# HG changeset patch
# User bgruening
# Date 1375462459 14400
# Node ID f9390e176b8fab17a1986b3dd83a9f05614c4513
# Parent e343dca92ee723e795530c07dad242571426d6d0
Uploaded
diff -r e343dca92ee7 -r f9390e176b8f bigwigCompare.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwigCompare.xml Fri Aug 02 12:54:19 2013 -0400
@@ -0,0 +1,120 @@
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+ compares two bigwig files based on the number of mapped reads
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+ bigwigCompare
+ --bigwig1 '$bigwigFile1'
+ --bigwig2 '$bigwigFile2'
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+ --outFileName '$outFileName'
+ --outFileFormat '$outFileFormat'
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+ --ratio $comparison_type
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+ #if $advancedOpt.showAdvancedOpt == "yes":
+ #if str($advancedOpt.region.value) != '':
+ --region '$advancedOpt.region'
+ #end if
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+ --missingDataAsZero $advancedOpt.missingDataAsZero
+ --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
+ --pseudocount '$advancedOpt.pseudocount'
+ --binSize $advancedOpt.binSize
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+ #end if
+ --numberOfProcessors 4
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+ argsparse
+ pysam
+ numpy
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+**What it does**
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+This tool compares two bigwig files based on the number of mapped reads. To
+compare the bigwig files the genome is partitioned into bins of equal size,
+then the number of reads found in each BAM file are counted for such bins and
+finally a summarizing value is reported. This vaule can be the ratio of the
+number of readsper bin, the log2 of the ratio, the sum or the difference.
+
+-----
+
+.. 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 e343dca92ee7 -r f9390e176b8f computeMatrix.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/computeMatrix.xml Fri Aug 02 12:54:19 2013 -0400
@@ -0,0 +1,191 @@
+
+ summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile
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+ computeMatrix
+ $mode.mode_select
+ --regionsFileName '$regionsFile'
+ --scoreFileName '$scoreFile'
+ --outFileName '$outFileName'
+
+ #if $output.showOutputSettings == "yes"
+ #if $output.saveData:
+ --outFileNameData '$outFileNameData'
+ #end if
+ #if $output.saveMatrix:
+ --outFileNameMatrix '$outFileNameMatrix'
+ #end if
+
+ #if $output.saveSortedRegions:
+ --outFileSortedRegions '$outFileSortedRegions'
+ #end if
+ #end if
+
+ #if $mode.mode_select == "reference-point":
+ --referencePoint $mode.referencePoint
+ $mode.nanAfterEnd
+ --beforeRegionStartLength $mode.beforeRegionStartLength
+ --afterRegionStartLength $mode.afterRegionStartLength
+ #else
+ --regionBodyLength $mode.regionBodyLength
+ --startLabel $mode.startLabel
+ --endLabel $mode.endLabel
+ #if $mode.regionStartLength.regionStartLength_select == "yes":
+ --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
+ --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
+ #end if
+ #end if
+
+ #if $advancedOpt.showAdvancedOpt == "yes":
+ --sortRegions '$advancedOpt.sortRegions'
+ --sortUsing '$advancedOpt.sortUsing'
+ --averageTypeBins '$advancedOpt.averageTypeBins'
+ $advancedOpt.missingDataAsZero
+ $advancedOpt.skipZeros
+
+ #if $advancedOpt.minThreshold:
+ --minThreshold $advancedOpt.minThreshold
+ #end if
+ #if $advancedOpt.maxThreshold:
+ --maxThreshold $advancedOpt.maxThreshold
+ #end if
+ #if $advancedOpt.scale:
+ --scale $advancedOpt.scale
+ #end if
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+ #end if
+ --numberOfProcessors 4
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+ (output['showOutputSettings'] == 'yes' and output['saveData'] == True)
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+ (output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)
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+ (output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)
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+**What it does**
+
+This tool summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile. Typically, these genomic regions are genes, but any other regions defined in a BED or GFF format can be used. This tool can also be used to filter and sort regions according to their score.
+
+-----
+
+.. class:: infomark
+
+Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+
+
+.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
+
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+
diff -r e343dca92ee7 -r f9390e176b8f correctGCBias.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/correctGCBias.xml Fri Aug 02 12:54:19 2013 -0400
@@ -0,0 +1,108 @@
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+ correctGCBias
+ --bamfile '$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 '$advancedOpt.region'
+ #end if
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+ --binSize '$advancedOpt.binSize'
+ #end if
+
+ #set newoutFileName="corrected."+str($outFileFormat)
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+ --correctedFile $newoutFileName; mv $newoutFileName $outFileName
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+**What it does**
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+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 e343dca92ee7 -r f9390e176b8f tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Aug 02 12:54:19 2013 -0400
@@ -0,0 +1,7 @@
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