# HG changeset patch # User bgruening # Date 1455550078 18000 # Node ID 36f655a04a57b3259d4e1ed273b2d411a50e68e1 # Parent 19a6007845ccec28ac32b1b8e2323e77bb3e04cf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 diff -r 19a6007845cc -r 36f655a04a57 bamCoverage.xml --- a/bamCoverage.xml Mon Jan 25 20:19:01 2016 -0500 +++ b/bamCoverage.xml Mon Feb 15 10:27:58 2016 -0500 @@ -21,13 +21,13 @@ #if $scaling.type=='rpkm': --normalizeUsingRPKM + --scaleFactor $scaling.scaleFactor #elif $scaling.type=='1x': #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize #else: --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt #end if - #elif $scaling.type=='own': --scaleFactor $scaling.scaleFactor #end if @@ -156,7 +156,9 @@ `_ +.. image:: $PATH_TO_IMAGES/bamCoverage_output.png + :width: 600 + :height: 450 -**Output files**: +Usage hints +------------ -- coverage file either in bigWig or bedGraph format +* A smaller ``bin size`` value will result in a higher resolution of the coverage track but also in a larger file size. +* The ``1x normalization`` (RPGC) requires the input of a value for the **effective genome size**, which is the mappable part of the reference genome. Of course, this value is species-specific. +* It might be useful for some studies to exclude certain chromosomes in order to avoid biases, e.g. chromosome X for many mammals where the males contain a pair of each autosome, but often only a single X chromosome. +* By default, the read length is **NOT** extended! This is the preferred setting for **spliced-read** data like RNA-seq, where one usually wants to rely on the detected read locations only. A read extension would neglect potential splice sites in the unmapped part of the fragment. + Other data, e.g. ChIP-seq, where fragments are known to map contiuously, should be processed with read extension (``--extendReads [INT]``). +* For paired-end data, the fragment length is generally defined by the two read mates. The user-provided fragment length is only used as a fallback for singletons or mate reads that map too far apart (with a distance greater than four times the fragment length or if the mates are located on different chromosomes). + +WARNING: If you already normalized for GC bias using ``correctGCbias``, you should absolutely **NOT** set the parameter ``--ignoreDuplicates``! + ----- diff -r 19a6007845cc -r 36f655a04a57 deepTools_macros.xml --- a/deepTools_macros.xml Mon Jan 25 20:19:01 2016 -0500 +++ b/deepTools_macros.xml Mon Feb 15 10:27:58 2016 -0500 @@ -72,12 +72,12 @@ --numberOfProcessors "\${GALAXY_SLOTS:-4}" - 2.0.1 + 2.1.0 python @BINARY@ - deepTools + deepTools @@ -104,6 +104,7 @@ + + + + @@ -126,6 +136,11 @@ --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 @@ -293,6 +308,12 @@ + + + + @@ -310,6 +331,7 @@ help="Title of the plot, to be printed on top of the generated image." /> + + + + + + + + + + + + + + + + + #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 $advancedOpt.samFlagExclude + #end if + + + + + + + + + + + #if str($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' + + + + + + + + + + + + + + + + + --numberOfProcessors "\${GALAXY_SLOTS:-4}" +<<<<<<< HEAD + 2.0.1.0 +======= + 2.1.0 +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + + + python + @BINARY@ +<<<<<<< HEAD + deepTools +======= + deepTools +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + + + + @BINARY@ --version + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. 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/ + + + + + 10.1093/nar/gku365 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $source.ref_source=="history": + --genome $source.input1 + #else: + --genome "$source.input1_2bit.fields.path" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveMatrix'] is True + )) + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveSortedRegions'] is True + )) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 19a6007845cc -r 36f655a04a57 readme.rst diff -r 19a6007845cc -r 36f655a04a57 static/images/GC_bias_simulated_reads_2L.png Binary file static/images/GC_bias_simulated_reads_2L.png has changed diff -r 19a6007845cc -r 36f655a04a57 static/images/QC_plotCoverage.png 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2016 -0500 @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + +<<<<<<< HEAD + + +======= + + + + + + + + +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + + + + + + + + + + + + + + + + + + + + + + + + + + + https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz + + + + $INSTALL_DIR/bin + $INSTALL_DIR + $INSTALL_DIR + $INSTALL_DIR + $INSTALL_DIR/bin + + $ENV[LIBPNG_LIB_PATH] + $ENV[LIBPNG_LIB_PATH] + + TRUE + + + + + Installation of deepTools from Fidel Ramirez. + https://github.com/fidelram/deepTools + + +