381589996 -GO:0005694 chromosome 0.0271872006 -GO:0005727 extrachromosomal circular DNA 121.82450720269999 -GO:0005737 cytoplasm 9919.697399687224 -GO:0005739 mitochondrion 193.03667393669969 -GO:0005773 vacuole 2.2073187229999993 -GO:0005783 endoplasmic reticulum 13.858678920100003 -GO:0005794 Golgi apparatus 11.580712904300004 -GO:0005840 ribosome 1635.3364950416994 -GO:0005856 cytoskeleton 0.1781304753 -GO:0005886 plasma membrane 2956.1483673840053 -GO:0009295 nucleoid 56.116239729200025 -GO:0009579 thylakoid 16.531472969800003 -GO:0016020 membrane 76.73590696070002 -GO:0019012 virion 0.2407286574 -GO:0019867 outer membrane 502.1513331402007 -GO:0031012 extracellular matrix 0.5991089999 -GO:0031982 vesicle 81.09742051820007 -GO:0042575 DNA polymerase complex 65.46696539999999 -GO:0042597 periplasmic space 130.1736765559 -GO:0043190 ATP-binding cassette (ABC) transporter complex 271.6521785019997 -GO:0070469 respiratory chain 2.0447839356 +GO:0005739 mitochondrion 68.84 |
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| diff -r cad28d7b49d2 -r fd2cf7c9d3ec test-data/expected_molecular_function_abundances.txt --- a/test-data/expected_molecular_function_abundances.txt Fri May 27 05:58:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,40 +0,0 @@ -GO id GO name Abundance -GO:0000156 phosphorelay response regulator activity 4.4347360838 -GO:0000166 nucleotide binding 11436.730254302318 -GO:0000988 transcription factor activity, protein binding 673.7839975407998 -GO:0003674 molecular_function 4087.6458012782 -GO:0003676 nucleic acid binding 3028.700666733601 -GO:0003924 GTPase activity 490.16358835940014 -GO:0004386 helicase activity 273.26291990489995 -GO:0004518 nuclease activity 708.2423017374001 -GO:0004672 protein kinase activity 626.4942495674997 -GO:0004812 aminoacyl-tRNA ligase activity 234.25362423819996 -GO:0004872 receptor activity 626.4846539767997 -GO:0005102 receptor binding 1.5301407557 -GO:0005215 transporter activity 1762.0709654024004 -GO:0008092 cytoskeletal protein binding 7.383357547800001 -GO:0008134 transcription factor binding 84.63172726779997 -GO:0008233 peptidase activity 1182.3108289962993 -GO:0016298 lipase activity 3.6081972003000002 -GO:0016301 kinase activity 937.2682550285 -GO:0016407 acetyltransferase activity 65.750125095 -GO:0016491 oxidoreductase activity 2051.3275224607996 -GO:0016740 transferase activity 2598.2115822036 -GO:0016746 transferase activity, transferring acyl groups 212.45457835869996 -GO:0016757 transferase activity, transferring glycosyl groups 319.0056774039 -GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups 161.48389564689995 -GO:0016787 hydrolase activity 280.95384492459993 -GO:0016788 hydrolase activity, acting on ester bonds 549.7984070913 -GO:0016791 phosphatase activity 148.29697741039996 -GO:0016798 hydrolase activity, acting on glycosyl bonds 650.9218081131 -GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 428.24025912369996 -GO:0016829 lyase activity 575.0019956493999 -GO:0016853 isomerase activity 1916.3316482209 -GO:0016874 ligase activity 675.5332395482 -GO:0016887 ATPase activity 965.0511058454001 -GO:0030234 enzyme regulator activity 31.695909846600003 -GO:0034061 DNA polymerase activity 290.6773463926 -GO:0034062 RNA polymerase activity 233.7752678209 -GO:0046872 metal ion binding 4116.705081461401 -GO:0048037 cofactor binding 2930.3128404498993 -GO:0051082 unfolded protein binding 203.18389855299998 |
