Mercurial > repos > galaxyp > unipept
changeset 9:21a560af5913 draft default tip
planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7
| author | galaxyp |
|---|---|
| date | Tue, 12 Mar 2024 11:44:08 +0000 |
| parents | 7863f1abcdda |
| children | |
| files | unipept.xml |
| diffstat | 1 files changed, 322 insertions(+), 324 deletions(-) [+] |
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--- a/unipept.xml Sat Jul 02 13:46:38 2022 +0000 +++ b/unipept.xml Tue Mar 12 11:44:08 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="unipept" name="Unipept" version="4.5.1"> +<tool id="unipept" name="Unipept" version="4.5.1" profile="22.05"> <description>retrieve taxonomy for peptides</description> <macros> <xml name="equate_il"> @@ -17,10 +17,10 @@ </param> </xml> <xml name="names"> - <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" > + <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names"> <help>return the names in complete taxonomic lineage</help> </param> - <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" > + <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields"> <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help> </param> </xml> @@ -39,13 +39,13 @@ </param> </xml> </macros> + <xrefs> + <xref type="bio.tools">unipept</xref> + </xrefs> <requirements> <requirement type="package" version="3">python</requirement> </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/unipept.py' ## --url 'http://morty.ugent.be/api/v1' -g -M 1 --api=$unipept.api @@ -106,142 +106,142 @@ #end if ]]></command> <inputs> - <conditional name="unipept"> - <param name="api" type="select" label="Unipept application" > - <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option> - <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option> - <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option> - <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option> - <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option> - <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option> - <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option> - <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option> - </param> - <when value="pept2lca"> - <expand macro="equate_il" /> - <expand macro="extra"> - <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help> - </expand> - <expand macro="names" /> - </when> - <when value="pept2taxa"> - <expand macro="equate_il" /> - <expand macro="extra_true"> - <help>Return the complete lineage of each organism, and include ID fields.</help> - </expand> - <expand macro="names" /> - </when> - <when value="pept2prot"> - <expand macro="equate_il" /> - <expand macro="extra"> - <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids + <conditional name="unipept"> + <param name="api" type="select" label="Unipept application"> + <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option> + <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option> + <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option> + <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option> + <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option> + <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option> + <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option> + <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option> + </param> + <when value="pept2lca"> + <expand macro="equate_il"/> + <expand macro="extra"> + <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help> + </expand> + <expand macro="names"/> + </when> + <when value="pept2taxa"> + <expand macro="equate_il"/> + <expand macro="extra_true"> + <help>Return the complete lineage of each organism, and include ID fields.</help> + </expand> + <expand macro="names"/> + </when> + <when value="pept2prot"> + <expand macro="equate_il"/> + <expand macro="extra"> + <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required. </help> - </expand> - </when> - <when value="pept2ec"> - <expand macro="equate_il" /> - <expand macro="extra_true"> - <help>Return the name of the EC-number. + </expand> + </when> + <when value="pept2ec"> + <expand macro="equate_il"/> + <expand macro="extra_true"> + <help>Return the name of the EC-number. </help> - </expand> - </when> - <when value="pept2go"> - <expand macro="equate_il" /> - <expand macro="extra_true"> - <help>Return the name of the GO-term. + </expand> + </when> + <when value="pept2go"> + <expand macro="equate_il"/> + <expand macro="extra_true"> + <help>Return the name of the GO-term. </help> - </expand> - <expand macro="domains" /> - </when> - <when value="pept2interpro"> - <expand macro="equate_il" /> - <expand macro="extra_true"> - <help>Return the name of the GO-term. + </expand> + <expand macro="domains"/> + </when> + <when value="pept2interpro"> + <expand macro="equate_il"/> + <expand macro="extra_true"> + <help>Return the name of the GO-term. </help> - </expand> - <expand macro="domains" /> - </when> - <when value="pept2funct"> - <expand macro="equate_il" /> - <expand macro="extra_true"> - <help>Return the name of the EC-number and GO-term. + </expand> + <expand macro="domains"/> + </when> + <when value="pept2funct"> + <expand macro="equate_il"/> + <expand macro="extra_true"> + <help>Return the name of the EC-number and GO-term. </help> - </expand> - <expand macro="domains" /> - </when> - <when value="peptinfo"> - <expand macro="equate_il" /> - <expand macro="extra_true"> - <help>Return the name of the EC-number and GO-term. + </expand> + <expand macro="domains"/> + </when> + <when value="peptinfo"> + <expand macro="equate_il"/> + <expand macro="extra_true"> + <help>Return the name of the EC-number and