# HG changeset patch
# User bgruening
# Date 1455550233 18000
# Node ID edc6597ff21e68175f666e8a0bb6b5ec54d0fadf
# Parent 268ab1ca409156891e82825a16719cc44c921a4c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
diff -r 268ab1ca4091 -r edc6597ff21e deepTools_macros.xml
--- a/deepTools_macros.xml Mon Jan 25 20:21:48 2016 -0500
+++ b/deepTools_macros.xml Mon Feb 15 10:30:33 2016 -0500
@@ -72,12 +72,12 @@
--numberOfProcessors "\${GALAXY_SLOTS:-4}"
- 2.0.1
+ 2.1.0
python
@BINARY@
- deepTools
+ deepTools
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--kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
#end if
#end if
+ #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
+ #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
+ --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
+ #end if
+ #end if
#end if
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help="Title of the plot, to be printed on top of the generated image." />
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+ #if $advancedOpt.doExtendCustom.doExtend == 'custom':
+ --extendReads $advancedOpt.doExtendCustom.extendReadsValue
+ #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
+ --extendReads
+ #end if
+ $advancedOpt.ignoreDuplicates
+ $advancedOpt.centerReads
+ #if $advancedOpt.minMappingQuality:
+ --minMappingQuality '$advancedOpt.minMappingQuality'
+ #end if
+ #if $advancedOpt.samFlagInclude:
+ --samFlagInclude $advancedOpt.samFlagInclude
+ #end if
+ #if $advancedOpt.samFlagExclude:
+ --samFlagExclude $advancedOpt.samFlagExclude
+ #end if
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+ #if str($plotting_type.zMin) != "":
+ --zMin $plotting_type.zMin
+ #end if
+ #if str($plotting_type.zMax) != "":
+ --zMax $plotting_type.zMax
+ #end if
+ --colorMap '$plotting_type.colorMap'
+ $plotting_type.plotNumbers
+ --plotTitle '$plotting_type.plotTitle'
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+ --numberOfProcessors "\${GALAXY_SLOTS:-4}"
+<<<<<<< HEAD
+ 2.0.1.0
+=======
+ 2.1.0
+>>>>>>> d56067f86089e75354a2fad266002db3730766d9
+
+
+ python
+ @BINARY@
+<<<<<<< HEAD
+ deepTools
+=======
+ deepTools
+>>>>>>> d56067f86089e75354a2fad266002db3730766d9
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+ @BINARY@ --version
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+ #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
+ #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
+ #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
+ --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
+ #end if
+ #end if
+ #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
+ #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
+ --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
+ #end if
+ #end if
+ #end if
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+.. class:: infomark
+
+For more information on the tools, please visit our `help site`_.
+
+If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
+
+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://www.ie-freiburg.mpg.de/bioinformaticsfac
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _help site: https://deeptools.readthedocs.org/
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+ 10.1093/nar/gku365
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+ #if $source.ref_source=="history":
+ --genome $source.input1
+ #else:
+ --genome "$source.input1_2bit.fields.path"
+ #end if
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+ ((
+ output['showOutputSettings'] == 'yes' and
+ output['saveMatrix'] is True
+ ))
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+ ((
+ output['showOutputSettings'] == 'yes' and
+ output['saveSortedRegions'] is True
+ ))
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diff -r 268ab1ca4091 -r edc6597ff21e plotCoverage.xml
--- a/plotCoverage.xml Mon Jan 25 20:21:48 2016 -0500
+++ b/plotCoverage.xml Mon Feb 15 10:30:33 2016 -0500
@@ -1,5 +1,5 @@
- plots a histogram of coverage on genomic regions
+ assesses the sequencing depth of BAM files
plotCoverage
deepTools_macros.xml
@@ -82,16 +82,37 @@
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diff -r 268ab1ca4091 -r edc6597ff21e tool_dependencies.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml.orig Mon Feb 15 10:30:33 2016 -0500
@@ -0,0 +1,76 @@
+
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+
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+<<<<<<< HEAD
+
+
+=======
+
+
+
+
+
+
+
+
+>>>>>>> d56067f86089e75354a2fad266002db3730766d9
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+ https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz
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+ $INSTALL_DIR/bin
+ $INSTALL_DIR
+ $INSTALL_DIR
+ $INSTALL_DIR
+ $INSTALL_DIR/bin
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+ $ENV[LIBPNG_LIB_PATH]
+ $ENV[LIBPNG_LIB_PATH]
+
+ TRUE
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+
+
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+ Installation of deepTools from Fidel Ramirez.
+ https://github.com/fidelram/deepTools
+
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+