comparison unipept.xml @ 5:917fd3ebc223 draft

"planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"

4:4953dcd7dd39

<tool id="unipept" name="Unipept" version="4.0.0">
    <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>

                <option value="unmatched">Unmatched peptides</option>
            </param>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[

        --ec_tsv $output_ec_tsv
      #end if
      #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
        --go_tsv $output_go_tsv
      #end if
      #if 'unmatched' in str($selected_outputs).split(','):
        --unmatched $output_unmatched
      #end if
    ]]></command>
    <inputs>

              <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="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" />

                  <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>

      <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="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"/>

        <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_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>

        <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>

        <param name="selected_outputs" value="tsv"/>
        <output name="output_tsv">
            <assert_contents>
              <has_text text="sapiens" />
              <has_text text="paniscus" />
              <has_text text="Gorilla" />
            </assert_contents>
        </output>
      </test>
      <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,unmatched"/>
        <output name="output_tsv">
            <assert_contents>
              <has_text text="GO:0004802" />
              <has_text text="2.2.1.1" />
            </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>
      </test>
    </tests>
    <help><![CDATA[

        go_term: The GO-term associated with the current tryptic peptide.
        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
        name: Optional, name of the GO-term. Included when the extra parameter is set to true.


    **pept2funct**  - http://unipept.ugent.be/apidocs/pept2funct

    Returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.

    By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::

        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
        name: Optional, name of the EC-number. Included when the extra parameter is set to true.
        go_term: The GO-term associated with the current tryptic peptide.
        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
        name: Optional, name of the GO-term. Included when the extra parameter is set to true.


    **Attributions**

    The Unipept metaproteomics analysis pipeline

5:917fd3ebc223

<tool id="unipept" name="Unipept" version="4.3.0">
    <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>

                <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[

        --ec_tsv $output_ec_tsv
      #end if
      #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
        --go_tsv $output_go_tsv
      #end if
      #if 'ipr_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2interpro', 'pept2funct', 'peptinfo']:
        --ipr_tsv $output_ipr_tsv
      #end if
      #if 'unmatched' in str($selected_outputs).split(','):
        --unmatched $output_unmatched
      #end if
    ]]></command>
    <inputs>

              <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" />

                  <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>

      <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"/>

        <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>

        <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>

        <param name="selected_outputs" value="tsv"/>
        <output name="output_tsv">
            <assert_contents>
              <has_text text="sapiens" />
              <has_text text="paniscus" />
            </assert_contents>
        </output>
      </test>
      <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>
    </tests>
    <help><![CDATA[

        go_term: The GO-term associated with the current tryptic peptide.
        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
        name: Optional, name of the GO-term. Included when the extra parameter is set to true.


    **pept2interpro**  - http://unipept.ugent.be/apidocs/pept2interpro

    Returns the functional InterPro entries associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.

    By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::

        peptide: the peptide that matched this record
        total_protein_count: Total amount of proteins matched with the given peptide
        code: InterPro entry code associated with the current tryptic peptide
        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
        type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
        name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.

    **pept2funct**  - http://unipept.ugent.be/apidocs/pept2funct

    Returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.

    By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::

        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
        name: Optional, name of the EC-number. Included when the extra parameter is set to true.
        go_term: The GO-term associated with the current tryptic peptide.
        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
        name: Optional, name of the GO-term. Included when the extra parameter is set to true.
        code: InterPro entry code associated with the current tryptic peptide
        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
        type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
        name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.


    **Attributions**

    The Unipept metaproteomics analysis pipeline