| Previous changeset 0:19a6007845cc (2016-01-25) Next changeset 2:8145727ba0f0 (2016-02-18) |
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Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 |
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modified:
bamCoverage.xml deepTools_macros.xml readme.rst test-data/bamCompare_result2.bw test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result4.bw test-data/bamPEFragmentSize_result1.txt test-data/bigwigCompare_result1.bw test-data/computeMatrix2.bed test-data/computeMatrix2.bw test-data/correctGCBias_result1.bam test-data/plotCoverage_result1.png test-data/plotCoverage_result1.tabular test-data/sequence.2bit test-data/test.bw tool-data/deepTools_seqs.loc.sample tool_dependencies.xml |
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added:
deepTools_macros.xml.orig static/images/GC_bias_simulated_reads_2L.png static/images/QC_plotCoverage.png static/images/bamCompare_output.png static/images/bamCoverage_output.png static/images/bamPEFragmentSize_output.png static/images/bigwigCompare_output.png static/images/computeGCBias_output.png static/images/computeMatrix_advancedOutput.png static/images/computeMatrix_output.png static/images/computeMatrix_overview.png static/images/computeMatrix_selectRegions.png static/images/computeMatrix_selectScores.png static/images/multiBamSummary_output.png static/images/multiBigwigSummary_output.png static/images/plotCorrelate_RNAseq.png static/images/plotCorrelation_output.png static/images/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png static/images/plotCoverage_annotated.png static/images/plotCoverage_output.png static/images/plotFingerprint_output.png static/images/plotHeatmap_example.png static/images/plotHeatmap_example02.png static/images/plotPCA_annotated.png static/images/plotProfiler_examples.png tool_dependencies.xml.orig |
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removed:
static/images/flowChart_computeMatrixetc.png |
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| 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 |
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| @@ -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 @@ </tests> <help> <![CDATA[ -**What it does** + +What it does +-------------- Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or read coverages. The way the method works is by first calculating all the @@ -168,15 +170,35 @@ pairs is present. This means that *each end* will be extended to match the fragment length. +See the usage hints below. + .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png + :width: 600 + :height: 336 +Output +------------- -You can find more details on the bamCoverage doc page: https://deeptools.readthedocs.org/en/master/content/tools/bamCoverage.html +``bamCoverage`` produces a coverage file, either in bigWig or bedGraph format, where for each bin the number of overlapping reads (possibly normalized) is noted. + +Like BAM files, bigWig files are compressed, binary files. If you would like to see the coverage values, choose the bedGraph output. For more information on typical NGS file formats, see our `Glossary <http://deeptools.readthedocs.org/en/latest/content/help_glossary.html#file-formats>`_ +.. 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``! + ----- |
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| 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 |
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| @@ -72,12 +72,12 @@ </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.0.1</token> + <token name="@WRAPPER_VERSION@">2.1.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> <requirement type="binary">@BINARY@</requirement> - <requirement type="package" version="2.0.1">deepTools</requirement> + <requirement type="package" version="2.1.0">deepTools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -104,6 +104,7 @@ <param name="clustering_options" type="select" label="Clustering algorithm"> <option value="none">No clustering</option> <option value="kmeans">Kmeans clustering</option> + <option value="hclust">Hierarchical clustering</option> </param> <when value="kmeans"> <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" @@ -112,6 +113,15 @@ If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software."/> </when> + <when value="hclust"> + <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." + help="WARNING: This option causes the tool to run for a very long time! When this option is + set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. + This only works for data that is not grouped, otherwise only the first group will be clustered. + Note that you must have used the '--missingDataAsZero' option within computeMatrix! + If more specific clustering methods are required it is advisable to save the underlying matrix and + run the clustering using other software."/> + </when> <when value="none" /> </conditional> </when> @@ -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 </token> @@ -293,6 +308,12 @@ </xml> <xml name="multiple_input_bams"> + <param argument="--bamfiles" type="data" format="bam" min="1" + label="Bam file" multiple="true" + help="The BAM file must be sorted."/> + </xml> + + <xml name="multiple_input_bams_min2"> <param argument="--bamfiles" type="data" format="bam" min="2" label="Bam file" multiple="true" help="The BAM file must be sorted."/> @@ -310,6 +331,7 @@ help="Title of the plot, to be printed on top of the generated image." /> </xml> + <token name="@multiple_input_bams@"> <![CDATA[ #set files=[] |
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| diff -r 19a6007845cc -r 36f655a04a57 deepTools_macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml.orig Mon Feb 15 10:27:58 2016 -0500 |
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| b'@@ -0,0 +1,639 @@\n+<macros>\n+\n+ <xml name="advancedOpt_scaffold">\n+ <conditional name="advancedOpt">\n+ <param name="showAdvancedOpt" type="select" label="Show advanced options" >\n+ <option value="no" selected="true">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <yield/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <token name="@ADVANCED_OPTS_READ_PROCESSING@">\n+ #if $advancedOpt.doExtendCustom.doExtend == \'custom\':\n+ --extendReads $advancedOpt.doExtendCustom.extendReadsValue\n+ #else if $advancedOpt.doExtendCustom.doExtend == \'yes\':\n+ --extendReads\n+ #end if\n+ $advancedOpt.ignoreDuplicates\n+ $advancedOpt.centerReads\n+ #if $advancedOpt.minMappingQuality:\n+ --minMappingQuality \'$advancedOpt.minMappingQuality\'\n+ #end if\n+ #if $advancedOpt.samFlagInclude:\n+ --samFlagInclude $advancedOpt.samFlagInclude\n+ #end if\n+ #if $advancedOpt.samFlagExclude:\n+ --samFlagExclude $advancedOpt.samFlagExclude\n+ #end if\n+ </token>\n+\n+ <xml name="heatmap_options">\n+ <expand macro="zMin_zMax" />\n+ <expand macro="colorMap" />\n+ <expand macro="plotTitle" />\n+ <expand macro="plotNumbers" />\n+ </xml>\n+\n+ <token name="@HEATMAP_OPTIONS@">\n+ #if str($plotting_type.zMin) != "":\n+ --zMin $plotting_type.zMin\n+ #end if\n+ #if str($plotting_type.zMax) != "":\n+ --zMax $plotting_type.zMax\n+ #end if\n+ --colorMap \'$plotting_type.colorMap\'\n+ $plotting_type.plotNumbers\n+ --plotTitle \'$plotting_type.plotTitle\'\n+ </token>\n+\n+\n+ <xml name="includeZeros">\n+ <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""\n+ label="Include zeros"\n+ help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />\n+ </xml>\n+\n+ <xml name="zMin_zMax">\n+ <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"\n+ help="If not specified the value is set automatically."/>\n+ <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"\n+ help="If not specified the value is set automatically."/>\n+ </xml>\n+\n+ <xml name="region_limit_operation">\n+ <param argument="--region" type="text" value=""\n+ label="Region of the genome to limit the operation to"\n+ help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." />\n+ </xml>\n+\n+ <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n+<<<<<<< HEAD\n+ <token name="@WRAPPER_VERSION@">2.0.1.0</token>\n+=======\n+ <token name="@WRAPPER_VERSION@">2.1.0</token>\n+>>>>>>> d56067f86089e75354a2fad266002db3730766d9\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="2.7.10">python</requirement>\n+ <requirement type="binary">@BINARY@</requirement>\n+<<<<<<< HEAD\n+ <requirement type="package" version="2.0.1">deepTools</requirement>\n+=======\n+ <requirement type="package" version="2.1.0">deepTools</requirement>\n+>>>>>>> d56067f86089e75354a2fad266002db3730766d9\n+ <yield />\n+ </requirements>\n+ <expand