comparison add_protein_features_mouse.xml @ 1:f10816a9dd0b draft

planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty

0:1e856941a888

<tool id="prot_features_mouse" name="Add protein features (Mouse)" version="2019.02.08">
<description>[UniProt]
</description>
<requirements>
  <requirement type="package" version="3.4.1">R</requirement>
</requirements>

  --input='$inputtype.genelist'

  #if $inputtype.filetype == "file" 
    --column='$inputtype.column' 
    --header=$inputtype.header
  #end if

  --pc_features='$pc_features'   
  --output='$output'  
  --uniprot_file=$__tool_directory__/tool-data/uniprot_features_mouse.tsv
    
]]></command>

<inputs>
  <conditional name="inputtype">

        </sanitizer>
      </param>
    </when>
    <when value="file">
      <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
      <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1"/> 
      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />

    </when>
  </conditional>
    <param name="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="true">
      <option value="Entry name" selected="false">Entry name (e.g. PLK3_MOUSE)</option>
      <option value="Protein names" selected="false">Protein names (e.g. Serine/threonine-protein kinase PLK3 (EC 2.7.11.21))</option>
      <option value="Length" selected="false">Sequence length</option>
      <option value="Mass" selected="false">Molecular Mass (Da)</option>
      <option value="Features" selected="false">Features (e.g. Chain (1); Transmembrane (4))</option>

      <option value="Involvement in disease" selected="false">Involvement in disease (e.g. DISEASE: Note=Defects in Btk are the cause of murine X-linked immunodeficiency (XID))</option>     
    </param>
</inputs>

<outputs>
  <data name="output" format="tsv" label="Add_information_from_UniProt on ${inputtype.genelist.name}">
    <filter>inputtype=="file"</filter>
  </data>
  <data name="output" format="tsv" label="Add_information_from_UniProt"/>
</outputs>

<tests>
  <test>
    <conditional name="inputtype">

      <param name="header" value="true"/>
    </conditional>

    <param name="pc_features" value='Entry name,Protein names,Length,Mass,Features,Intramembrane,Transmembrane,Topological domain,Pathway,Function [CC],Post-translational modification,Subcellular location [CC],Subunit structure [CC],Domain [CC],Tissue specificity,Involvement in disease'/> 
      
    <output name="output" file="results_wilson-foie-souris-up.tsv"/>
  </test>
</tests>

<help><![CDATA[

1:f10816a9dd0b

<tool id="prot_features_mouse" name="Add protein features (Mouse)" version="2019.02.21">
<description>[UniProt]
</description>
<requirements>
  <requirement type="package" version="3.4.1">R</requirement>
</requirements>

  --input='$inputtype.genelist'

  #if $inputtype.filetype == "file" 
    --column='$inputtype.column' 
    --header=$inputtype.header
    --output='$output' 
  #else
    --output='$output2'
  #end if

  --pc_features='$pc_features'   
  --uniprot_file=$__tool_directory__/tool-data/uniprot_features_mouse.tsv 
    
]]></command>

<inputs>
  <conditional name="inputtype">

        </sanitizer>
      </param>
    </when>
    <when value="file">
      <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
      <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1">
        <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
      </param>
      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />

    </when>
  </conditional>
    <param name="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="false">
      <option value="Entry name" selected="false">Entry name (e.g. PLK3_MOUSE)</option>
      <option value="Protein names" selected="false">Protein names (e.g. Serine/threonine-protein kinase PLK3 (EC 2.7.11.21))</option>
      <option value="Length" selected="false">Sequence length</option>
      <option value="Mass" selected="false">Molecular Mass (Da)</option>
      <option value="Features" selected="false">Features (e.g. Chain (1); Transmembrane (4))</option>

      <option value="Involvement in disease" selected="false">Involvement in disease (e.g. DISEASE: Note=Defects in Btk are the cause of murine X-linked immunodeficiency (XID))</option>     
    </param>
</inputs>

<outputs>
  <data name="output" format="tsv" label="Add_Mouse_ProteinFeatures_UP_on_${inputtype.genelist.name}">
    <filter>inputtype['filetype'] == 'file'</filter>
  </data>
  <data name="output2" format="tsv" label="Add_Mouse_ProteinFeatures_UP">
    <filter>inputtype['filetype'] == 'copy_paste'</filter>
  </data>
</outputs>

<tests>
  <test>
    <conditional name="inputtype">

      <param name="header" value="true"/>
    </conditional>

    <param name="pc_features" value='Entry name,Protein names,Length,Mass,Features,Intramembrane,Transmembrane,Topological domain,Pathway,Function [CC],Post-translational modification,Subcellular location [CC],Subunit structure [CC],Domain [CC],Tissue specificity,Involvement in disease'/> 
      
    <output name="output2" file="results_wilson-foie-souris-up.tsv"/>
  </test>
</tests>

<help><![CDATA[