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| diff -r cad28d7b49d2 -r fd2cf7c9d3ec test-data/go_02_22_2016.obo --- a/test-data/go_02_22_2016.obo Fri May 27 05:58:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,597223 +0,0 @@\n-format-version: 1.2\n-data-version: releases/2016-02-20\n-date: 19:02:2016 13:43\n-saved-by: tanyaberardini\n-auto-generated-by: OBO-Edit 2.3.1\n-subsetdef: goantislim_grouping "Grouping classes that can be excluded"\n-subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"\n-subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"\n-subsetdef: goslim_aspergillus "Aspergillus GO slim"\n-subsetdef: goslim_candida "Candida GO slim"\n-subsetdef: goslim_chembl "ChEMBL protein targets summary"\n-subsetdef: goslim_generic "Generic GO slim"\n-subsetdef: goslim_goa "GOA and proteome slim"\n-subsetdef: goslim_metagenomics "Metagenomics GO slim"\n-subsetdef: goslim_pir "PIR GO slim"\n-subsetdef: goslim_plant "Plant GO slim"\n-subsetdef: goslim_pombe "Fission yeast GO slim"\n-subsetdef: goslim_synapse "synapse GO slim"\n-subsetdef: goslim_virus "Viral GO slim"\n-subsetdef: goslim_yeast "Yeast GO slim"\n-subsetdef: gosubset_prok "Prokaryotic GO subset"\n-subsetdef: mf_needs_review "Catalytic activity terms in need of attention"\n-subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"\n-subsetdef: virus_checked "Viral overhaul terms"\n-synonymtypedef: systematic_synonym "Systematic synonym" EXACT\n-default-namespace: gene_ontology\n-remark: cvs version: $Revision: 31531 $\n-ontology: go\n-\n-[Term]\n-id: GO:0000001\n-name: mitochondrion inheritance\n-namespace: biological_process\n-def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764]\n-synonym: "mitochondrial inheritance" EXACT []\n-is_a: GO:0048308 ! organelle inheritance\n-is_a: GO:0048311 ! mitochondrion distribution\n-\n-[Term]\n-id: GO:0000002\n-name: mitochondrial genome maintenance\n-namespace: biological_process\n-def: "The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome." [GOC:ai, GOC:vw]\n-is_a: GO:0007005 ! mitochondrion organization\n-\n-[Term]\n-id: GO:0000003\n-name: reproduction\n-namespace: biological_process\n-alt_id: GO:0019952\n-alt_id: GO:0050876\n-def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732]\n-subset: goslim_chembl\n-subset: goslim_generic\n-subset: goslim_pir\n-subset: goslim_plant\n-subset: gosubset_prok\n-synonym: "reproductive physiological process" EXACT []\n-xref: Wikipedia:Reproduction\n-is_a: GO:0008150 ! biological_process\n-disjoint_from: GO:0044848 ! biological phase\n-\n-[Term]\n-id: GO:0000005\n-name: obsolete ribosomal chaperone activity\n-namespace: molecular_function\n-def: "OBSOLETE. Assists in the correct assembly of ribosomes or ribosomal subunits in vivo, but is not a component of the assembled ribosome when performing its normal biological function." [GOC:jl, PMID:12150913]\n-comment: This term was made obsolete because it refers to a class of gene products and a biological process rather than a molecular function.\n-synonym: "ribosomal chaperone activity" EXACT []\n-is_obsolete: true\n-consider: GO:0042254\n-consider: GO:0044183\n-consider: GO:0051082\n-\n-[Term]\n-id: GO:0000006\n-name: high-affinity zinc uptake transmembrane transporter activity\n-namespace: molecular_function\n-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+(out) = Zn2+(in), probably powered by proton motive force. In high-affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations." [TC:2.A.5.1.1]\n-synonym: "high affinity zinc uptake transmembrane transporter activity" EXACT []\n-is_a: GO:0005385 ! zinc ion transmembrane transporter activity\n-\n-[Term]\n-id: G'..b' GO:2001313 ! UDP-4-deoxy-4-formamido-beta-L-arabinopyranose metabolic process\n-created_by: pr\n-creation_date: 2012-03-22T01:20:05Z\n-\n-[Term]\n-id: