| Next changeset 1:0240a81c3ae6 (2017-01-24) |
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Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 |
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added:
computeMatrixOperations.xml datatypes_conf.xml deepTools_macros.xml deepTools_macros.xml.orig readme.rst repository_dependencies.xml static/images/GC_bias_simulated_reads_2L.png static/images/QC_GCplots_input.png static/images/QC_fingerprint.png static/images/QC_multiBamSummary_humanSamples.png static/images/QC_plotCoverage.png static/images/bamCompare_output.png static/images/bamCoverage_output.png static/images/bamFP_galaxy_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/norm_IGVsnapshot_indFiles.png static/images/plotCorrelate_RNAseq.png static/images/plotCorrelation_galaxy_bw_heatmap_output.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/plotEnrichment_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 static/images/visual_hm_DmelPolII.png static/images/visual_profiler_DmelPolII.png test-data/bamCompare_result1.bg test-data/bamCompare_result2.bw test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result3.bg test-data/bamCoverage_result4.bg test-data/bamCoverage_result4.bw test-data/bamCoverage_result5.bw test-data/bamCoverage_result6.bw test-data/bamPEFragmentSize_histogram_result1.png test-data/bamPEFragmentSize_result1.txt test-data/bigwigCompare_result1.bw test-data/bigwigCompare_result2.bg test-data/bowtie2 test1.bam test-data/computeGCBias_result1.png test-data/computeGCBias_result1.tabular test-data/computeMatrix1.bed test-data/computeMatrix2.bed test-data/computeMatrix2.bw test-data/computeMatrixOperations.txt test-data/computeMatrixOperations_result2.mat.gz test-data/computeMatrix_result1.gz test-data/computeMatrix_result2.gz test-data/computeMatrix_result3.gz test-data/correctGCBias_result1.bam test-data/heatmapper_result1.png test-data/heatmapper_result2.png test-data/heatmapper_result2.tabular test-data/multiBamSummary_regions.bed test-data/multiBamSummary_result1.npz test-data/multiBamSummary_result2.npz test-data/multiBigwigSummary_result1.npz test-data/multiBigwigSummary_result1.png test-data/paired_chr2L.bam test-data/phiX.2bit test-data/phiX.bam test-data/phiX.bam.bai test-data/phiX.fasta test-data/plotCorrelation_result1.png test-data/plotCorrelation_result1.tabular test-data/plotCorrelation_result2.png test-data/plotCoverage_result1.png test-data/plotCoverage_result1.tabular test-data/plotEnrichment_output.png test-data/plotEnrichment_output.txt test-data/plotFingerprint_quality_metrics.tabular test-data/plotFingerprint_result1.png test-data/plotFingerprint_result2.png test-data/plotFingerprint_result2.tabular test-data/plotPCA_result1.png test-data/plotPCA_result2.png test-data/plotPCA_result2.tabular test-data/profiler_result1.png test-data/profiler_result2.png test-data/profiler_result2.tabular test-data/sequence.2bit test-data/test.bw tool-data/deepTools_seqs.loc.sample tool-data/lastz_seqs.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r 1638c02b28b5 computeMatrixOperations.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatrixOperations.xml Mon Dec 05 08:09:05 2016 -0500 |
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| b'@@ -0,0 +1,179 @@\n+<tool id="deeptools_compute_matrix_operations" name="computeMatrixOperations" version="@WRAPPER_VERSION@.0">\n+ <description>Modify or combine the output of computeMatrix in a variety of ways.</description>\n+ <macros>\n+ <token name="@BINARY@">computeMatrixOperations</token>\n+ <import>deepTools_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command>\n+<![CDATA[\n+ @BINARY@\n+ #if $submodule.command == "info":\n+ info\n+ -m $submodule.matrixFile\n+ > $outFileTxt\n+ #else if $submodule.command == "subset":\n+ subset\n+ -m $submodule.matrixFile\n+ #if $submodule.groups is not None and str($submodule.groups) != \'\':\n+ --groups $submodule.groups\n+ #end if\n+ #if $submodule.samples is not None and str($submodule.samples) != \'\':\n+ --samples $submodule.samples\n+ #end if\n+ -o $outFileName\n+ #else if $submodule.command == "filterStrand":\n+ filterStrand\n+ -m $submodule.matrixFile\n+ --strand $submodule.strand\n+ -o $outFileName\n+ #else if $submodule.command == "rbind":\n+ #set $files=[]\n+ #for $f in $submodule.matrixFiles:\n+ #silent $files.append(str($f.matrixFile))\n+ #end for\n+ rbind\n+ -m \'#echo "\' \'".join($files)#\'\n+ -o $outFileName\n+ #else if $submodule.command == "cbind":\n+ cbind\n+ #set $files=[]\n+ #for $f in $submodule.matrixFiles:\n+ #silent $files.append(str($f.matrixFile))\n+ #end for\n+ -m \'#echo "\' \'".join($files)#\'\n+ -o $outFileName\n+ #else if $submodule.command == "sort":\n+ sort\n+ #set $files=[]\n+ #for $f in $submodule.regionsFiles:\n+ #silent $files.append(str($f.regionsFile))\n+ #end for\n+ -m $submodule.matrixFile\n+ -R \'#echo "\' \'".join($files)#\'\n+ -o $outFileName\n+ #end if\n+]]>\n+ </command>\n+ <inputs>\n+ <conditional name="submodule">\n+ <param name="command" type="select" label="Operation type">\n+ <option value="info" selected="true">Print information (info)</option>\n+ <option value="subset">Subset by samples and/or groups of regions (subset)</option>\n+ <option value="filterStrand">Filter by strand (filterStrand)</option>\n+ <option value="rbind">Bind matrices, top to bottom (rbind)</option>\n+ <option value="cbind">Bind matrices, left to right (cbind)</option>\n+ <option value="sort">Sort by region order in specified files (sort)</option>\n+ </param>\n+ <when value="info">\n+ <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"\n+ label="Matrix file from the computeMatrix tool" help=""/>\n+ </when>\n+\n+ <when value="subset">\n+ <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"\n+ label="Matrix file from the computeMatrix tool" help=""/>\n+ <param argument="groups" type="text" optional="true" label="Region groups to include."\n+ help="If blank, all region groups are output. Alternatively, one or more groups listed in the output of the \'info\' command can be used (separate groups by a space and enclose in quotes if needed)" />\n+ <param argument="samples" type="text" optional="true" label="Samples to include."\n+ help="If blank, all samples are output. Alternatively, one or mo'..b'ool.name} ${submodule.command} on ${on_string}">\n+ <filter>\n+ ((\n+ submodule[\'command\'] != "info"\n+ ))\n+ </filter>\n+ </data>\n+ <data format="txt" name="outFileTxt" label="${tool.name} info on ${on_string}">\n+ <filter>\n+ ((\n+ submodule[\'command\'] == "info"\n+ ))\n+ </filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="command" value="info" />\n+ <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />\n+ <output name="outFileTxt" file="computeMatrixOperations.txt" ftype="txt" />\n+ </test>\n+ <test>\n+ <param name="command" value="rbind" />\n+ <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />\n+ <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />\n+ <output name="outFileName" file="computeMatrixOperations_result2.mat.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" delta="100"/>\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+\n+What it does\n+------------\n+\n+``computeMatrixOperations`` can perform a variety of operations on one or more files produced by ``computeMatrix`` (N.B., the output is always written to a new file):\n+\n++----------------+--------------------------------------------------------------------------------------------------------------------------+\n++ **Subcommand** | **What it does** |\n++----------------+--------------------------------------------------------------------------------------------------------------------------+\n++ info | Prints out the sample and region group names in the order in which they appear. |\n++----------------+--------------------------------------------------------------------------------------------------------------------------+\n++ subset | Subsets a file by the desired samples/region group names. This can also change the order of these samples/region groups. |\n++----------------+--------------------------------------------------------------------------------------------------------------------------+\n++ filterStrand | Filters the file to only include regions annotated as being on a particular strand. |\n++----------------+--------------------------------------------------------------------------------------------------------------------------+\n++ rbind | Concatenates multiple matrices together, top to bottom. |\n++----------------+--------------------------------------------------------------------------------------------------------------------------+\n++ cbind | Merges multiple matrices, left to right. |\n++----------------+--------------------------------------------------------------------------------------------------------------------------+\n++ sort | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s). |\n++----------------+--------------------------------------------------------------------------------------------------------------------------+\n+\n+\n+These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file.\n+\n+-----\n+\n+@REFERENCES@\n+]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 1638c02b28b5 datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Mon Dec 05 08:09:05 2016 -0500 |
