diff imgt_locus_split.xml @ 1:418b7dbc8947 draft

Uploaded

--- a/imgt_locus_split.xml	Thu Jul 13 10:24:39 2017 -0400
+++ b/imgt_locus_split.xml	Mon Jul 17 08:54:02 2017 -0400
@@ -4,9 +4,16 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python3 $__tool_directory__/imgt_locus_split.py 
-            --input $input
-            --loci $loci
-            --output $output
+            --input $input 
+            --output-ig ${output_ig}
+            --output-igh ${output_igh}
+            --output-igk ${output_igk}
+            --output-igl ${output_igl}
+            --output-tr ${output_tr}
+            --output-tra ${output_tra}
+            --output-trb ${output_trb}
+            --output-trd ${output_trd}
+            --output-trg ${output_trg}
     ]]></command>
     <inputs>
         <param name="input" type="data" format="data" label="The IMGT zip file to be split"/>
@@ -23,7 +30,33 @@
         </param>
     </inputs>
     <outputs>
-        <data format="imgt_archive" name="output" label="${input.name} $loci" />
+        <data format="imgt_archive" name="output_ig" label="Filtered IMGT IG: ${input.name}">
+            <filter>loci.__contains__('IG')</filter>
+        </data>
+        <data format="imgt_archive" name="output_igh" label="Filtered IMGT IGH: ${input.name}">
+            <filter>loci.__contains__('IGH')</filter>
+        </data>
+        <data format="imgt_archive" name="output_igk" label="Filtered IMGT IGK: ${input.name}">
+            <filter>loci.__contains__('IGK')</filter>
+        </data>
+        <data format="imgt_archive" name="output_igl" label="Filtered IMGT IGL: ${input.name}">
+            <filter>loci.__contains__('IGL')</filter>
+        </data>
+        <data format="imgt_archive" name="output_tr" label="Filtered IMGT TR: ${input.name}">
+            <filter>loci.__contains__('TR')</filter>
+        </data>
+        <data format="imgt_archive" name="output_tra" label="Filtered IMGT TRA: ${input.name}">
+            <filter>loci.__contains__('TRA')</filter>
+        </data>
+        <data format="imgt_archive" name="output_trb" label="Filtered IMGT TRB: ${input.name}">
+            <filter>loci.__contains__('TRB')</filter>
+        </data>
+        <data format="imgt_archive" name="output_trd" label="Filtered IMGT TRD: ${input.name}">
+            <filter>loci.__contains__('TRD')</filter>
+        </data>
+        <data format="imgt_archive" name="output_trg" label="Filtered IMGT TRG: ${input.name}">
+            <filter>loci.__contains__('TRG')</filter>
+        </data>
     </outputs>
     <help><![CDATA[
         Creates a new IMGT zip file for every checked locus with sequences from only that locus.