GO:2001316\n-name: kojic acid metabolic process\n-namespace: biological_process\n-def: "The chemical reactions and pathways involving kojic acid." [CHEBI:43572, GOC:di]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one metabolic process" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one metabolism" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 metabolic process" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 metabolism" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "kojic acid metabolism" EXACT [GOC:obol]\n-is_a: GO:0034308 ! primary alcohol metabolic process\n-is_a: GO:0042180 ! cellular ketone metabolic process\n-is_a: GO:0046483 ! heterocycle metabolic process\n-is_a: GO:1901360 ! organic cyclic compound metabolic process\n-created_by: rfoulger\n-creation_date: 2012-04-18T09:22:42Z\n-\n-[Term]\n-id: GO:2001317\n-name: kojic acid biosynthetic process\n-namespace: biological_process\n-def: "The chemical reactions and pathways resulting in the formation of kojic acid." [CHEBI:43572, GOC:di]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one anabolism" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one biosynthesis" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one biosynthetic process" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one formation" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one synthesis" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 anabolism" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 biosynthesis" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 biosynthetic process" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 formation" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 synthesis" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "kojic acid anabolism" EXACT [GOC:obol]\n-synonym: "kojic acid biosynthesis" EXACT [GOC:obol]\n-synonym: "kojic acid formation" EXACT [GOC:obol]\n-synonym: "kojic acid synthesis" EXACT [GOC:obol]\n-is_a: GO:0018130 ! heterocycle biosynthetic process\n-is_a: GO:0034309 ! primary alcohol biosynthetic process\n-is_a: GO:0042181 ! ketone biosynthetic process\n-is_a: GO:1901362 ! organic cyclic compound biosynthetic process\n-is_a: GO:2001316 ! kojic acid metabolic process\n-created_by: rfoulger\n-creation_date: 2012-04-18T09:22:46Z\n-\n-[Typedef]\n-id: ends_during\n-name: ends_during\n-namespace: external\n-xref: RO:0002093\n-\n-[Typedef]\n-id: happens_during\n-name: happens_during\n-namespace: external\n-xref: RO:0002092\n-is_transitive: true\n-is_a: ends_during ! ends_during\n-\n-[Typedef]\n-id: has_part\n-name: has_part\n-namespace: external\n-xref: BFO:0000051\n-is_transitive: true\n-\n-[Typedef]\n-id: negatively_regulates\n-name: negatively regulates\n-namespace: external\n-xref: RO:0002212\n-is_a: regulates ! regulates\n-transitive_over: part_of ! part of\n-\n-[Typedef]\n-id: never_in_taxon\n-name: never_in_taxon\n-namespace: external\n-xref: RO:0002161\n-expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y" []\n-is_metadata_tag: true\n-is_class_level: true\n-\n-[Typedef]\n-id: occurs_in\n-name: occurs in\n-namespace: external\n-xref: BFO:0000066\n-holds_over_chain: part_of occurs_in\n-transitive_over: part_of ! part of\n-\n-[Typedef]\n-id: part_of\n-name: part of\n-namespace: external\n-xref: BFO:0000050\n-is_transitive: true\n-inverse_of: has_part ! has_part\n-\n-[Typedef]\n-id: positively_regulates\n-name: positively regulates\n-namespace: external\n-xref: RO:0002213\n-holds_over_chain: negatively_regulates negatively_regulates\n-is_a: regulates ! regulates\n-transitive_over: part_of ! part of\n-\n-[Typedef]\n-id: regulates\n-name: regulates\n-namespace: external\n-xref: RO:0002211\n-is_transitive: true\n-transitive_over: part_of ! part of\n-\n-[Typedef]\n-id: starts_during\n-name: starts_during\n-namespace: external\n-xref: RO:0002091\n-\n' |
