diff bamCorrelate.xml @ 1:21d563d5f2b2 draft

Uploaded

--- a/bamCorrelate.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/bamCorrelate.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,20 +1,36 @@
-<tool id="bamCorrelate" name="bamCorrelate" version="1.0">
+<tool id="bamCorrelate" name="bamCorrelate" version="1.0.1">
   <description>corrlates pairs of bam files</description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
   <command>
-  #set files=[]
-  #set labels=[]
-  #for $i in $inputs
-    #set $files += [str($i.bamfile)]
-    #if str($i.label.value) != "":
-        #set $labels += ["\"%s\"" % ($i.label.value)]
-    #else
-        #set $labels += ["\"%s\"" % ($i.bamfile.name)]
-    #end if
-  #end for
+    #import tempfile
+    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+
+    #set files=[]
+    #set labels=[]
+    #for $i in $inputs
+
+        #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.bamfile), $temp_input_path))
+        #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
+        #silent $files.append('%s.bam' % $temp_input_path)
+
+
+        ##set $files += [str($i.bamfile)]
+        #if str($i.label.value) != "":
+            #set $labels += ["\"%s\"" % ($i.label.value)]
+        #else
+            #set $labels += ["\"%s\"" % ($i.bamfile.name)]
+        #end if
+    #end for
   bamCorrelate
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --bamfiles #echo " ".join($files)
   --labels #echo " ".join($labels)
   
@@ -25,12 +41,8 @@
   --plotFile $newoutFileName
   
   #if $outputOpt.showOutputOpt == "yes"
-      #if $outputOpt.outFileRawCounts:
-        --outRawCounts '$outputOpt.outFileRawCounts' 
-      #end if
-      #if $outputOpt.outFileCorMatrix:
-        --outFileCorMatrix '$outputOpt.outFileCorMatrix'
-      #end if
+        --outRawCounts '$outFileRawCounts' 
+        --outFileCorMatrix '$outFileCorMatrix'
   #end if
   
   #if $advancedOpt.showAdvancedOpt == "yes":
@@ -53,12 +65,11 @@
       --minMappingQuality '$advancedOpt.minMappingQuality'
     #end if
   #end if
-  
-  --numberOfProcessors 4; mv $newoutFileName $outFileName
+  ; mv $newoutFileName $outFileName
+  ; rm $temp_dir -rf
   </command>
 
   <inputs>
-  
   <repeat name="inputs" title="Input files" min="2">
     <param name="bamfile" type="data" format="bam" 
         label="Bam file" 
@@ -67,7 +78,7 @@
         label="Label"
         help="Label to use in the output. If not given the dataset name will be used instead."/>
   </repeat>
-  
+
   <param name="fragmentLength" type="integer" value="300" min="1"
        label="Length of the average fragment size"
        help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>