view scde_list_compare.xml @ 0:b1d730728d5f default tip

Initial commit.

<tool id="scde-list-compare" name="SCDE ListCompare" version="1.0" hidden="false">
<description>compare multiple lists against one or more selected reference lists</description>
<version_string>scde --version</version_string>

<command interpreter="perl">
    scde compare --source $source

                 #for $i in $lists
                 --file     ${i.filename}
                 --column   ${i.column}
                 --organism ${i.organism}
                 --symbol   ${i.symbol_type}
                 #end for
                 --output   $format 

                 #if str($output_html) != "None"
                 > $output_html
                 #else
                 > $output_tab
                 #end if
</command>

<inputs>
  <param name="source" type="select" label="Compare your gene lists to">
    <option value="wikipathways">Wikipathways</option>
    <option value="genesigdb">GeneSigDB</option>
    <option value="msigdb">MSigDB</option>
    <option value="scd">SCDE Repository - Public</option>
  </param>

  <repeat name="lists" title="Add List" min="2" >
    <param name="filename" type="data" format="txt" label="Dataset" help="Select a list for comparison from your History." />

    <param name="column" type="select" label="Gene Column" help="Select the column number corresponding to the gene identifier">
      <option value="1">c1</option>
      <option value="2">c2</option>
      <option value="3">c3</option>
      <option value="4">c4</option>
      <option value="5">c5</option>
      <option value="6">c6</option>
      <option value="7">c7</option>
      <option value="8">c8</option>
      <option value="9">c9</option>
      <option value="10">c10</option>
    </param>

    <param name="organism" type="select" label="Query Organism" help="Which organism do your gene lists come from?">
      <option value="human">Human</option>
      <option value="mouse">Mouse</option>
    </param>

    <param name="symbol_type" type="select" label="Query Gene ID Type" help="Select the gene identifier type to search with.">
      <option value="symbol">Gene Symbol</option>
      <option value="ensembl">Ensembl ID</option>
      <option value="entrez">Entrez ID</option>
    </param>
  </repeat>

  <param name="format" type="select" label="Output Format" help="Select the Format for the Output File">
    <option value="html">HTML</option>
    <option value="tab">Tab Delimited</option>
  </param>
</inputs>

<outputs>
  <data format="html" name="output_html">
    <filter>format == "html"</filter>
  </data>
  <data format="tabular" name="output_tab">
    <filter>format == "tab"</filter>
  </data>
</outputs> 

<help>
**What it does**

This tool compares two or more sets of gene lists against one or more selected reference lists.

-----

.. class:: infomark

Upload data in tabular format to your history using the "Get Data" -> "Upload File" tool.

.. class:: infomark

Additional lists may be added using the "Add new List" button.
</help>
</tool>