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| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<datatypes> + <registration> + <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/> + <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/> + </registration> +</datatypes> |
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| diff -r 000000000000 -r 1638c02b28b5 deepTools_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml Mon Dec 05 08:09:05 2016 -0500 |
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| b'@@ -0,0 +1,811 @@\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+ #if $advancedOpt.minFragmentLength:\n+ --minFragmentLength $advancedOpt.minFragmentLength\n+ #end if\n+ #if $advancedOpt.maxFragmentLength:\n+ --maxFragmentLength $advancedOpt.maxFragmentLength\n+ #end if\n+ </token>\n+\n+ <token name="@ADVANCED_OPTS_GTF@">\n+ $advancedOpt.metagene\n+ #if $advancedOpt.transcriptID:\n+ --transcriptID $advancedOpt.transcriptID\n+ #end if\n+ #if $advancedOpt.exonID:\n+ --exonID $advancedOpt.exonID\n+ #end if\n+ #if $advancedOpt.transcript_id_designator:\n+ --transcript_id_designator $advancedOpt.transcript_id_designator\n+ #end if\n+ </token>\n+\n+ <xml name="heatmap_options">\n+ <expand macro="zMin_zMax" />\n+ <expand macro="colorMap" />\n+ <expand macro="plotTitle" />\n+ <expand macro="plotNumbers" />\n+ </xml>\n+\n+ <token name="@HEATMAP_OPTIONS@">\n+ #if str($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="text" 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="text" 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+ <sanitizer>\n+ <valid initial="string.letters,string.digits">\n+ <add value="|"/>\n+ <add value=":"/>\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ </xml>\n+\n+ <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n+ <token name="@WRAPPER_VERSION@">2.4.1</token>\n+ <x'..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 000000000000 -r 1638c02b28b5 deepTools_macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml.orig Mon Dec 05 08:09:05 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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| @@ -0,0 +1,74 @@ +======================== +Galaxy deeptools wrapper +======================== + +deepTools are user-friendly tools for the normalization and visualization of +deep-sequencing data. +They address the challenge of visualizing the large amounts of data that are now +routinely generated from sequencing centers in a meaningful way. +To do so, deepTools contain useful routines to process the mapped reads data +through removal of duplicates and different filtering options to create coverage +files in standard bedGraph and bigWig file formats. deepTools allow the creation +of normalized coverage files or the comparison between two files +(for example, treatment and control). Finally, using such normalized and +standardized files, multiple visualizations can be created to identify +enrichments with functional annotations of the genome. +For a gallery of images that can be produced and a description +of the tools see our poster_. + +.. _poster: http://f1000.com/posters/browse/summary/1094053 + +deeptools is developed under here: + + https://github.com/fidelram/deepTools + +For support, questions, or feature requests contact: deeptools@googlegroups.com + + +============ +Installation +============ + +Requirements: python-2.7 + +Galaxy should be able to automatically install all other dependencies, such as numpy or scipy. + +For the best performance we recommend to install blas/lapack/atlas in your environment before +installing deepTools from the Tool Shed. + + +======== +Citation +======== + +deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. + + +======= +History +======= + + * v1.0: Initial public release + * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="74b09c8e5f6e" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| @@ -0,0 +1,1 @@ +chrM 0 16569 1 |
