diff multiqc.xml @ 9:df99138d2776 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945

--- a/multiqc.xml	Fri Apr 20 01:06:25 2018 -0400
+++ b/multiqc.xml	Wed Apr 25 07:59:52 2018 -0400
@@ -8,6 +8,10 @@
         ]]></token>
         <token name="@CHECK_LN_FILE@">
 <![CDATA[
+#if $file_path in $file_paths
+    #set $file_path += '_' + str($file_paths.count($file_path))
+#end if
+#set $file_paths += [$file_path]
 grep -q "$pattern" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
 ln -s '$file' '$file_path'  &&
         ]]></token>
@@ -23,6 +27,7 @@
         ]]></token>
         <token name="@LN_FILES@">
 <![CDATA[
+#set file_paths = []
 #for $file in $repeat.software_cond.input
     @ESCAPE_IDENTIFIER@
     #set file_path = os.path.join($software_dir, str($identifier))
@@ -31,6 +36,7 @@
         ]]></token>
         <token name="@LN_2_FILES@">
 <![CDATA[
+#set file_paths = []
 @CREATE_REPEAT_DIR_1@
 #for $file in $repeat2.input
     #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
@@ -40,6 +46,7 @@
         ]]></token>
         <token name="@LN_3_FILES@">
 <![CDATA[
+#set file_paths = []
 #for $file in $repeat2.type.input
     #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
     #set file_path = os.path.join($repeat_dir, str($identifier))
@@ -868,7 +875,7 @@
             <repeat name="results">
                 <conditional name="software_cond">
                     <param name="software" value="hicexplorer" />
-                    <param name="input" value="hicexplorer1.log,hicexplorer2.log" />
+                    <param name="input" value="hicexplorer1.log,hicexplorer1.log,hicexplorer2.log" />
                 </conditional>
             </repeat>
             <repeat name="results">
@@ -910,7 +917,7 @@
                     <has_text text="star_alignment_plot" />
                     <has_text text="tophat_alignment" />
                     <has_text text="hicexplorer" />
-                    
+                    <has_text text="hicexplorer1_log_1" />
                 </assert_contents>
             </output>
             <output_collection name="stats" type="list">