Mercurial > repos > davidvanzessen > report_clonality_tcell_igg

diff report_tcell.xml @ 0:1d429107cd26 draft

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author davidvanzessen
date Fri, 07 Mar 2014 05:42:31 -0500
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children b850200d4335
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_tcell.xml	Fri Mar 07 05:42:31 2014 -0500
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+<tool id="report_clonality_t-cells" name="Report Clonality T-Cells" version="1.0">
+	<description> </description>
+	<command interpreter="bash">
+		r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" "$species"
+	</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>
+	<param name="species" type="select" label="Human or Mouse (Does nothing)">
+		<option value="human">Human</option>
+		<option value="mouse">Mouse</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>