# HG changeset patch
# User iuc
# Date 1491395710 14400
# Node ID 0c48a4ed47a07849a27daf75514f8b43b1cdf19d
# Parent  b3eef7e04ea9de2dcedc283d99425e63249909c9
Uploaded

diff -r b3eef7e04ea9 -r 0c48a4ed47a0 multigps.xml
--- a/multigps.xml	Tue Apr 04 21:38:01 2017 -0400
+++ b/multigps.xml	Wed Apr 05 08:35:10 2017 -0400
@@ -165,13 +165,13 @@
 condition_repeat = params['condition_repeat']
 fh = open('design.tabular', 'w')
 fh.write('%s\n' % str(params))
-"""
-for cond_i, condition_items in enumerate(condition_repeat):
+for condition_items in condition_repeat:
     for signal_items in condition_items['signal_repeat']:
         signal = signal_items['signal']
+        condition_name = signal_items['condition_name']
         replicate_name = signal_items['replicate_name']
         experiment_type = signal['experiment_type']
-        line_items = [signal.file_name, 'Signal', signal.ext.upper(), cond_i, replicate_name, experiment_type]
+        line_items = [signal.file_name, 'Signal', signal.ext.upper(), condition_name, replicate_name, experiment_type]
         fixedreadcount_cond = signal_items['fixedreadcount_cond']
         fixedreadcount_select = fixedreadcount_cond['fixedreadcount_select']
         if fixedreadcount_select == 'yes':
@@ -180,7 +180,8 @@
     for control_items in condition_items['control_repeat']:
         control = control_items['control']
         experiment_type = control_items['experiment_type']
-        line_items = [control.file_name, 'Control', control.ext.upper(), cond_i]
+        condition_name = control_items['condition_name']
+        line_items = [control.file_name, 'Control', control.ext.upper(), condition_name]
         specify_replicate_name_cond = control_items['specify_replicate_name_cond']
         specify_replicate_name = specify_replicate_name_cond['specify_replicate_name']
         if specify_replicate_name == 'yes':
@@ -191,7 +192,6 @@
         if fixedreadcount_select == 'yes':
             line_items.append(fixedreadcount_cond['fixedreadcount'])
         fh.write('%s\n' % '\t'.join(line_items))
-"""
 fh.close()
 ]]>
         </configfile>
@@ -203,6 +203,7 @@
                     <validator type="unspecified_build" />
                 </param>
                 <expand macro="param_experiment_type" />
+                <param name="condition_name" type="text" label="Condition name" />
                 <param name="replicate_name" type="text" label="Replicate name" />
                 <expand macro="cond_fixedreadcount" />
             </repeat>
@@ -211,6 +212,7 @@
                     <validator type="unspecified_build" />
                 </param>
                 <expand macro="param_experiment_type" />
+                <param name="condition_name" type="text" label="Condition name" />
                 <conditional name="specify_replicate_name_cond">
                     <param  name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control.  If used, the control will only be used for the corresponding named signal replicate">
                         <option value="no" selected="True">No</option>
@@ -536,3 +538,4 @@
         </citation>
     </citations>
 </tool>
+