comparison unipept.xml @ 1:0c1ee95282fa draft

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0:6430407e5869

<tool id="unipept" name="Unipept" version="0.1.0">
    <description>retrieve taxonomy for peptides</description>
    <macros>
        <xml name="equate_il">
            <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Equate isoleucine and leucine">
                <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
            </param >
        </xml>
        <xml name="extra">
            <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" 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 of taxons</help>
            </param >
        </xml>
    </macros>
    <requirements>
    </requirements>

    <command interpreter="python"><![CDATA[
      unipept.py 
      --api=$unipept.api
      $unipept.equate_il $unipept.extra 
      #if $unipept.api != 'pept2prot':
        $unipept.names 
      #end if
      $strict
      #if str($peptide_src.fmt) == 'proteomic':
        #if $peptide_src.input.datatype.file_ext == 'fasta':
          --fasta="$peptide_src.input"

        --tsv $output_tsv
      #end if
      #if 'csv' in str($outputs).split(','):
        --csv $output_csv
      #end if
      #if 'mismatch' in str($outputs).split(','):
        --mismatch $output_mismatch
      #end if
    ]]></command>
    <inputs>
      <conditional name="unipept">
          <param name="api" type="select" label="Unipept application" >
              <option value="pept2taxa" selected="true">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
              <option value="pept2lca">pept2lca: lowest common ancestor</option>
              <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
          </param>
          <when value="pept2taxa">
              <expand macro="equate_il" />
              <expand macro="extra">
                  <checked>true</checked>
                  <help>Return the complete lineage of each organism.</help>
              </expand>
              <expand macro="names" />
          </when>
          <when value="pept2lca">
              <expand macro="equate_il" />
              <expand macro="extra">
                  <help>Return the complete lineage of the taxonomic lowest common ancestor.</help>
              </expand>
              <expand macro="names" />
          </when>
          <when value="pept2prot">
              <expand macro="equate_il" />

      </conditional>
      <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
        <option value="tsv" selected="true">tabular</option>
        <option value="csv">Comma Separated Values (.csv)</option>
        <option value="json">JSON</option>
        <option value="mismatch">Mismatches</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="json" label="${tool.name} ${unipept.api} on ${on_string} json"> 

        <filter>'tsv' in outputs</filter>
      </data> 
      <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> 
        <filter>'csv' in outputs</filter>
      </data> 
      <data name="output_mismatch" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} mismatch"> 
        <filter>'mismatch' in outputs</filter>
      </data> 
    </outputs>
    <tests>
      <test>
        <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="outputs" value="tsv,mismatch"/>
        <output name="output_tsv">
            <assert_contents>
              <has_text text="AIPQLEVARPADAYETAEAYR" />
            </assert_contents>
        </output>
        <output name="output_mismatch">
            <assert_contents>
              <has_text text="DQIAHEGK" />
            </assert_contents>
        </output>
      </test>
      <test>
        <param name="fmt" value="fasta"/>
        <param name="input_tsv" value="input.fasta"/>
        <param name="equate_il" value="True"/>
        <param name="extra" value="True"/>
        <param name="names" value="True"/>
        <param name="outputs" value="json,mismatch"/>
        <output name="output_json">
            <assert_contents>
              <has_text text="AIPQLEVARPADAYETAEAYR" />
            </assert_contents>
        </output>
        <output name="output_mismatch">
            <assert_contents>
              <has_text text="DQIAHEGK" />
            </assert_contents>
        </output>
      </test>
    </tests>
    <help><![CDATA[
    **Unipept** 

    Retrieve Uniprot and taxanomic information for trypic peptides.

