# HG changeset patch
# User bgruening
# Date 1375460927 14400
# Node ID c3793b7dee24e7c9eb3547e4d5dfd89951ac648c
# Parent 7f8dc9e3df053a5bfb1fd93b8b1b705728130258
Uploaded
diff -r 7f8dc9e3df05 -r c3793b7dee24 computeGCBias.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/computeGCBias.xml Fri Aug 02 12:28:47 2013 -0400
@@ -0,0 +1,144 @@
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+ computeGCBias
+ --bamfile '$bamInput'
+ --species '$species'
+ --GCbiasFrequenciesFile $outFileName
+ --fragmentLength $fragmentLength
+
+ #if $source.ref_source=="history":
+ --genome $source.input1
+ #else:
+ --genome "${source.input1_2bit.fields.path}"
+ #end if
+
+ #if $advancedOpt.showAdvancedOpt == "yes":
+ #if str($advancedOpt.region.value) != '':
+ --region '$advancedOpt.region'
+ #end if
+
+ --binSize '$advancedOpt.binSize'
+ --sampleSize '$advancedOpt.sampleSize'
+ --regionSize '$advancedOpt.regionSize'
+
+ #if $advancedOpt.filterOut:
+ --filterOut $advancedOpt.filterOut
+ #end if
+
+ #if $advancedOpt.extraSampling:
+ --extraSampling $advancedOpt.extraSampling
+ #end if
+
+ #end if
+
+ #set move=""
+ #if $output.showOutputSettings == "yes"
+ #if $output.saveBiasPlot:
+ --biasPlot biasPlot.png
+ #set move="mv biasPlot.png $biasPlot"
+ #end if
+ #end if
+ ; $move
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+ (output['showOutputSettings'] == 'yes' and output['saveBiasPlot'] == True)
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+**What it does**
+
+Computes the GC bias ussing Benjamini's method [citation]. The resulting GC
+bias can later be used to plot the bias or to correct the bias.
+
+-----
+
+.. class:: infomark
+
+Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+
+
+.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
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diff -r 7f8dc9e3df05 -r c3793b7dee24 correctGCBias.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/correctGCBias.xml Fri Aug 02 12:28:47 2013 -0400
@@ -0,0 +1,108 @@
+
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+ correctGCBias
+ --bamfile '$bamInput'
+ --species '$species'
+ --GCbiasFrequenciesFile $GCbiasFrequenciesFile
+
+ #if $source.ref_source=="history":
+ --genome $source.input1
+ #else:
+ --genome "${source.input1_2bit.fields.path}"
+ #end if
+
+ #if $advancedOpt.showAdvancedOpt == "yes":
+ #if str($advancedOpt.region.value) != '':
+ --region '$advancedOpt.region'
+ #end if
+
+ --binSize '$advancedOpt.binSize'
+ #end if
+
+ #set newoutFileName="corrected."+str($outFileFormat)
+
+ --correctedFile $newoutFileName; mv $newoutFileName $outFileName
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+**What it does**
+
+Computes the GC bias ussing Benjamini's method [citation]. The resulting GC
+bias can later be used to plot the bias or to correct the bias.
+
+-----
+
+.. class:: infomark
+
+Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+
+
+.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
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diff -r 7f8dc9e3df05 -r c3793b7dee24 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Aug 02 12:22:29 2013 -0400
+++ b/tool_dependencies.xml Fri Aug 02 12:28:47 2013 -0400
@@ -50,6 +50,7 @@
git clone --recursive https://github.com/fidelram/deepTools.git
git reset --hard 98e5d8a61431ea8605c0643d991a1a5d8999b4dc
+ $INSTALL_DIR/lib/python
export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin