comparison unipept.xml @ 9:21a560af5913 draft default tip

planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7

8:7863f1abcdda

<tool id="unipept" name="Unipept" version="4.5.1">
    <description>retrieve taxonomy for peptides</description>
    <macros>
        <xml name="equate_il">
            <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
                <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>

            <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="true" label="retrieve extra information">
                <yield/>
            </param>
        </xml>
        <xml name="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" >
                <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
            </param>
        </xml>
        <xml name="domains">
            <param name="domains" type="boolean" truevalue="-D" falsevalue="" checked="false" label="group responses by GO namespace (biological process, molecular function, cellular component)">

                <yield/>
                <option value="unmatched">Unmatched peptides</option>
            </param>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="3">python</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
      python '$__tool_directory__/unipept.py' 
      ## --url 'http://morty.ugent.be/api/v1' -g -M 1  
      --api=$unipept.api
      $unipept.equate_il $unipept.extra 
      #if $unipept.api in ['pept2lca', 'pept2taxa', 'peptinfo']:

      #if 'unmatched' in str($selected_outputs).split(','):
        --unmatched $output_unmatched
      #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
                        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.
                  </help>
              </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.
                  </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.
                  </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.
                  </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>
        </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"/>
    </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" />
            <!--
            <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" />
                </when>
                <when value="pept2go">

                <when value="pept2ec">
                    <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
                </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> 
    </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>
    </tests>
    <help><![CDATA[
    **Unipept** 

    Retrieve Uniprot and taxanomic information for trypic peptides.

    Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
    Article first published online: 11 FEB 2015
    DOI: 10.1002/pmic.201400361

    ]]></help>
  <citations>
    <citation type="doi">doi:10.1002/pmic.201400361</citation>
  </citations>

</tool>

9:21a560af5913

<tool id="unipept" name="Unipept" version="4.5.1" profile="22.05">
    <description>retrieve taxonomy for peptides</description>
    <macros>
        <xml name="equate_il">
            <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
                <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>

            <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="true" label="retrieve extra information">
                <yield/>
            </param>
        </xml>
        <xml name="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">
                <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
            </param>
        </xml>
        <xml name="domains">
            <param name="domains" type="boolean" truevalue="-D" falsevalue="" checked="false" label="group responses by GO namespace (biological process, molecular function, cellular component)">

                <yield/>
                <option value="unmatched">Unmatched peptides</option>
            </param>
        </xml>
    </macros>
    <xrefs>
        <xref type="bio.tools">unipept</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="3">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      python '$__tool_directory__/unipept.py' 
      ## --url 'http://morty.ugent.be/api/v1' -g -M 1  
      --api=$unipept.api
      $unipept.equate_il $unipept.extra 
      #if $unipept.api in ['pept2lca', 'pept2taxa', 'peptinfo']:

      #if 'unmatched' in str($selected_outputs).split(','):
        --unmatched $output_unmatched
      #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
                        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.
                  </help>
                </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.
                  </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.
                  </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.
                  </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>
            </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"/>
    </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"/>
                <!--
            <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" />
                </when>
                <when value="pept2go">

                <when value="pept2ec">
                    <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
                </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>
    </outputs>
    <tests>
        <!-- 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** 

    Retrieve Uniprot and taxanomic information for trypic peptides.

    Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
    Article first published online: 11 FEB 2015
    DOI: 10.1002/pmic.201400361

    ]]></help>
    <citations>
        <citation type="doi">doi:10.1002/pmic.201400361</citation>
    </citations>
</tool>