# HG changeset patch
# User bgruening
# Date 1385661508 18000
# Node ID 351cd1f8791beb1fcbd695f6c9328e2206902d62
# Parent  b0d64a9930d6247a6235bdcc64acf40145057386
Uploaded

diff -r b0d64a9930d6 -r 351cd1f8791b bamCorrelate.xml
--- a/bamCorrelate.xml	Thu Nov 14 05:43:15 2013 -0500
+++ b/bamCorrelate.xml	Thu Nov 28 12:58:28 2013 -0500
@@ -15,6 +15,15 @@
 
         bamCorrelate
 
+        #if $mode.modeOpt == "bins":
+            bins
+            --binSize '$mode.binSize'
+            --numberOfSamples '$mode.numberOfSamples'
+        #else:
+            BED-file
+            --BED $mode.region_file
+        #end if
+
         @THREADS@
 
         --bamfiles #echo " ".join($files)
@@ -31,13 +40,6 @@
             --outFileCorMatrix '$outFileCorMatrix'
         #end if
 
-        #if $mode.modeOpt == "bins":
-            --binSize '$mode.binSize'
-            --numberOfSamples '$modenumberOfSamples'
-        #else:
-            --BED $mode.region_file
-        #end if
-
         ## options available in both modes
         #if $mode.advancedOpt.showAdvancedOpt == "yes":
 
diff -r b0d64a9930d6 -r 351cd1f8791b bigwigCompare.xml
--- a/bigwigCompare.xml	Thu Nov 14 05:43:15 2013 -0500
+++ b/bigwigCompare.xml	Thu Nov 28 12:58:28 2013 -0500
@@ -29,6 +29,10 @@
 
         #end if
     </command>
+    <stdio>
+        <regex match="Error:" />
+        <regex match="EXception:" />
+    </stdio>
     <inputs>
         <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
         <param name="bigwigFile2" format="bigwig" type="data" label="Input bigwig file" />
diff -r b0d64a9930d6 -r 351cd1f8791b computeGCBias.xml
--- a/computeGCBias.xml	Thu Nov 14 05:43:15 2013 -0500
+++ b/computeGCBias.xml	Thu Nov 28 12:58:28 2013 -0500
@@ -8,63 +8,52 @@
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
-        #import tempfile
-        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+        ln -s $bamInput local_bamInput.bam;
+        ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
 
-    #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))
+        computeGCBias
 
-  computeGCBias
-
-    @THREADS@
+            @THREADS@
 
-  --bamfile '$temp_bam_path'
-  --GCbiasFrequenciesFile $outFileName
-  --fragmentLength $fragmentLength
+            --bamfile 'local_bamInput.bam'
+            --GCbiasFrequenciesFile $outFileName
+            --fragmentLength $fragmentLength
 
-    @reference_genome_source@
-
+            @reference_genome_source@
 
-  #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
-    --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
-  #else:
-    --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
-  #end if
-
+            #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
+            #else:
+                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
+            #end if
 
-  #if $advancedOpt.showAdvancedOpt == "yes":
-    #if str($advancedOpt.region.value) != '':
-      --region '$advancedOpt.region'
-    #end if
-    
-    --sampleSize '$advancedOpt.sampleSize'
-    --regionSize '$advancedOpt.regionSize'
+            #if $advancedOpt.showAdvancedOpt == "yes":
+                #if str($advancedOpt.region.value) != '':
+                    --region '$advancedOpt.region'
+                #end if
 
-    #if $advancedOpt.filterOut:
-      --filterOut $advancedOpt.filterOut
-    #end if
+                --sampleSize '$advancedOpt.sampleSize'
+                --regionSize '$advancedOpt.regionSize'
+
+                #if $advancedOpt.filterOut:
+                    --filterOut $advancedOpt.filterOut
+                #end if
 
-    #if $advancedOpt.extraSampling:
-      --extraSampling $advancedOpt.extraSampling
-    #end if
-
-  #end if
+                #if $advancedOpt.extraSampling:
+                    --extraSampling $advancedOpt.extraSampling
+                #end if
+            #end if
 
-  #if $saveBiasPlot:
-    --biasPlot $biasPlot
-  #end if
+            #if $saveBiasPlot:
+                --biasPlot $biasPlot
+            #end if
 
-##  #if $output.showOutputSettings == "yes"
-##      #if $output.saveBiasPlot:
-##        --biasPlot biasPlot.png ;
-##        mv biasPlot.png $biasPlot
-##      #end if
-##  #end if
-
-  ; rm $temp_dir -rf
+        ##  #if $output.showOutputSettings == "yes"
+        ##      #if $output.saveBiasPlot:
+        ##        --biasPlot biasPlot.png ;
+        ##        mv biasPlot.png $biasPlot
+        ##      #end if
+        ##  #end if
 
     </command>
     <inputs>
diff -r b0d64a9930d6 -r 351cd1f8791b deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Nov 14 05:43:15 2013 -0500
+++ b/deepTools_macros.xml	Thu Nov 28 12:58:28 2013 -0500
@@ -40,14 +40,14 @@
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
     <macro name="requirements">
         <requirements>
-            <requirement type="package" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b">deepTools</requirement>
-            <requirement type="package" version="0.1">ucsc_tools</requirement>
-            <requirement type="package" version="1.7.1">numpy</requirement>
-            <requirement type="package" version="0.7.6">pysam</requirement>
-            <requirement type="package" version="0.1.19">samtools</requirement>
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
+            <requirement type="package" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">deepTools</requirement>
+            <requirement type="package" version="0.1">ucsc_tools</requirement>
+            <requirement type="package" version="1.7.1">numpy</requirement>
+            <requirement type="package" version="0.7.7">pysam</requirement>
+            <requirement type="package" version="0.1.19">samtools</requirement>
             <yield />
         </requirements>
         </macro>
diff -r b0d64a9930d6 -r 351cd1f8791b tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 14 05:43:15 2013 -0500
+++ b/tool_dependencies.xml	Thu Nov 28 12:58:28 2013 -0500
@@ -12,8 +12,8 @@
     <package name="scipy" version="0.12.0">
         <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="pysam" version="0.7.6">
-        <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="pysam" version="0.7.7">
+        <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="ucsc_tools" version="0.1">
@@ -54,17 +54,17 @@
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-    <package name="deepTools" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b">
+    <package name="deepTools" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">
         <install version="1.0">
             <actions>
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="pysam" version="0.7.5" />
+                    <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="pysam" version="0.7.7" />
                     </repository>
                 </action>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
-                <action type="shell_command">git reset --hard 91b873c095bb4ca44da99e57d8b49784508aa98b</action>
+                <action type="shell_command">git reset --hard 323fa6bf083c9d40e5092a6364a4ab8fee57507a</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
@@ -73,7 +73,7 @@
 
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                     <!-- disable the config file of deepTools -->
                     <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
                 </action>