# HG changeset patch
# User bgruening
# Date 1417634607 18000
# Node ID 6947d8ed51cc93052642b6a3b186f62f08ba4909
# Parent  05a4f4e317a015c80278f9c862a9f21464e74bf5
Uploaded

diff -r 05a4f4e317a0 -r 6947d8ed51cc deseq2.xml
--- a/deseq2.xml	Wed Nov 26 12:16:47 2014 -0500
+++ b/deseq2.xml	Wed Dec 03 14:23:27 2014 -0500
@@ -24,8 +24,8 @@
                 #set $temp_factor = list()
                 #for $level in $factor.rep_factorLevel:
                     #set $count_files = list()
-                    #for $file in $level.rep_countsFile:
-                        $count_files.append(str($file.countsFile))
+                    #for $file in $level.countsFile:
+                        $count_files.append(str($file))
                     #end for
                     $temp_factor.append( {str($level.factorLevel): $count_files} )
                 #end for
@@ -66,9 +66,7 @@
                         <valid initial="string.letters,string.digits"><add value="_" /></valid>
                     </sanitizer>
                 </param>
-                <repeat name="rep_countsFile" title="biological replicate" min="1">
-                    <param name="countsFile" type="data" label="Counts file"/>
-                </repeat>
+                <param name="countsFile" type="data" multiple="true" label="Counts file"/>
             </repeat>
         </repeat>
         <conditional name="filtermode">
@@ -83,7 +81,7 @@
                 <param name="count_quant" size="10" type="float" value="10.0" min="0" max="100" label="Filter out features with mean normalized counts lower than this % of values" />
             </when>
         </conditional>
-        <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" label="Visualising the analysis results"
+        <param name="pdf" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Visualising the analysis results"
             help="output an additional PDF files" />
     </inputs>
 
@@ -101,32 +99,14 @@
                 <param name="factorName" value="Treatment"/>
                 <repeat name="rep_factorLevel">
                     <param name="factorLevel" value="Treated"/>
-                    <repeat name="rep_countsFile">
-                        <param name="countsFile" value="GSM461179_treat_single.counts"/>
-                    </repeat>
-                    <repeat name="rep_countsFile">
-                        <param name="countsFile" value="GSM461180_treat_paired.counts"/>
-                    </repeat>
-                    <repeat name="rep_countsFile">
-                        <param name="countsFile" value="GSM461181_treat_paired.counts"/>
-                    </repeat>
+                    <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
                 </repeat>
                 <repeat name="rep_factorLevel">
                     <param name="factorLevel" value="Untreated"/>
-                    <repeat name="rep_countsFile">
-                        <param name="countsFile" value="GSM461176_untreat_single.counts"/>
-                    </repeat>
-                    <repeat name="rep_countsFile">
-                        <param name="countsFile" value="GSM461177_untreat_paired.counts"/>
-                    </repeat>
-                    <repeat name="rep_countsFile">
-                        <param name="countsFile" value="GSM461178_untreat_paired.counts"/>
-                    </repeat>
-                    <repeat name="rep_countsFile">
-                        <param name="countsFile" value="GSM461182_untreat_single.counts"/>
-                    </repeat>
+                    <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
                 </repeat>
             </repeat>
+            <param name="pdf" value="no"/>
             <output name="deseq_out" file="deseq2_out.tab"/>
             <output name="deseq_out_filtered" file="deseq2_out_filtered.tab"/>
         </test>