GO-term. </help> - </expand> - <expand macro="domains" /> - <expand macro="names" /> - </when> - </conditional> - <conditional name="peptide_src"> - <param name="fmt" type="select" label="Peptides input format" > - <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option> - <option value="tabular">tabular</option> - <option value="fasta">fasta</option> - <option value="mzid">mzid</option> - <option value="pepxml">pepxml</option> + </expand> + <expand macro="domains"/> + <expand macro="names"/> + </when> + </conditional> + <conditional name="peptide_src"> + <param name="fmt" type="select" label="Peptides input format"> + <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option> + <option value="tabular">tabular</option> + <option value="fasta">fasta</option> + <option value="mzid">mzid</option> + <option value="pepxml">pepxml</option> + </param> + <when value="proteomic"> + <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input"/> + </when> + <when value="tabular"> + <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column"/> + <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv"/> + </when> + <when value="fasta"> + <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input"/> + </when> + <when value="mzid"> + <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input"/> + </when> + <when value="pepxml"> + <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input"/> + </when> + </conditional> + <param name="peptide_match" type="select" label="Match input peptides by"> + <option value="full">Match to the full input peptide</option> + <option value="best" selected="true">Best match to tryptic parts of the input peptide</option> + <option value="report">Best match to tryptic parts, add tryptic_match column</option> </param> - <when value="proteomic"> - <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" /> - </when> - <when value="tabular"> - <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" /> - <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" /> - </when> - <when value="fasta"> - <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" /> - </when> - <when value="mzid"> - <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" /> - </when> - <when value="pepxml"> - <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" /> - </when> - </conditional> - <param name="peptide_match" type="select" label="Match input peptides by"> - <option value="full">Match to the full input peptide</option> - <option value="best" selected="true">Best match to tryptic parts of the input peptide</option> - <option value="report">Best match to tryptic parts, add tryptic_match column</option> - </param> - <param name="unmatched_aa" type="select" label="Show tryptic_match as:"> - <option value="default">List of matched tryptic parts</option> - <option value=".">peptide with unmatched AAs as .</option> - <option value="x">peptide with unmatched AAs as x</option> - </param> - <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> - <option value="tsv" selected="true">Tabular with one line per peptide</option> - <option value="csv">Comma Separated Values (.csv) with one line per peptide</option> - <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option> - <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option> - <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option> - <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option> - <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option> - <option value="unmatched">Unmatched peptides</option> - </param> - <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/> + <param name="unmatched_aa" type="select" label="Show tryptic_match as:"> + <option value="default">List of matched tryptic parts</option> + <option value=".">peptide with unmatched AAs as .</option> + <option value="x">peptide with unmatched AAs as x</option> + </param> + <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> + <option value="tsv" selected="true">Tabular with one line per peptide</option> + <option value="csv">Comma Separated Values (.csv) with one line per peptide</option> + <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option> + <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option> + <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option> + <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option> + <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option> + <option value="unmatched">Unmatched peptides</option> + </param> + <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/> </inputs> <outputs> - <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json"> - <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter> - <change_format> - <when input="api" value="pept2prot" format="json" /> - </change_format> - </data> - <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json"> - <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter> - </data> - <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> - <filter>'tsv' in selected_outputs</filter> - <actions> - <action name="comment_lines" type="metadata" default="1" /> - <!-- + <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json"> + <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter> + <change_format> + <when input="api" value="pept2prot" format="json"/> + </change_format> + </data> + <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json"> + <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter> + </data> + <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> + <filter>'tsv' in selected_outputs</filter> + <actions> + <action name="comment_lines" type="metadata" default="1"/> + <!