diff region_motif_compare.xml @ 35:4ce22698acb0 draft

Uploaded

--- a/region_motif_compare.xml	Tue Feb 10 02:03:15 2015 -0500
+++ b/region_motif_compare.xml	Thu Feb 26 22:54:09 2015 -0500
@@ -4,18 +4,28 @@
     <requirement type="set_environment">RMOTIF_PATH</requirement>
   </requirements>
   <command interpreter="Rscript">
-    region_motif_compare.r --args \$RMOTIF_PATH $db_type $in_tab_1 $in_tab_2 $out_enriched $out_depleted $out_plots
+    region_motif_compare.r --args \$RMOTIF_PATH $pwm_file.fields.path $in_tab_1 $in_tab_2 
+    $out_enriched 
+    $out_depleted 
+    $out_plots
   </command>
   <inputs>
     <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/>
     <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/>
+
+    <param name="pwm_file" type="select" label="Using motif database PWM file">
+      <options from_data_table="motif_databases"/>
+    </param>
+    
+    <!-- COMBINED OPTION IS LOST
     <param name="db_type" type="select" label="Select Motif Database" >
-      <option value="t">Test Pouya Subset (hg19)</option>
-      <option value="p">Pouya Encode Motifs (hg19)</option>
+      <option value="t">Test Encode Motifs (hg19)</option>
+      <option value="e">Encode Motifs (hg19)</option>
       <option value="j">Jaspar and Jolma Motifs (hg19)</option>
       <option value="m">Mouse Motifs (mm9)</option>
       <option value="c">Pouya, Jaspar, and Jolma Combined (hg19)</option>
-    </param>
+    </param> -->
+
   </inputs>
   <outputs>
     <data name="out_enriched" format="tabular" label="Enriched Motifs"/>