changeset 71:106cd88dc9da draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty

--- a/deepTools_macros.xml	Fri Sep 18 06:17:07 2015 -0400
+++ b/deepTools_macros.xml	Fri Sep 18 07:34:39 2015 -0400
@@ -198,14 +198,9 @@
     </xml>
 
     <xml name="multiple_input_bigwigs">
-        <repeat name="input_files" title="BigWig files" min="2">
-            <param name="bigwigfile" type="data" format="bigwig" 
-                label="Bigwig file" 
-                help="The Bigwig file must be sorted."/>
-            <param name="label" type="text" size="30" optional="true" value=""
-                label="Label"
-                help="Label to use in the output. If not given the dataset name will be used instead."/>
-        </repeat>
+        <param name="bigwigfile" type="data" format="bigwig" multiple="True"
+            label="Bigwig file" 
+            help="The Bigwig file must be sorted."/>
     </xml>
 
     <xml name="plotTitle">
@@ -215,41 +210,28 @@
     </xml>
 
     <token name="@multiple_input_bams@">
-        #import tempfile
-        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+<![CDATA[
         #set files=[]
         #set labels=[]
-        #for $i in $bamfiles:
-            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
-            #set $temp_input_path = $temp_input_handle.name
-            #silent $temp_input_handle.close()
-            #silent os.system("ln -s %s %s.bam" % (str($i), $temp_input_path))
-            #silent os.system("ln -s %s %s.bam.bai" % (str($i.metadata.bam_index), $temp_input_path))
-            #silent $files.append('%s.bam' % $temp_input_path)
-
-            #silent $labels.append("\"%s\"" % ($i.name))
+        #for $counter, $bamfile in enumerate($bamfiles):
+            ln -s "${bamfile}" "./${counter}.bam" &&
+            ln -s "${bamfile}" "./${counter}.bam.bai" &&
+            #silent $files.append('%s.bam' % $counter)
+            #silent $labels.append("'%s'" % ($bamfile.name))
         #end for
+]]>
     </token>
 
     <token name="@multiple_input_bigwigs@">
-        #import tempfile
-        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+<![CDATA[
         #set files=[]
         #set labels=[]
-        #for $i in $input_files:
-            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
-            #set $temp_input_path = $temp_input_handle.name
-            #silent $temp_input_handle.close()
-            #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
-            #silent $files.append('%s.bw' % $temp_input_path)
-
-            ##set $files += [str($i.bigwigfile)]
-            #if str($i.label.value) != "":
-                #set $labels += ["\"%s\"" % ($i.label.value)]
-            #else
-                #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
-            #end if
+        #for $counter, $bigwig in enumerate($input_files):
+            ln -s "${bigwig}" "${counter}.bw" &&
+            #silent $files.append('%s.bw' % $counter)
+            #silent $labels.append("'%s'" % ($bigwig.name))
         #end for
+]]>
     </token>
 
     <xml name="reference_genome_source">