# HG changeset patch
# User bgruening
# Date 1385733544 18000
# Node ID c54d31467be4a4e6ac7a3d3aebb30c1043e2f96f
# Parent  ac935c35437ab61db0036ac32118bf48c0ca2271
Uploaded

diff -r ac935c35437a -r c54d31467be4 bamCorrelate.xml
--- a/bamCorrelate.xml	Sat Nov 16 07:54:13 2013 -0500
+++ b/bamCorrelate.xml	Fri Nov 29 08:59:04 2013 -0500
@@ -15,14 +15,7 @@
 
         bamCorrelate
 
-        #if $mode.modeOpt == "bins":
-            bins
-            --binSize '$mode.binSize'
-            --numberOfSamples '$mode.numberOfSamples'
-        #else:
-            BED-file
-            --BED $mode.region_file
-        #end if
+        $mode.modeOpt
 
         @THREADS@
 
@@ -40,6 +33,13 @@
             --outFileCorMatrix '$outFileCorMatrix'
         #end if
 
+        #if $mode.modeOpt == "bins":
+            --binSize '$mode.binSize'
+            --numberOfSamples '$mode.numberOfSamples'
+        #else:
+            --BED $mode.region_file
+        #end if
+
         ## options available in both modes
         #if $mode.advancedOpt.showAdvancedOpt == "yes":
 
diff -r ac935c35437a -r c54d31467be4 computeGCBias.xml
--- a/computeGCBias.xml	Sat Nov 16 07:54:13 2013 -0500
+++ b/computeGCBias.xml	Fri Nov 29 08:59:04 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 ac935c35437a -r c54d31467be4 correctGCBias.xml
--- a/correctGCBias.xml	Sat Nov 16 07:54:13 2013 -0500
+++ b/correctGCBias.xml	Fri Nov 29 08:59:04 2013 -0500
@@ -16,6 +16,9 @@
 
 
   correctGCBias
+
+    @THREADS@
+
   --bamfile '$temp_bam_path'
   --GCbiasFrequenciesFile $GCbiasFrequenciesFile
 
diff -r ac935c35437a -r c54d31467be4 deepTools_macros.xml
--- a/deepTools_macros.xml	Sat Nov 16 07:54:13 2013 -0500
+++ b/deepTools_macros.xml	Fri Nov 29 08:59:04 2013 -0500
@@ -46,7 +46,7 @@
             <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="0.7.6">pysam</requirement>
+            <requirement type="package" version="0.7.7">pysam</requirement>
             <requirement type="package" version="0.1.19">samtools</requirement>
             <yield />
         </requirements>
diff -r ac935c35437a -r c54d31467be4 readme.rst
--- a/readme.rst	Sat Nov 16 07:54:13 2013 -0500
+++ b/readme.rst	Fri Nov 29 08:59:04 2013 -0500
@@ -29,7 +29,7 @@
 Citation
 ========
 
-deeptools are currently under review. In the meantime please refere to
+deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
 
 
 =======
@@ -39,25 +39,23 @@
 - v1.0: Initial public release
 
 
-===============================
-Wrapper Licence (MIT/BSD style)
-===============================
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
-
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff -r ac935c35437a -r c54d31467be4 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Nov 16 07:54:13 2013 -0500
+++ b/tool_dependencies.xml	Fri Nov 29 08:59:04 2013 -0500
@@ -4,16 +4,16 @@
         <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="796c0081adad" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.2.1">
         <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="303d29ec30e5" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d277bf006c3e" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="pysam" version="0.7.6">
-        <repository changeset_revision="9d817cc2c290" name="package_pysam_0_7_6" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <package name="pysam" version="0.7.7">
+        <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="ucsc_tools" version="0.1">
@@ -59,8 +59,8 @@
             <actions>
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="f3f4b6121444" name="package_pysam_0_7_5" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
-                        <package name="pysam" version="0.7.5" />
+                    <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.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>