macro="stdio" />\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+\n+ <xml name="smoothLength">\n+ <param argument="--smoothLength" type="integer" value="" optional="True" min="1"\n+ label="Smooth values using the following length (in bases)"\n+ help '..b'k2 reversed</option>\n+ <option value="Reds_r">Reds reversed</option>\n+ <option value="Oranges_r">Oranges reversed</option>\n+ <option value="Greens_r">Greens reversed</option>\n+ <option value="Blues_r">Blues reversed</option>\n+ <option value="Greys_r">Greys reversed</option>\n+ <option value="Purples_r">Purples reversed</option>\n+ <option value="Paired_r">Paired reversed</option>\n+ <option value="Pastel1_r">Pastel1 reversed</option>\n+ <option value="Pastel2_r">Pastel2 reversed</option>\n+ <option value="spring_r">spring reversed</option>\n+ <option value="summer_r">summer reversed</option>\n+ <option value="autumn_r">autumn reversed</option>\n+ <option value="winter_r">winter reversed</option>\n+ <option value="hot_r">hot reversed</option>\n+ <option value="coolwarm_r">coolwarm reversed</option>\n+ <option value="cool_r">cool reversed</option>\n+ <option value="seismic_r">seismic reversed</option>\n+ <option value="terrain_r">terrain reversed</option>\n+ <option value="ocean_r">ocean reversed</option>\n+ <option value="rainbow_r">rainbow reversed</option>\n+ <option value="bone_r">bone reversed</option>\n+ <option value="flag_r">flag reversed</option>\n+ <option value="prism_r">prism reversed</option>\n+ <option value="cubehelix_r">cubehelix reversed</option>\n+ <option value="binary_r">binary reversed</option>\n+ <option value="pink_r">pink reversed</option>\n+ <option value="gray_r">gray reversed</option>\n+ <option value="copper_r">copper reversed</option>\n+ <option value="BrBG_r">BrBG reversed</option>\n+ <option value="BuGn_r">BuGn reversed</option>\n+ <option value="BuPu_r">BuPu reversed</option>\n+ <option value="GnBu_r">GnBu reversed</option>\n+ <option value="OrRd_r">OrRd reversed</option>\n+ <option value="PiYG_r">PiYG reversed</option>\n+ <option value="PRGn_r">PRGn reversed</option>\n+ <option value="PuOr_r">PuOr reversed</option>\n+ <option value="PuRd_r">PuRd reversed</option>\n+ <option value="PuBu_r">PuBu reversed</option>\n+ <option value="RdBu_r">RdBu reversed</option>\n+ <option value="RdGy_r">RdGy reversed</option>\n+ <option value="RdPu_r">RdPu reversed</option>\n+ <option value="YlGn_r">YlGn reversed</option>\n+ <option value="PuBuGn_r">PuBuGn reversed</option>\n+ <option value="RdYlBu_r">RdYlBu reversed</option>\n+ <option value="RdYlGn_r">RdYlGn reversed</option>\n+ <option value="YlGnBu_r">YlGnBu reversed</option>\n+ <option value="YlOrBr_r">YlOrBr reversed</option>\n+ <option value="YlOrRd_r">YlOrRd reversed</option>\n+ <option value="gist_gray_r">gist_gray reversed</option>\n+ <option value="gist_stern_r">gist_stern reversed</option>\n+ <option value="gist_earth_r">gist_earth reversed</option>\n+ <option value="gist_yarg_r">gist_yarg reversed</option>\n+ <option value="gist_ncar_r">gist_ncar reversed</option>\n+ <option value="gist_rainbow_r">gist_rainbow reversed</option>\n+ <option value="gist_heat_r">gist_heat reversed</option>\n+ <option value="gnuplot_r">gnuplot reversed</option>\n+ <option value="gnuplot2_r">gnuplot2 reversed</option>\n+ <option value="CMRmap_r">CMRmap reversed</option>\n+ <option value="bwr_r">bwr reversed</option>\n+ <option value="hsv_r">hsv reversed</option>\n+ <option value="brg_r">brg reversed</option>\n+ <option value="jet_r">jet reversed</option>\n+ <option value="afmhot_r">afmhot reversed</option>\n+ </param>\n+\n+ </xml>\n+\n+</macros>\n' |
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| diff -r 19a6007845cc -r 36f655a04a57 test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Mon Jan 25 20:19:01 2016 -0500 +++ b/test-data/bamPEFragmentSize_result1.txt Mon Feb 15 10:27:58 2016 -0500 |
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| @@ -2,19 +2,19 @@ Fragment lengths: -Min.: 241 +Min.: 241.0 1st Qu.: 241.5 Mean: 244.666666667 Median: 242.0 3rd Qu.: 246.5 -Max.: 251 +Max.: 251.0 Std: 4.49691252108 Read lengths: -Min.: 251 +Min.: 251.0 1st Qu.: 251.0 Mean: 251.0 Median: 251.0 3rd Qu.: 251.0 -Max.: 251 +Max.: 251.0 Std: 0.0 |