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| diff -r cad28d7b49d2 -r fd2cf7c9d3ec test-data/humann2_gene_families.csv --- a/test-data/humann2_gene_families.csv Fri May 27 05:58:11 2016 -0400 +++ b/test-data/humann2_gene_families.csv Fri Jun 14 11:12:44 2019 -0400 |
| b |
| b'@@ -19343,243017 +19343,4 @@\n UniRef50_B2UQ61\t2.1263395375\n UniRef50_UPI000368D15E: MULTISPECIES: hypothetical protein\t2.1262980593\n UniRef50_R6R0Z2\t2.1256067481\n-UniRef50_R5U0R8\t2.1254369173\n-UniRef50_R5B2T7\t2.1253996911\n-UniRef50_D4K9R8: Diguanylate cyclase (GGDEF) domain\t2.1253174959\n-UniRef50_UPI00029A5B10: GTP-binding protein Obg/CgtA\t2.1253053684\n-UniRef50_D6DIW4: Mn-containing catalase\t2.1252628511\n-UniRef50_R6XRM1: Conserved domain protein\t2.1251776727\n-UniRef50_I9VLK3\t2.1250915415\n-UniRef50_R6IWE7: Alpha-N-acetylglucosaminidase\t2.1249967738\n-UniRef50_D1XVA1\t2.1249541547\n-UniRef50_H1A261\t2.1249143546\n-UniRef50_UPI00034DC1F6: hypothetical protein\t2.1247712089\n-UniRef50_UPI000370BC44: hypothetical protein\t2.1245363910\n-UniRef50_UPI0003FA8561: beta-glucosidase\t2.1243762599\n-UniRef50_R6D019\t2.1242068651\n-UniRef50_R5ENA5\t2.1241111600\n-UniRef50_UPI00046FE20A: hypothetical protein\t2.1238477210\n-UniRef50_R7CV67\t2.1236930472\n-UniRef50_R7JHG3: Protein-export membrane protein SecD/SecF\t2.1236897545\n-UniRef50_R6L8R3: Aldose 1-epimerase\t2.1234803843\n-UniRef50_B0MUJ3\t2.1231422505\n-UniRef50_D4K2G4: Response regulator of the LytR/AlgR family\t2.1231422505\n-UniRef50_K1TX91: ABC-type transport system, involved in lipoprotein release, permease component (Fragment)\t2.1231422505\n-UniRef50_O34814: Cell division ATP-binding protein FtsE\t2.1231422505\n-UniRef50_R5ALE4\t2.1231422505\n-UniRef50_R5ZZ62: Transporter gate domain protein\t2.1231422505\n-UniRef50_R6LX35\t2.1231422505\n-UniRef50_R7CTA2: 5-nitroimidazole antibiotic resistance protein\t2.1231422505\n-UniRef50_R7DSG2\t2.1231422505\n-UniRef50_R7JKX7\t2.1231422505\n-UniRef50_UPI0003AAF731: nitroreductase\t2.1231422505\n-UniRef50_W4PQ74: NADH-ubiquinone oxidoreductase chain N\t2.1230986988\n-UniRef50_A8S6R6\t2.1227911115\n-UniRef50_Q73RR5: Glycine--tRNA ligase\t2.1227550794\n-UniRef50_B0NDY5\t2.1226972671\n-UniRef50_K7UZK8\t2.1226967078\n-UniRef50_R6JGZ6\t2.1225569302\n-UniRef50_G2T2N1\t2.1224624320\n-UniRef50_R5WW77\t2.1224207367\n-UniRef50_R7EF78\t2.1223866265\n-UniRef50_R6TH84\t2.1220087858\n-UniRef50_G4KSD2: Putative transposase\t2.1220012777\n-UniRef50_UPI0002EFB599: hypothetical protein\t2.1219035183\n-UniRef50_Q5FL71: Prolipoprotein diacylglyceryl transferase\t2.1218594866\n-UniRef50_UPI00047D203D: hypothetical protein\t2.1217660864\n-UniRef50_UPI00046FE9EE: hypothetical protein\t2.1217363383\n-UniRef50_R9M703\t2.1217253358\n-UniRef50_UPI000466F216: methyltransferase, partial\t2.1215409673\n-UniRef50_R7GP35: 4Fe-4S binding domain protein\t2.1215109149\n-UniRef50_Q5WEG9: Dephospho-CoA kinase\t2.1214637411\n-UniRef50_R6D053: Stage V sporulation protein AD\t2.1212670737\n-UniRef50_UPI00047EA506: MFS transporter\t2.1210325494\n-UniRef50_UPI00038250F8: hypothetical protein, partial\t2.1209851518\n-UniRef50_UPI000404485D: hypothetical protein\t2.1209793874\n-UniRef50_R5IQT2\t2.1208150178\n-UniRef50_R7HJY8\t2.1206470304\n-UniRef50_D4JT75: Cellulase (Glycosyl hydrolase family 5)\t2.1204871683\n-UniRef50_R5GT82\t2.1203786583\n-UniRef50_L2I5G3\t2.1203181195\n-UniRef50_UPI0001B44A6B: