diff correctGCBias.xml @ 1:21d563d5f2b2 draft

Uploaded

--- a/correctGCBias.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/correctGCBias.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,13 +1,23 @@
-<tool id="correctGCBias" name="correctGCBias" version="1.0">
+<tool id="correctGCBias" name="correctGCBias" version="1.0.1">
   <description>
   </description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
   </requirements>
   <command>
+    #import tempfile
+    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+
+    #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
+    #set $temp_bam_path = $temp_bam_handle.name + '.bam'
+    #silent $temp_bam_handle.close()
+    #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
+    #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
+
+
   correctGCBias
-  --bamfile '$bamInput'
+  --bamfile '$temp_bam_path'
   --species '$species'
   --GCbiasFrequenciesFile $GCbiasFrequenciesFile
   
@@ -32,13 +42,18 @@
   </command>
 
   <inputs>
-  
+
   <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
-  
+
   <param name="bamInput" format="bam" type="data" label="Input BAM file" help="The BAM file must be sorted and indexed."/>
-  
-  <param name="species" type="text" value="" label="Species name abbreviation" />
-  
+
+  <param name="species" type="select" label="Species name abbreviation">
+    <option value="hg19">hg19</option>
+    <option value="ce10">ce10</option>
+    <option value="dm3">dm3</option>
+    <option value="mm9">mm9</option>
+  </param>
+
   <conditional name="source">
     <param name="ref_source" type="select" label="Reference genome">
         <option value="cached">locally cached</option>