view exclusive_clonotype_computation.xml @ 1:acaa8e8a0b88 draft default tip

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<tool id="exclClonoComput" name="Exclusive Clonotypes" version="1.0">
<description>Compute exclusive clonotypes between 2 repertoires</description>
<requirements>
      <requirement type="package" version="0.19">pandas</requirement>
</requirements>
<command interpreter="python">exclusive_clonotype_computation.py "$clono" "$output_file" "$Th.thres" "$inputA" "$inputA.name" "$inputB" "$inputB.name"
</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>
	<param format="txt" name="inputA" type="data" label="First Clonotypes File (A)"/>
	<param format="txt" name="inputB" type="data" label="Second Clonotypes File (B)"/>
</inputs>

<outputs>
<data format="tabular" name="output_file" label="exclusiveClonotypes"/>
</outputs>
<help>
This tool extracts the exclusive (i.e., found in the 1st dataset but not in the 2nd) clonotypes between 2 clonotype repertoires (1st output of the Clonotype Diversity &amp; Expression tool) according to 3 of the 5 supported clonotype definitions.
</help>
</tool>