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changeset 3:d78ff3764fe5 draft

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Uploaded
author iuc
date Mon, 03 Apr 2017 13:38:23 -0400
parents 91127c200437
children 0bec3b2df784
files macros.xml multigps.xml
diffstat 2 files changed, 31 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Apr 03 11:21:10 2017 -0400
+++ b/macros.xml	Mon Apr 03 13:38:23 2017 -0400
@@ -5,4 +5,22 @@
         <param name="mememinw" type="integer" min="0" value="6" label="Minimum motif width for MEME" />
         <param name="mememaxw" type="integer" min="0" value="16" label="Maximum motif width for MEME" />
     </xml>
+    <xml name="label_cond_params_start">
+        <param name="input" type="data" format="bam,bed,scidx" label="Run multigps on" help="Supported formats are bam, bed and scidx">
+            <validator type="unspecified_build" />
+        </param>
+        <param name="control" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" />
+        <param name="condition_name" type="text" label="Condition name" />
+    </xml>
+    <xml name="label_cond_params_end">
+        <param name="experiment_type" type="select" label="Experiment type for this replicate">
+            <option value="None" selected="True">Do not set</option>
+            <option value="chipseq">ChIP-seq</option>
+            <option value="chipexo">ChIP-exo</option>
+        </param>
+        <param  name="fixedreadcount" type="select" label="Use fixed per-base read count limit for this replicate?" help="Selecting No uses a global per-base limit that is estimated from a Poisson distribution.">
+            <option value="None" selected="True">No</option>
+            <option value="P">Yes</option>
+        </param>
+    </xml>
 </macros>
--- a/multigps.xml	Mon Apr 03 11:21:10 2017 -0400
+++ b/multigps.xml	Mon Apr 03 13:38:23 2017 -0400
@@ -13,20 +13,20 @@
             #set single_or_multi_expt = $single_or_multi_expt_cond.single_or_multi_expt
             #if str($single_or_multi_expt) == 'multi':
                 #for $i in $single_or_multi_expt_cond['input_items']:
-                    #set file_name = $i['input']
                     #set label_cond = $i['label_cond']
+                    #set file_name = $label_cond.input
                     #set label = $label_cond.label
-                    #set file_format = $i['input'].ext
-                    #set condition_name = $i['condition_name']
+                    #set file_format = $label_cond.input.ext
+                    #set condition_name = $label_cond.condition_name
                     #set replicate_name = 'None'
-                    #set experiment_type = $i['experiment_type']
-                    #set fixed_read_count = $i['fixedreadcount']
+                    #set experiment_type = $label_cond.experiment_type
+                    #set fixed_read_count = $label_cond.fixedreadcount
                     #if str($label) == 'Signal':
-                        #set replicate_name = $label_cond['replicate_name']
+                        #set replicate_name = $label_cond.replicate_name
                     #else if str($label) == 'Control':
-                        #set rncond = $label_cond['replicate_name_cond']
-                        #if str($rncond['specify_replicate_name']) == 'yes':
-                            #set replicate_name = $rncond['replicate_name']
+                        #set rncond = $label_cond.replicate_name_cond
+                        #if str($rncond.specify_replicate_name) == 'yes':
+                            #set replicate_name = $rncond.replicate_name
                         #end if
                     #end if
                     --input_item '$file_name' '$label' '$file_format' '$condition_name' '$replicate_name' '$experiment_type' '$fixed_read_count'
@@ -186,18 +186,18 @@
             </param>
             <when value="multi">
                 <repeat name="input_items" title="Input files, attributes and options" min="2">
-                    <param name="input" type="data" format="bam,bed,scidx" label="Run multigps on" help="Supported formats are bam, bed and scidx">
-                        <validator type="unspecified_build" />
-                    </param>
                     <conditional name="label_cond">
                         <param name="label" type="select" label="This experiment is">
                             <option value="Signal" selected="True">Signal</option>
                             <option value="Control">Control</option>
                         </param>
                         <when value="Signal">
+                            <expand macro="label_cond_params_start" />
                             <param name="replicate_name" type="text" label="Replicate name" />
+                            <expand macro="label_cond_params_end" />
                         </when>
                         <when value="Control">
+                            <expand macro="label_cond_params_start" />
                             <conditional name="replicate_name_cond">
                                 <param  name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control experiments.  If used, the control will only be used for the corresponding named signal replicate">
                                     <option value="no" selected="True">No</option>
@@ -208,18 +208,9 @@
                                 </when>
                                 <when value="no" />
                             </conditional>
+                            <expand macro="label_cond_params_end" />
                         </when>
                     </conditional>
-                    <param name="condition_name" type="text" label="Condition name" />
-                    <param name="experiment_type" type="select" label="Experiment type for this replicate">
-                        <option value="None" selected="True">Do not set</option>
-                        <option value="chipseq">ChIP-seq</option>
-                        <option value="chipexo">ChIP-exo</option>
-                    </param>
-                    <param  name="fixedreadcount" type="select" label="Use fixed per-base read count limit for this replicate?" help="Selecting No uses a global per-base limit that is estimated from a Poisson distribution.">
-                        <option value="None" selected="True">No</option>
-                        <option value="P">Yes</option>
-                    </param>
                 </repeat>
             </when>
             <when value="single">