Mercurial > repos > davidvanzessen > report_clonality_tcell_igg

diff plotting_merged.xml @ 2:fd1b76816395 draft

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author davidvanzessen
date Thu, 27 Mar 2014 10:54:03 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotting_merged.xml	Thu Mar 27 10:54:03 2014 -0400
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+<tool id="report_clonality_igg" name="Report Clonality" version="1.0">
+	<description> </description>
+	<command interpreter="bash">
+		r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select"
+	</command>
+	<inputs>
+	<param name="in_file" format="tabular" type="data" label="Data to Process" />
+	<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>
+		Step 4 of the Immune Repertoire tools, plots the merged data, generating 3 bar charts for V, D and J frequencies and 3 heatmaps for every sample (V-D, V-J, D-J)
+	</help>
+</tool>