view scde_list_match.xml @ 0:b1d730728d5f default tip

Initial commit.

<?xml version="1.0"?>
<tool id="scde-list-match" name="SCDE ListMatch" version="1.0" hidden="false">
<description>match a list against one or more selected reference gene lists</description>
<version_string>scde --version</version_string>

<command interpreter="perl">
    scde match --source   $source
               --organism    $organism

               #if str($symbol_type) != ""
               --symbol      $symbol_type
               #end if

               #if $query.type == "file"
               --file        $query.filename
               --column      $query.column
               #else
                             $query.source
               #end if
               --min-matches $min_matches
               --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 list to">
    <option value="wikipathways">Wikipathways</option>
    <option value="genesigdb">GeneSigDB</option>
    <option value="msigdb">MSigDB</option>
    <option value="scd">SCDE Repository - Public</option>
  </param>

  <param name="organism" type="select" label="Query Organism" help="Which organism did your gene list 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>

  <conditional name="query">
    <param name="type" type="select" label="Query source" help="You may select a file from your User History or enter a list of genes as text.">
      <option value="file">History File</option>
      <option value="text">Enter Text</option>
    </param> 

    <when value="file"> 
      <param name="filename" format="txt" type="data" label="Query History File" help="Select a file from your History"/>
      <param name="column" type="data_column" data_ref="filename" label="Query File Column Number" help="Column numbers start at 1. Verify that the column number corresponds to the Gene ID Type you specified."/>
    </when>

    <when value="text">
      <param name="source" type="text" area="true" size="5x60" label="Query using Text Entry" help="Paste a list of gene symbols here, separated by a space, tab, new line or a comma."/>
    </when>
  </conditional>

  <param name="min_matches" type="select" label="Minimum Number of Matches" help="Select the minimum number of genes that must be matched per reference gene list.">
    <option value="1">1</option>
    <option value="2">2</option>
    <option value="3">3</option>
    <option value="4">4</option>
    <option value="5">5</option>
  </param>

  <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 a list of genes as a query against one or more selected reference lists.

-----

.. class:: infomark

Please upload your data as a tab-delimited text file. If the column number does not appear as a dropdown menu, make sure the file type is 'Tabular'.

-----

**Screencast!**

Watch the SCDE ListMatch Screencast_ (right click to open this link in another window).

.. _Screencast: http://discovery.hsci.harvard.edu/screencasts/galaxy.html
</help>
</tool>