Mercurial > repos > davidvanzessen > imgt_immunerepertoire_igg

diff combined_imgt.xml @ 0:3cce6e04b1e8 draft

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author davidvanzessen
date Thu, 23 Jan 2014 08:35:31 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combined_imgt.xml	Thu Jan 23 08:35:31 2014 -0500
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+<tool id="imgt_immunerepertoire_igg" name="IMGT ImmuneRepertoire" version="1.0">
+	<description> </description>
+	<command interpreter="bash">
+		combined.sh
+		#for $i, $f in enumerate($patients)
+			${f.id}
+            #for $j, $g in enumerate($f.samples)
+            	${g.sample}
+            #end for
+		#end for
+		"$clonaltype_select" $out_file $out_file.files_path
+	</command>
+	<inputs>
+		<repeat name="patients" title="Patients" min="1" default="1">
+            <repeat name="samples" title="Sample" min="1" default="1">
+                <param name="sample" type="data" label="Sample to Process" />
+            </repeat>
+			<param name="id" type="text" label="ID" />
+		</repeat>
+		<param name="clonaltype_select" type="select" label="Clonal Type Definition">
+			<option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
+			<option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
+			<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
+			<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
+			<option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
+		</param>
+	</inputs>
+	<outputs>
+		<data format="html" name="out_file" />
+	</outputs>
+	<help>
+		The entire Immune Repertoire pipeline as a single tool, input several IMGT zip files, give them an ID and it will parse, merge and plot them.
+	</help>
+</tool>
+