Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg

diff complete_immunerepertoire.xml @ 1:778a9d130904 draft

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Uploaded
author davidvanzessen
date Thu, 04 Sep 2014 07:46:23 -0400
parents 7d97fa9a0423
children 0dafe2f9ceb8
line wrap: on
line diff
--- a/complete_immunerepertoire.xml	Fri May 09 09:35:32 2014 -0400
+++ b/complete_immunerepertoire.xml	Thu Sep 04 07:46:23 2014 -0400
@@ -1,20 +1,20 @@
 <tool id="complete_immunerepertoire_igg" name="Complete ImmuneRepertoire" version="1.0">
 	<description> </description>
 	<command interpreter="bash">
-		complete.sh
+		complete.sh "
 		#for $i, $f in enumerate($patients)
-			${f.id}
+ ${f.id}
             #for $j, $g in enumerate($f.samples)
-            	${g.sample}
+ ${g.sample}
             #end for
 		#end for
-		"$clonaltype_select" $out_file $out_file.files_path $species $locus $selection
+" $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection
 	</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>
+			<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">
@@ -34,6 +34,10 @@
 			<option value="igh">IGH</option>
 			<option value="igk">IGK</option>
 			<option value="igl">IGL</option>
+			<option value="trb">TRB</option>
+			<option value="tra">TRA</option>
+			<option value="trg">TRG</option>
+			<option value="trd">TRD</option>
 		</param>
 
 		<param name="selection" type="select" label="Selection">