    **pept2prot**
    Returns the list of UniProt entries containing a given tryptic peptide. This is the same information as provided on the Protein matches tab 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::

        peptide: the peptide that matched this record

        refseq_ids: a space separated list of associated RefSeq accession numbers
        refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
        insdc_ids: a space separated list of associated insdc accession numbers
        insdc_protein_ids: a space separated list of associated insdc protein accession numbers

    http://unipept.ugent.be/apidocs/pept2prot

    **pept2taxa**
    Returns the set of organisms associated with the UniProt entries containing a given tryptic peptide. This is the same information as provided on the Lineage table tab 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

        species_id
        subspecies_id
        varietas_id
        forma_id

    http://unipept.ugent.be/apidocs/pept2taxa

    **pept2lca** 
    Returns the taxonomic lowest common ancestor for 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

        species_id
        subspecies_id
        varietas_id
        forma_id

    http://unipept.ugent.be/apidocs/pept2lca

    **Attributions**

    The Unipept metaproteomics analysis pipeline
    Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1

1:0c1ee95282fa

<tool id="unipept" name="Unipept" version="1.1.0">
    <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>
            </param >
        </xml>
        <xml name="extra">
            <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" 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>
    </macros>
    <requirements>
    </requirements>

    <command interpreter="python"><![CDATA[
      unipept.py 
      --api=$unipept.api
      $unipept.equate_il $unipept.extra 
      #if $unipept.api != 'pept2prot':
        $unipept.names $unipept.allfields
      #end if
      $strict
      #if str($peptide_src.fmt) == 'proteomic':
        #if $peptide_src.input.datatype.file_ext == 'fasta':
          --fasta="$peptide_src.input"

        --tsv $output_tsv
      #end if
      #if 'csv' in str($outputs).split(','):
        --csv $output_csv
      #end if
      #if 'unmatched' in str($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>
          </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">
                  <checked>true</checked>
                  <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" />

      </conditional>
      <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
        <option value="tsv" selected="true">tabular</option>
        <option value="csv">Comma Separated Values (.csv)</option>
        <option value="json">JSON</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="json" label="${tool.name} ${unipept.api} on ${on_string} json"> 

        <filter>'tsv' in outputs</filter>
      </data> 
      <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> 
        <filter>'csv' in outputs</filter>
      </data> 
      <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched"> 
        <filter>'unmatched' in outputs</filter>
      </data> 
    </outputs>
    <tests>
      <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="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>
        <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="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="9598" />
            </assert_contents>
        </output>
      </test>
      <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="outputs" value="tsv"/>
        <output name="output_tsv">
            <assert_contents>
              <has_text text="sapiens" />
              <has_text text="troglodytes" />
              <has_text text="Gorilla" />
              <has_text text="Macaca" />
            </assert_contents>
        </output>
      </test>
    </tests>
    <help><![CDATA[
    **Unipept** 

    Retrieve Uniprot and taxanomic information for trypic peptides.
    
    Unipept API documentation - http://unipept.ugent.be/apidocs 

    **Input**

    Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets.  
 
    Processing deatils::

        The input peptides are split into typtic peptide fragments in order to match the Unipept records.   
        Only fragments that are complete tryptic peptides between 5 and 50 animo acid in length will be matched by Unipept.
        The match to the most specific tryptic fragment is reported.


    **Unipept APIs**

    **pept2prot**  - http://unipept.ugent.be/apidocs/pept2prot

    Returns the list of UniProt entries containing a given tryptic peptide. This is the same information as provided on the Protein matches tab 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::

        peptide: the peptide that matched this record

        refseq_ids: a space separated list of associated RefSeq accession numbers
        refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
        insdc_ids: a space separated list of associated insdc accession numbers
        insdc_protein_ids: a space separated list of associated insdc protein accession numbers


    **pept2taxa**  - http://unipept.ugent.be/apidocs/pept2taxa

    Returns the set of organisms associated with the UniProt entries containing a given tryptic peptide. This is the same information as provided on the Lineage table tab 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

        species_id
        subspecies_id
        varietas_id
        forma_id


    **pept2lca**  - http://unipept.ugent.be/apidocs/pept2lca

    Returns the taxonomic lowest common ancestor for 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

        species_id
        subspecies_id
        varietas_id
        forma_id


    **Attributions**

    The Unipept metaproteomics analysis pipeline
    Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1