-- <conditional name="unipept.api"> <when value="pept2funct"> <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" /> @@ -254,195 +254,194 @@ </when> </conditional> --> - </actions> - </data> - <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> - <filter>'csv' in selected_outputs</filter> - </data> - <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv"> - <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter> - <actions> - <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" /> - </actions> - </data> - <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv"> - <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter> - <actions> - <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" /> - </actions> - </data> - <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv"> - <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter> - <actions> - <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name" /> - </actions> - </data> - - <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched"> - <filter>'unmatched' in selected_outputs</filter> - <actions> - <action name="column_names" type="metadata" default="Unmatched Peptide" /> - </actions> - </data> + </actions> + </data> + <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> + <filter>'csv' in selected_outputs</filter> + </data> + <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv"> + <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter> + <actions> + <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name"/> + </actions> + </data> + <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv"> + <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter> + <actions> + <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name"/> + </actions> + </data> + <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv"> + <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter> + <actions> + <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name"/> + </actions> + </data> + <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched"> + <filter>'unmatched' in selected_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="Unmatched Peptide"/> + </actions> + </data> </outputs> <tests> - <!-- Test-1 --> - <test> - <param name="api" value="pept2lca"/> - <param name="fmt" value="tabular"/> - <param name="input_tsv" value="tryptic.tsv"/> - <param name="column" value="2"/> - <param name="extra" value="True"/> - <param name="names" value="True"/> - <param name="selected_outputs" value="tsv,unmatched"/> - <output name="output_tsv"> - <assert_contents> - <has_text text="Homininae" /> - </assert_contents> - </output> - <output name="output_unmatched"> - <assert_contents> - <has_text text="QTAMAV" /> - </assert_contents> - </output> - </test> - <!-- Test-2 --> - <test> - <param name="api" value="pept2lca"/> - <param name="fmt" value="fasta"/> - <param name="input_fasta" value="peptide.fa"/> - <param name="equate_il" value="True"/> - <param name="extra" value="True"/> - <param name="names" value="True"/> - <param name="selected_outputs" value="json,tsv"/> - <output name="output_json"> - <assert_contents> - <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" /> - </assert_contents> - </output> - <output name="output_tsv"> - <assert_contents> - <has_text text="9606" /> - <has_text text="9596" /> - </assert_contents> - </output> - </test> - <!-- Test-3 --> - <test> - <param name="api" value="pept2taxa"/> - <param name="fmt" value="fasta"/> - <param name="input_fasta" value="peptide.fa"/> - <param name="equate_il" value="True"/> - <param name="extra" value="False"/> - <param name="names" value="False"/> - <param name="selected_outputs" value="tsv"/> - <output name="output_tsv"> - <assert_contents> - <has_text text="sapiens" /> - <has_text text="troglodytes" /> - </assert_contents> - </output> - </test> - <!-- Test-4 --> - <test> - <param name="api" value="pept2funct"/> - <param name="fmt" value="tabular"/> - <param name="input_tsv" value="input.tsv"/> - <param name="column" value="2"/> - <param name="extra" value="True"/> - <param name="names" value="True"/> - <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/> - <output name="output_tsv"> - <assert_contents> - <has_text text="GO:0004802" /> - <has_text text="2.2.1.1" /> - <has_text text="IPR005475" /> - </assert_contents> - </output> - <output name="output_ec_tsv"> - <assert_contents> - <has_text text="2.2.1.1" /> - </assert_contents> - </output> - <output name="output_go_tsv"> - <assert_contents> - <has_text text="GO:0004802" /> - </assert_contents> - </output> - <output name="output_ipr_tsv"> - <assert_contents> - <has_text text="IPR005475" /> - </assert_contents> - </output> - </test> - <!-- Test-5 --> - <test> - <param name="api" value="pept2funct"/> - <param name="fmt" value="tabular"/> - <param name="input_tsv" value="input.tsv"/> - <param name="column" value="2"/> - <param name="extra" value="True"/> - <param name="names" value="True"/> - <param name="peptide_match" value="full"/> - <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/> - <output name="output_tsv"> - <assert_contents> - <has_text text="GO:0004802" /> - <has_text text="2.2.1.1" /> - <has_text text="IPR005475" /> - <has_text_matching expression="FAPLLEEYKAEDWVQK\t0" /> - </assert_contents> - </output> - <output name="output_ec_tsv"> - <assert_contents> - <has_text text="2.2.1.1" /> - </assert_contents> - </output> - <output name="output_go_tsv"> - <assert_contents> - <has_text text="GO:0004802" /> - </assert_contents> - </output> - <output name="output_ipr_tsv"> - <assert_contents> - <has_text text="IPR005475" /> - </assert_contents> - </output> - </test> - <!