| Previous changeset 8:7863f1abcdda (2022-07-02) |
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Commit message:
planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 |
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modified:
unipept.xml |
| b |
| diff -r 7863f1abcdda -r 21a560af5913 unipept.xml --- a/unipept.xml Sat Jul 02 13:46:38 2022 +0000 +++ b/unipept.xml Tue Mar 12 11:44:08 2024 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="unipept" name="Unipept" version="4.5.1">\n+<tool id="unipept" name="Unipept" version="4.5.1" profile="22.05">\n <description>retrieve taxonomy for peptides</description>\n <macros>\n <xml name="equate_il">\n@@ -17,10 +17,10 @@\n </param>\n </xml>\n <xml name="names">\n- <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >\n+ <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names">\n <help>return the names in complete taxonomic lineage</help>\n </param>\n- <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >\n+ <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields">\n <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>\n </param>\n </xml>\n@@ -39,13 +39,13 @@\n </param>\n </xml>\n </macros>\n+ <xrefs>\n+ <xref type="bio.tools">unipept</xref>\n+ </xrefs>\n <requirements>\n <requirement type="package" version="3">python</requirement>\n </requirements>\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n- <command><![CDATA[\n+ <command detect_errors="exit_code"><![CDATA[\n python \'$__tool_directory__/unipept.py\' \n ## --url \'http://morty.ugent.be/api/v1\' -g -M 1 \n --api=$unipept.api\n@@ -106,142 +106,142 @@\n #end if\n ]]></command>\n <inputs>\n- <conditional name="unipept">\n- <param name="api" type="select" label="Unipept application" >\n- <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>\n- <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>\n- <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>\n- <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>\n- <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>\n- <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option>\n- <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>\n- <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>\n- </param>\n- <when value="pept2lca">\n- <expand macro="equate_il" />\n- <expand macro="extra">\n- <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>\n- </expand>\n- <expand macro="names" />\n- </when>\n- <when value="pept2taxa">\n- <expand macro="equate_il" />\n- <expand macro="extra_true">\n- <help>Return the complete lineage of each organism, and include ID fields.</help>\n- </expand>\n- <expand macro="names" />\n- </when>\n- <when value="pept2prot">\n- <expand macro="equate_il" />\n- <expand macro="extra">\n- <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids\n+ <conditional name="unipept">\n+ <param name="api" type="select" label="Unipept application">\n+ <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>\n+ <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>\n+ <option value'..b' <has_text text="GO:0004802"/>\n+ <has_text text="2.2.1.1"/>\n+ <has_text text="IPR005475"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_ec_tsv">\n+ <assert_contents>\n+ <has_text text="2.2.1.1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_go_tsv">\n+ <assert_contents>\n+ <has_text text="GO:0004802"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_ipr_tsv">\n+ <assert_contents>\n+ <has_text text="IPR005475"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test-5 -->\n+ <test expect_num_outputs="5">\n+ <param name="api" value="pept2funct"/>\n+ <param name="fmt" value="tabular"/>\n+ <param name="input_tsv" value="input.tsv"/>\n+ <param name="column" value="2"/>\n+ <param name="extra" value="True"/>\n+ <param name="names" value="True"/>\n+ <param name="peptide_match" value="full"/>\n+ <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>\n+ <output name="output_tsv">\n+ <assert_contents>\n+ <has_text text="GO:0004802"/>\n+ <has_text text="2.2.1.1"/>\n+ <has_text text="IPR005475"/>\n+ <has_text_matching expression="FAPLLEEYKAEDWVQK\\t0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_ec_tsv">\n+ <assert_contents>\n+ <has_text text="2.2.1.1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_go_tsv">\n+ <assert_contents>\n+ <has_text text="GO:0004802"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_ipr_tsv">\n+ <assert_contents>\n+ <has_text text="IPR005475"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test-6 -->\n+ <test expect_num_outputs="5">\n+ <param name="api" value="pept2funct"/>\n+ <param name="fmt" value="tabular"/>\n+ <param name="input_tsv" value="input.tsv"/>\n+ <param name="column" value="2"/>\n+ <param name="extra" value="True"/>\n+ <param name="names" value="True"/>\n+ <param name="peptide_match" value="report"/>\n+ <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>\n+ <output name="output_tsv">\n+ <assert_contents>\n+ <has_text text="GO:0004802"/>\n+ <has_text text="2.2.1.1"/>\n+ <has_text text="IPR005475"/>\n+ <has_text_matching expression="AAEGGLSR\\tAAEGGLSR\\t6"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_ec_tsv">\n+ <assert_contents>\n+ <has_text text="2.2.1.1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_go_tsv">\n+ <assert_contents>\n+ <has_text text="GO:0004802"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_ipr_tsv">\n+ <assert_contents>\n+ <has_text text="IPR005475"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help><![CDATA[\n **Unipept** \n@@ -637,8 +636,7 @@\n DOI: 10.1002/pmic.201400361\n \n ]]></help>\n- <citations>\n- <citation type="doi">doi:10.1002/pmic.201400361</citation>\n- </citations>\n-\n+ <citations>\n+ <citation type="doi">doi:10.1002/pmic.201400361</citation>\n+ </citations>\n </tool>\n' |