aminopeptidase\t2.1201835274\n-UniRef50_UPI00016C0C6A: PemK family transcriptional regulator\t2.1200845309\n-UniRef50_Q9RCA1: DNA polymerase III subunit beta\t2.1198832616\n-UniRef50_R7ILZ7\t2.1197959963\n-UniRef50_R7N6I1: Thiamine pyrophosphate protein domain protein TPP-binding\t2.1197844441\n-UniRef50_C0D2R2\t2.1196663632\n-UniRef50_UPI00031520C8: hypothetical protein\t2.1196271107\n-UniRef50_U6Q383\t2.1193933984\n-UniRef50_R5IRC1\t2.1193437355\n-UniRef50_Q4EGL3\t2.1192860279\n-UniRef50_UPI00046748E9: phosphotyrosine protein phosphatase\t2.1192843519\n-UniRef50_D4JSS7: DNA polymerase III, delta subunit\t2.1192402197\n-UniRef50_R5WK50\t2.1189397636\n-UniRef50_UPI0003FC4FE6: hypothetical protein\t2.1188532567\n-UniRef50_R7JM06\t2.1188302136\n-UniRef50_D4KWJ7: Carbohydrate ABC transporter substrate-binding protein, CUT1 family (TC 3.A.1.1.-)\t2.1186097857\n-UniRef50_R6Q8X3: ABC transporter substrate-binding protein family 5\t2.1186078878\n-UniRef50_G6C259\t2.1183573040\n-UniRef50_F4XCR5\t2.1183247305\n-UniRef50_R6Z2Y9: O'..b'954\n-UniRef50_U6MSM9\t0.0011965468\n-UniRef50_F0VFF5: NLI interacting factor-like phosphatase domain-containing protein\t0.0011959757\n-UniRef50_B8FR62: Putative cell wall binding repeat 2-containing protein\t0.0011666455\n-UniRef50_U6LM67\t0.0011647859\n-UniRef50_Q0B8X3: Peptidoglycan-binding LysM\t0.0011536482\n-UniRef50_U6LQ59: Oxysterol-binding protein, putative\t0.0011517523\n-UniRef50_UPI000359AA1F\t0.0011490494\n-UniRef50_V4ZWS2\t0.0011479842\n-UniRef50_UPI000185D8BE: hypothetical protein TGME49_070730\t0.0011469376\n-UniRef50_U6GBK4\t0.0011001954\n-UniRef50_UPI000378A2B2: hypothetical protein\t0.0010981606\n-UniRef50_D7FYV2\t0.0010914836\n-UniRef50_M1GDM0\t0.0010904319\n-UniRef50_U6N0W5\t0.0010903061\n-UniRef50_X1XYJ5\t0.0010820624\n-UniRef50_UPI0001AF2BF7: hypothetical protein, partial\t0.0010488365\n-UniRef50_F0VF93: Leucine rich repeat containing protein / ankyrin repeat containing protein\t0.0010223409\n-UniRef50_F0VNR1\t0.0010214275\n-UniRef50_UPI0003631483: hypothetical protein\t0.0010189849\n-UniRef50_F0VCV6\t0.0010050266\n-UniRef50_D2E8D4: Protein ORF83\t0.0009938652\n-UniRef50_B3L8W7\t0.0009832699\n-UniRef50_UPI0004545162: PREDICTED: LOW QUALITY PROTEIN: histone-lysine N-methyltransferase 2D, partial\t0.0009680217\n-UniRef50_UPI0003A778AD: hypothetical protein\t0.0009629950\n-UniRef50_B4MT58: GK20098\t0.0009553027\n-UniRef50_U6GVJ1\t0.0009486734\n-UniRef50_L0M6B5\t0.0009363698\n-UniRef50_UPI00045725E2: PREDICTED: LOW QUALITY PROTEIN: collagen alpha-3(VI) chain\t0.0009350960\n-UniRef50_UPI0003B680A3: hypothetical protein\t0.0009303525\n-UniRef50_UPI0004561B03: hypothetical protein PFL1_03196\t0.0009273358\n-UniRef50_E6RNZ7\t0.0009165506\n-UniRef50_UPI00044441FD: PREDICTED: hemicentin-1\t0.0009152235\n-UniRef50_A0A058Z170\t0.0009134866\n-UniRef50_U3JEJ7\t0.0009005083\n-UniRef50_UPI00036A6291: hypothetical protein\t0.0008978087\n-UniRef50_F4QIB0: Outer membrane autotransporter barrel domain protein\t0.0008881072\n-UniRef50_U6GK87\t0.0008878935\n-UniRef50_UPI0003836527: PREDICTED: collagen alpha-4(VI) chain\t0.0008775396\n-UniRef50_UPI0004445290: PREDICTED: trinucleotide repeat-containing gene 18 protein\t0.0008733433\n-UniRef50_W9PH85\t0.0008632389\n-UniRef50_UPI000444A032: hypothetical protein STEHIDRAFT_170927\t0.0008621167\n-UniRef50_UPI000273C102\t0.0008557976\n-UniRef50_UPI0003F1A505: PREDICTED: spectrin beta chain, non-erythrocytic 4\t0.0008485597\n-UniRef50_Q89ZD7\t0.0008459523\n-UniRef50_B2A8V7: Podospora anserina S mat+ genomic DNA chromosome 1, supercontig 1\t0.0008342783\n-UniRef50_F0V7P3: Putative SET domain-containing