-- Test-6 --> - <test> - <param name="api" value="pept2funct"/> - <param name="fmt" value="tabular"/> - <param name="input_tsv" value="input.tsv"/> - <param name="column" value="2"/> - <param name="extra" value="True"/> - <param name="names" value="True"/> - <param name="peptide_match" value="report"/> - <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/> - <output name="output_tsv"> - <assert_contents> - <has_text text="GO:0004802" /> - <has_text text="2.2.1.1" /> - <has_text text="IPR005475" /> - <has_text_matching expression="FAPLLEEYKAEDWVQK\tAEDWVQK\t1" /> - </assert_contents> - </output> - <output name="output_ec_tsv"> - <assert_contents> - <has_text text="2.2.1.1" /> - </assert_contents> - </output> - <output name="output_go_tsv"> - <assert_contents> - <has_text text="GO:0004802" /> - </assert_contents> - </output> - <output name="output_ipr_tsv"> - <assert_contents> - <has_text text="IPR005475" /> - </assert_contents> - </output> - </test> + <!-- Test-1 --> + <test expect_num_outputs="2"> + <param name="api" value="pept2lca"/> + <param name="fmt" value="tabular"/> + <param name="input_tsv" value="tryptic.tsv"/> + <param name="column" value="2"/> + <param name="extra" value="True"/> + <param name="names" value="True"/> + <param name="selected_outputs" value="tsv,unmatched"/> + <output name="output_tsv"> + <assert_contents> + <has_text text="Homininae"/> + </assert_contents> + </output> + <output name="output_unmatched"> + <assert_contents> + <has_text text="QTAMAV"/> + </assert_contents> + </output> + </test> + <!-- Test-2 --> + <test expect_num_outputs="2"> + <param name="api" value="pept2lca"/> + <param name="fmt" value="fasta"/> + <param name="input_fasta" value="peptide.fa"/> + <param name="equate_il" value="True"/> + <param name="extra" value="True"/> + <param name="names" value="True"/> + <param name="selected_outputs" value="json,tsv"/> + <output name="output_json"> + <assert_contents> + <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV"/> + </assert_contents> + </output> + <output name="output_tsv"> + <assert_contents> + <has_text text="9606"/> + <has_text text="9596"/> + </assert_contents> + </output> + </test> + <!-- Test-3 --> + <test expect_num_outputs="1"> + <param name="api" value="pept2taxa"/> + <param name="fmt" value="fasta"/> + <param name="input_fasta" value="peptide.fa"/> + <param name="equate_il" value="True"/> + <param name="extra" value="False"/> + <param name="names" value="False"/> + <param name="selected_outputs" value="tsv"/> + <output name="output_tsv"> + <assert_contents> + <has_text text="sapiens"/> + <has_text text="Cercocebus"/> + </assert_contents> + </output> + </test> + <!-- Test-4 --> + <test expect_num_outputs="5"> + <param name="api" value="pept2funct"/> + <param name="fmt" value="tabular"/> + <param name="input_tsv" value="input.tsv"/> + <param name="column" value="2"/> + <param name="extra" value="True"/> + <param name="names" value="True"/> + <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/> + <output name="output_tsv"> + <assert_contents> + <has_text text="GO:0004802"/> + <has_text text="2.2.1.1"/> + <has_text text="IPR005475"/> + </assert_contents> + </output> + <output name="output_ec_tsv"> + <assert_contents> + <has_text text="2.2.1.1"/> + </assert_contents> + </output> + <output name="output_go_tsv"> + <assert_contents> + <has_text text="GO:0004802"/> + </assert_contents> + </output> + <output name="output_ipr_tsv"> + <assert_contents> + <has_text text="IPR005475"/> + </assert_contents> + </output> + </test> + <!-- Test-5 --> + <test expect_num_outputs="5"> + <param name="api" value="pept2funct"/> + <param name="fmt" value="tabular"/> + <param name="input_tsv" value="input.tsv"/> + <param name="column" value="2"/> + <param name="extra" value="True"/> + <param name="names" value="True"/> + <param name="peptide_match" value="full"/> + <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/> + <output name="output_tsv"> + <assert_contents> + <has_text text="GO:0004802"/> + <has_text text="2.2.1.1"/> + <has_text text="IPR005475"/> + <has_text_matching expression="FAPLLEEYKAEDWVQK\t0"/> + </assert_contents> + </output> + <output name="output_ec_tsv"> + <assert_contents> + <has_text text="2.2.1.1"/> + </assert_contents> + </output> + <output name="output_go_tsv"> + <assert_contents> + <has_text text="GO:0004802"/> + </assert_contents> + </output> + <output name="output_ipr_tsv"> + <assert_contents> + <has_text text="IPR005475"/> + </assert_contents> + </output> + </test> + <!-- Test-6 --> + <test expect_num_outputs="5"> + <param name="api" value="pept2funct"/> + <param name="fmt" value="tabular"/> + <param name="input_tsv" value="input.tsv"/> + <param name="column" value="2"/> + <param name="extra" value="True"/> + <param name="names" value="True"/> + <param name="peptide_match" value="report"/> + <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/> + <output name="output_tsv"> + <assert_contents> + <has_text text="GO:0004802"/> + <has_text text="2.2.1.1"/> + <has_text text="IPR005475"/> + <has_text_matching expression="AAEGGLSR\tAAEGGLSR\t6"/> + </assert_contents> + </output> + <output name="output_ec_tsv"> + <assert_contents> + <has_text text="2.2.1.1"/> + </assert_contents> + </output> + <output name="output_go_tsv"> + <assert_contents> + <has_text text="GO:0004802"/> + </assert_contents> + </output> + <output name="output_ipr_tsv"> + <assert_contents> + <has_text text="IPR005475"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ **Unipept** @@ -637,8 +636,7 @@ DOI: 10.1002/pmic.201400361 ]]></help> - <citations> - <citation type="doi">doi:10.1002/pmic.201400361</citation> - </citations> - + <citations> + <citation type="doi">doi:10.1002/pmic.201400361</citation> + </citations> </tool>