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| diff -r 19a6007845cc -r 36f655a04a57 test-data/plotCoverage_result1.tabular --- a/test-data/plotCoverage_result1.tabular Mon Jan 25 20:19:01 2016 -0500 +++ b/test-data/plotCoverage_result1.tabular Mon Feb 15 10:27:58 2016 -0500 |
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| b"@@ -1,16570 +1,16570 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t0.0\t0.0\n+chrM\t16565\t16566\t0.0\t0.0\n+chrM\t16566\t16567\t0.0\t0.0\n+chrM\t16567\t16568\t0.0\t0.0\n+chrM\t16568\t16569\t0.0\t0.0\n' |
| b |
| diff -r 19a6007845cc -r 36f655a04a57 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jan 25 20:19:01 2016 -0500 +++ b/tool_dependencies.xml Mon Feb 15 10:27:58 2016 -0500 |
| b |
| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="python" version="2.7.10"> - <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="deepTools" version="2.0.1"> - <repository changeset_revision="1fb61fa32733" name="package_python_2_7_deeptools_2_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="deepTools" version="2.1.0"> + <repository changeset_revision="2c54c7c38299" name="package_python_2_7_deeptools_2_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
| b |
| diff -r 19a6007845cc -r 36f655a04a57 tool_dependencies.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml.orig Mon Feb 15 10:27:58 2016 -0500 |
| [ |
| @@ -0,0 +1,76 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool_dependency> + <package name="numpy" version="1.9"> + <repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" /> + </package> + <package name="pybigwig" version="0.2.4"> + <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc" prior_installation_required="True"/> + </package> + <package name="matplotlib" version="1.4"> + <repository name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" /> + </package> + <package name="scipy" version="0.14"> + <repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" /> + </package> +<<<<<<< HEAD + <package name="deepTools" version="2.0.1"> + <repository name="package_python_2_7_deeptools_2_0_1" owner="iuc"/> +======= + <package name="pysam" version="0.8.3"> + <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" /> + </package> + <package name="bx-python" version="0.7.2"> + <repository name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" /> + </package> + <package name="python" version="2.7.10"> + <repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" /> +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + </package> + <package name="deepTools" version="2.1.0"> + <install version="1.0"> + <actions> + <action type="setup_python_environment"> + <repository name="package_python_2_7_10" owner="iuc"> + <package name="python" version="2.7.10" /> + </repository> + <repository name="package_python_2_7_pysam_0_8_3" owner="iuc"> + <package name="pysam" version="0.8.3" /> + </repository> + <repository name="package_python_2_7_numpy_1_9" owner="iuc"> + <package name="numpy" version="1.9" /> + </repository> + <repository name="package_python_2_7_matplotlib_1_4" owner="iuc"> + <package name="matplotlib" version="1.4" /> + </repository> + <repository name="package_python_2_7_scipy_0_14" owner="iuc"> + <package name="scipy" version="0.14" /> + </repository> + <repository name="package_python_2_7_bx_python_0_7" owner="iuc"> + <package name="bx-python" version="0.7.2" /> + </repository> + <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc"> + <package name="pybigwig" version="0.2.4" /> + </repository> + <package sha256sum="3bf835afde02cd5247198db3e01f690899e1fdb86e1821a83ac940d807baa857">https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz</package> + </action> + + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable> + <environment_variable name="DEEPTOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="DEEPTOOLS_PYTHONPATH" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="DEEPTOOLS_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable> + <!-- libpng lib path --> + <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable> + <!-- disable the config file of deepTools --> + <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable> + </action> + </actions> + </install> + <readme> + Installation of deepTools from Fidel Ramirez. + https://github.com/fidelram/deepTools + </readme> + </package> +</tool_dependency> |