protein\t0.0008127623\n-UniRef50_UPI00034F3DF3\t0.0008068023\n-UniRef50_Q18DY9: Cell surface glycoprotein\t0.0007961722\n-UniRef50_UPI00022478B3: PREDICTED: hypothetical protein LOC100679692\t0.0007839742\n-UniRef50_C1EHI5: Predicted protein\t0.0007696542\n-UniRef50_A8IXH7: Predicted protein (Fragment)\t0.0007631858\n-UniRef50_F0VMX2\t0.0007580465\n-UniRef50_UPI000350FB63: PREDICTED: tenascin-X\t0.0007536189\n-UniRef50_G0SBI6\t0.0007534253\n-UniRef50_F4W8Q4\t0.0007410022\n-UniRef50_Q0RLJ2\t0.0007364271\n-UniRef50_UPI0003EC164A: PREDICTED: titin-like\t0.0007344948\n-UniRef50_G1XEY7\t0.0007281788\n-UniRef50_E2ARB2: Titin\t0.0007131677\n-UniRef50_UPI0003D0722E: PREDICTED: LOW QUALITY PROTEIN: titin\t0.0006937288\n-UniRef50_G6D6Y2\t0.0006776634\n-UniRef50_UPI000328967C: PREDICTED: LOW QUALITY PROTEIN: tenascin-X\t0.0006549464\n-UniRef50_UPI00046BEF15: PREDICTED: titin\t0.0006449421\n-UniRef50_U6MUQ3\t0.0006155478\n-UniRef50_UPI0002B4C97A: PREDICTED: hydrocephalus-inducing protein homolog\t0.0005870219\n-UniRef50_UPI000302F3DC: hypothetical protein\t0.0005564568\n-UniRef50_E9BX32\t0.0005394883\n-UniRef50_E3GPY4: TPR repeat-containing cell adhesion protein\t0.0005228216\n-UniRef50_UPI0003316881\t0.0005073666\n-UniRef50_A5K9D5\t0.0004675759\n-UniRef50_V4Z5P5\t0.0004671084\n-UniRef50_UPI0003BBD5E2: PREDICTED: mucin-5B\t0.0004041705\n-UniRef50_D8U832\t0.0003381003\n-UniRef50_UPI0003691979: hypothetical protein\t0.0003177584\n-UniRef50_UPI0003C020B8: PREDICTED: mucin-5B\t0.0002890962\n+UniRef50_R5U0R8\t2.1254369173\n\\ No newline at end of file\n' |
| b |
| diff -r cad28d7b49d2 -r fd2cf7c9d3ec test-data/map_infogo1000_uniref50_02_22_2016.txt --- a/test-data/map_infogo1000_uniref50_02_22_2016.txt Fri May 27 05:58:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,931 +0,0 @@\n-GO:0006596:BP:07:polyamine biosynthetic 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|
| b |
| diff -r cad28d7b49d2 -r fd2cf7c9d3ec test-data/map_infogo1000_uniref50_02_22_2016_trimmed.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/map_infogo1000_uniref50_02_22_2016_trimmed.txt Fri Jun 14 11:12:44 2019 -0400 |
| b |
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| diff -r cad28d7b49d2 -r fd2cf7c9d3ec test-data/o_02_22_2016.obo --- a/test-data/o_02_22_2016.obo Fri May 27 05:58:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,602460 +0,0 @@\n-format-version: 1.2\n-data-version: releases/2016-04-19\n-date: 18:04:2016 13:50\n-saved-by: bf\n-auto-generated-by: TermGenie 1.0\n-subsetdef: goantislim_grouping "Grouping classes that can be excluded"\n-subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"\n-subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"\n-subsetdef: goslim_aspergillus "Aspergillus GO slim"\n-subsetdef: goslim_candida "Candida GO slim"\n-subsetdef: goslim_chembl "ChEMBL protein targets summary"\n-subsetdef: goslim_generic "Generic GO slim"\n-subsetdef: goslim_goa "GOA and proteome slim"\n-subsetdef: goslim_metagenomics "Metagenomics GO slim"\n-subsetdef: goslim_pir "PIR GO slim"\n-subsetdef: goslim_plant "Plant GO slim"\n-subsetdef: goslim_pombe "Fission yeast GO slim"\n-subsetdef: goslim_synapse "synapse GO slim"\n-subsetdef: goslim_virus "Viral GO slim"\n-subsetdef: goslim_yeast "Yeast GO slim"\n-subsetdef: gosubset_prok "Prokaryotic GO subset"\n-subsetdef: mf_needs_review "Catalytic activity terms in need of attention"\n-subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"\n-subsetdef: virus_checked "Viral overhaul terms"\n-synonymtypedef: systematic_synonym "Systematic synonym" EXACT\n-default-namespace: gene_ontology\n-remark: cvs version: $Revision: 32767 $\n-ontology: go\n-\n-[Term]\n-id: GO:0000001\n-name: mitochondrion inheritance\n-namespace: biological_process\n-def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764]\n-synonym: "mitochondrial inheritance" EXACT []\n-is_a: GO:0048308 ! organelle inheritance\n-is_a: GO:0048311 ! mitochondrion distribution\n-\n-[Term]\n-id: GO:0000002\n-name: mitochondrial genome maintenance\n-namespace: biological_process\n-def: "The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome." [GOC:ai, GOC:vw]\n-is_a: GO:0007005 ! mitochondrion organization\n-\n-[Term]\n-id: GO:0000003\n-name: reproduction\n-namespace: biological_process\n-alt_id: GO:0019952\n-alt_id: GO:0050876\n-def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732]\n-subset: goslim_chembl\n-subset: goslim_generic\n-subset: goslim_pir\n-subset: goslim_plant\n-subset: gosubset_prok\n-synonym: "reproductive physiological process" EXACT []\n-xref: Wikipedia:Reproduction\n-is_a: GO:0008150 ! biological_process\n-disjoint_from: GO:0044848 ! biological phase\n-\n-[Term]\n-id: GO:0000005\n-name: obsolete ribosomal chaperone activity\n-namespace: molecular_function\n-def: "OBSOLETE. Assists in the correct assembly of ribosomes or ribosomal subunits in vivo, but is not a component of the assembled ribosome when performing its normal biological function." [GOC:jl, PMID:12150913]\n-comment: This term was made obsolete because it refers to a class of gene products and a biological process rather than a molecular function.\n-synonym: "ribosomal chaperone activity" EXACT []\n-is_obsolete: true\n-consider: GO:0042254\n-consider: GO:0044183\n-consider: GO:0051082\n-\n-[Term]\n-id: GO:0000006\n-name: high-affinity zinc uptake transmembrane transporter activity\n-namespace: molecular_function\n-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+(out) = Zn2+(in), probably powered by proton motive force. In high-affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations." [TC:2.A.5.1.1]\n-synonym: "high affinity zinc uptake transmembrane transporter activity" EXACT []\n-is_a: GO:0005385 ! zinc ion transmembrane transporter activity\n-\n-[Term]\n-id: GO:0000007\n-na'..b' GO:2001313 ! UDP-4-deoxy-4-formamido-beta-L-arabinopyranose metabolic process\n-created_by: pr\n-creation_date: 2012-03-22T01:20:05Z\n-\n-[Term]\n-id: GO:2001316\n-name: kojic acid metabolic process\n-namespace: biological_process\n-def: "The chemical reactions and pathways involving kojic acid." [CHEBI:43572, GOC:di]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one metabolic process" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one metabolism" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 metabolic process" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 metabolism" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "kojic acid metabolism" EXACT [GOC:obol]\n-is_a: GO:0034308 ! primary alcohol metabolic process\n-is_a: GO:0042180 ! cellular ketone metabolic process\n-is_a: GO:0046483 ! heterocycle metabolic process\n-is_a: GO:1901360 ! organic cyclic compound metabolic process\n-created_by: rfoulger\n-creation_date: 2012-04-18T09:22:42Z\n-\n-[Term]\n-id: GO:2001317\n-name: kojic acid biosynthetic process\n-namespace: biological_process\n-def: "The chemical reactions and pathways resulting in the formation of kojic acid." [CHEBI:43572, GOC:di]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one anabolism" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one biosynthesis" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one biosynthetic process" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one formation" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one