# HG changeset patch
# User greg
# Date 1503577118 14400
# Node ID 4afd642aa3ce64d1e7ef4bd65ec8b7a95cc5bd9b
# Parent  f2aaf4b141af397dc72303bde5c194474086b5ce
Uploaded

diff -r f2aaf4b141af -r 4afd642aa3ce ideas.xml
--- a/ideas.xml	Thu Aug 24 08:12:05 2017 -0400
+++ b/ideas.xml	Thu Aug 24 08:18:38 2017 -0400
@@ -109,9 +109,12 @@
 && mv ./*.state $output_state
     ]]></command>
     <configfiles>
-        <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
+        <configfile name="prep_input_config"><![CDATA[
+#if $input_type_cond == "datasets" and $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual":
+    #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
-#end for ]]></configfile>
+    #end for
+#end if]]></configfile>
     </configfiles>
     <inputs>
         <conditional name="input_type_cond">
@@ -122,8 +125,8 @@
             <when value="datasets">
                 <conditional name="cell_type_epigenetic_factor_cond">
                     <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by">
-                        <option value="extract">extracting them from the selected input file names</option>
-                        <option value="manual" selected="true">manually setting them for each selected input</option>
+                        <option value="extract" selected="true">extracting them from the selected input file names</option>
+                        <option value="manual">manually setting them for each selected input</option>
                     </param>
                     <when value="extract">
                         <param name="input" type="data" format="bigwig,bam" multiple="True" label="BAM or BigWig file">