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| @@ -0,0 +1,7 @@ +chrM 0 210 9.76876e+06 +chrM 210 220 9.56092e+06 +chrM 220 230 7.6903e+06 +chrM 230 240 5.19615e+06 +chrM 240 250 3.32554e+06 +chrM 250 260 623538 +chrM 260 16569 0 |
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| @@ -0,0 +1,22 @@ + + +BAM file : 0.bam +Sample size: 3 + +Fragment lengths: +Min.: 241.0 +1st Qu.: 241.5 +Mean: 244.666666667 +Median: 242.0 +3rd Qu.: 246.5 +Max.: 251.0 +Std: 4.49691252108 + +Read lengths: +Min.: 251.0 +1st Qu.: 251.0 +Mean: 251.0 +Median: 251.0 +3rd Qu.: 251.0 +Max.: 251.0 +Std: 0.0 |
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| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/computeMatrix1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrix1.bed Mon Dec 05 08:09:05 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +phiX174 1000 1500 CG11023 0 + +phiX174 150 1750 cda5 0 - +phiX174 150 177 cda8 0 - +phiX174 75 1500 cda9 0 + +phiX174 101 175 C11023 0 + +phiX174 125 150 ca5 0 - +phiX174 450 1750 ca8 0 + +phiX174 80 1500 cda9 0 + |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/computeMatrix2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrix2.bed Mon Dec 05 08:09:05 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +ch1 100 150 CG11023 0 + +ch2 150 175 cda5 0 - +ch3 100 125 cda8 0 + +ch1 75 125 C11023 0 + +ch2 125 150 ca5 0 - +ch3 75 100 ca8 0 + |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/computeMatrix2.bw |
| b |
| Binary file test-data/computeMatrix2.bw has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/computeMatrixOperations.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrixOperations.txt Mon Dec 05 08:09:05 2016 -0500 |
| b |
| @@ -0,0 +1,4 @@ +Groups: + genes +Samples: + file_0 |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/computeMatrixOperations_result2.mat.gz |
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| Binary file test-data/computeMatrixOperations_result2.mat.gz has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/computeMatrix_result1.gz |
| b |
| Binary file test-data/computeMatrix_result1.gz has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/computeMatrix_result2.gz |
| b |
| Binary file test-data/computeMatrix_result2.gz has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/computeMatrix_result3.gz |
| b |
| Binary file test-data/computeMatrix_result3.gz has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/correctGCBias_result1.bam |
| b |
| Binary file test-data/correctGCBias_result1.bam has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/heatmapper_result1.png |
| b |
| Binary file test-data/heatmapper_result1.png has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/heatmapper_result2.png |
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| Binary file test-data/heatmapper_result2.png has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/heatmapper_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmapper_result2.tabular Mon Dec 05 08:09:05 2016 -0500 |
| b |
| @@ -0,0 +1,3 @@ +bin labels -0.0Kb 0.0Kb +bins 1 2 +file_0 genes 2477942.34473 2610259.65234 |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/multiBamSummary_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiBamSummary_regions.bed Mon Dec 05 08:09:05 2016 -0500 |
| b |
| @@ -0,0 +1,3 @@ +chrM 1 10 +chrM 5 15 +chrM 10 20 |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/multiBamSummary_result1.npz |
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| Binary file test-data/multiBamSummary_result1.npz has changed |
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| diff -r 000000000000 -r 1638c02b28b5 test-data/multiBamSummary_result2.npz |
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| Binary file test-data/multiBamSummary_result2.npz has changed |
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| diff -r 000000000000 -r 1638c02b28b5 test-data/multiBigwigSummary_result1.npz |
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| Binary file test-data/multiBigwigSummary_result1.npz has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/multiBigwigSummary_result1.png |
| b |