synthesis" EXACT [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 anabolism" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 biosynthesis" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 biosynthetic process" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 formation" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "C6H6O4 synthesis" RELATED [CHEBI:43572, GOC:obol]\n-synonym: "kojic acid anabolism" EXACT [GOC:obol]\n-synonym: "kojic acid biosynthesis" EXACT [GOC:obol]\n-synonym: "kojic acid formation" EXACT [GOC:obol]\n-synonym: "kojic acid synthesis" EXACT [GOC:obol]\n-is_a: GO:0018130 ! heterocycle biosynthetic process\n-is_a: GO:0034309 ! primary alcohol biosynthetic process\n-is_a: GO:0042181 ! ketone biosynthetic process\n-is_a: GO:1901362 ! organic cyclic compound biosynthetic process\n-is_a: GO:2001316 ! kojic acid metabolic process\n-created_by: rfoulger\n-creation_date: 2012-04-18T09:22:46Z\n-\n-[Typedef]\n-id: ends_during\n-name: ends_during\n-namespace: external\n-xref: RO:0002093\n-\n-[Typedef]\n-id: happens_during\n-name: happens_during\n-namespace: external\n-xref: RO:0002092\n-is_transitive: true\n-is_a: ends_during ! ends_during\n-\n-[Typedef]\n-id: has_part\n-name: has_part\n-namespace: external\n-xref: BFO:0000051\n-is_transitive: true\n-\n-[Typedef]\n-id: negatively_regulates\n-name: negatively regulates\n-namespace: external\n-xref: RO:0002212\n-is_a: regulates ! regulates\n-transitive_over: part_of ! part of\n-\n-[Typedef]\n-id: never_in_taxon\n-name: never_in_taxon\n-namespace: external\n-xref: RO:0002161\n-expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y" []\n-is_metadata_tag: true\n-is_class_level: true\n-\n-[Typedef]\n-id: occurs_in\n-name: occurs in\n-namespace: external\n-xref: BFO:0000066\n-holds_over_chain: part_of occurs_in\n-transitive_over: part_of ! part of\n-\n-[Typedef]\n-id: part_of\n-name: part of\n-namespace: external\n-xref: BFO:0000050\n-is_transitive: true\n-inverse_of: has_part ! has_part\n-\n-[Typedef]\n-id: positively_regulates\n-name: positively regulates\n-namespace: external\n-xref: RO:0002213\n-holds_over_chain: negatively_regulates negatively_regulates\n-is_a: regulates ! regulates\n-transitive_over: part_of ! part of\n-\n-[Typedef]\n-id: regulates\n-name: regulates\n-namespace: external\n-xref: RO:0002211\n-is_transitive: true\n-transitive_over: part_of ! part of\n-\n-[Typedef]\n-id: starts_during\n-name: starts_during\n-namespace: external\n-xref: RO:0002091\n-\n' |
| b |
| diff -r cad28d7b49d2 -r fd2cf7c9d3ec tool_dependencies.xml --- a/tool_dependencies.xml Fri May 27 05:58:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="numpy" version="1.9"> - <repository changeset_revision="57b37f63cb84" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="humann2" version="0.6.1"> - <repository changeset_revision="655e87ac3364" name="package_humann2_0_6_1" owner="bebatut" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="goatools" version="0.6.4"> - <repository changeset_revision="25b614b3491f" name="package_goatools_0_6_4" owner="bebatut" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="group_humann2_uniref_abundances_to_go" version="1.2.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://github.com/ASaiM/group_humann2_uniref_abundances_to_GO/archive/v1.2.0.zip</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/</destination_directory> - </action> - <action type="set_environment"> - <environment_variable action="set_to" name="GROUP_UNIREF_GO_DIR">$INSTALL_DIR/</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme /> - </package> -</tool_dependency> |