annotate public_clonotype_computation.xml @ 1:acaa8e8a0b88 draft default tip

Uploaded test-data & added tool help

<tool id="pubClonoComput" name="Public Clonotypes" version="1.0">
    <description>Compute public clonotypes from multiple repertoires</description>
    <requirements>
      <requirement type="package" version="0.19">pandas</requirement>
		</requirements>
    <command interpreter="python">public_clonotype_computation.py "$clonotype" "$output_file" "$Th.thres"
#for x in $clono_files
  "$x.clfile"
  "$x.clfile.name"
#end for
</command>
    <inputs>
        <param name="clonotype" type="select" label="Clonotype definition">
            <option value="CDR3">CDR3</option>
            <option value="VCDR3">V+CDR3</option>
            <option value="JCDR3">J+CDR3</option>
        </param>
        <conditional name="Th">
            <param name="thres_select" type="select" label="Remove Clonotypes With Reads Fewer Than Threshold?">
                <option value="y">Yes</option>
                <option value="n" selected="true">No</option>
            </param>
            <when value="y">
                <param name="thres" type="integer" size="4" value="1" min="1" label="Keep Clonotypes with Number of Reads more than" />
            </when>
            <when value="n">
                <param name="thres" type="hidden" value="null" />
            </when>
        </conditional>
        <repeat name="clono_files" title="Files to be append" min="2">
            <param name="clfile" type="data" label="Clonotype_File" format="tabular" />
        </repeat>
    </inputs>
    <outputs>
        <data format="tabular" name="output_file" label="publicClonotypes" />
    </outputs>
    <help>
This tool extracts the public (i.e., shared in at least two datasets) clonotypes between 2 or more clonotype repertoires (1st output of the Clonotype Diversity &amp; Expression tool) according to 3 of the 5 supported clonotype definitions.
</help>
</tool>