| Binary file test-data/multiBigwigSummary_result1.png has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/paired_chr2L.bam |
| b |
| Binary file test-data/paired_chr2L.bam has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/phiX.2bit |
| b |
| Binary file test-data/phiX.2bit has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/phiX.bam |
| b |
| Binary file test-data/phiX.bam has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/phiX.bam.bai |
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| Binary file test-data/phiX.bam.bai has changed |
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| diff -r 000000000000 -r 1638c02b28b5 test-data/phiX.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta Mon Dec 05 08:09:05 2016 -0500 |
| b |
| @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/plotCorrelation_result1.png |
| b |
| Binary file test-data/plotCorrelation_result1.png has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/plotCorrelation_result1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotCorrelation_result1.tabular Mon Dec 05 08:09:05 2016 -0500 |
| b |
| @@ -0,0 +1,3 @@ + 'bowtie2-test1.bam' 'bowtie2-test1.bam' +'bowtie2-test1.bam' 1.0000 1.0000 +'bowtie2-test1.bam' 1.0000 1.0000 |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/plotCorrelation_result2.png |
| b |
| Binary file test-data/plotCorrelation_result2.png has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/plotCoverage_result1.png |
| b |
| Binary file test-data/plotCoverage_result1.png has changed |
| b |
| diff -r 000000000000 -r 1638c02b28b5 test-data/plotCoverage_result1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotCoverage_result1.tabular Mon Dec 05 08:09:05 2016 -0500 |
| b |
| b"@@ -0,0 +1,16570 @@\n+#'chr'\t'start'\t'end'\t'bowtie2 test1.bam'\t'bowtie2 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|
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| diff -r 000000000000 -r 1638c02b28b5 test-data/plotEnrichment_output.png |
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| Binary file test-data/plotEnrichment_output.png has changed |
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| diff -r 000000000000 -r 1638c02b28b5 test-data/plotEnrichment_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotEnrichment_output.txt Mon Dec 05 08:09:05 2016 -0500 |
| b |
| @@ -0,0 +1,5 @@ +file featureType percent +bowtie2 test1.bam down 100.00 +bowtie2 test1.bam up 100.00 +bowtie2 test1.bam down 100.00 +bowtie2 test1.bam up 100.00 |
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| diff -r 000000000000 -r 1638c02b28b5 test-data/plotFingerprint_quality_metrics.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotFingerprint_quality_metrics.tabular Mon Dec 05 08:09:05 2016 -0500 |
| b |
| @@ -0,0 +1,3 @@ +Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269861238192 NA NA NA +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269861238192 NA NA NA |
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| diff -r 000000000000 -r 1638c02b28b5 test-data/plotFingerprint_result1.png |
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| Binary file test-data/plotFingerprint_result1.png has changed |
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| diff -r 000000000000 -r 1638c02b28b5 test-data/plotFingerprint_result2.png |
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| Binary file test-data/plotFingerprint_result2.png has changed |
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| diff -r 000000000000 -r 1638c02b28b5 test-data/plotFingerprint_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotFingerprint_result2.tabular Mon Dec 05 08:09:05 2016 -0500 |
| b |
| b"@@ -0,0 +1,16071 @@\n+'bowtie2 test1.bam'\t'bowtie2 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| diff -r 000000000000 -r 1638c02b28b5 test-data/plotPCA_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotPCA_result2.tabular Mon Dec 05 08:09:05 2016 -0500 |
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| @@ -0,0 +1,3 @@ +Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue +1 -0.707106781187 -0.707106781187 6.0 +2 -0.707106781187 0.707106781187 1.23259516441e-32 |
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| diff -r 000000000000 -r 1638c02b28b5 test-data/profiler_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/profiler_result2.tabular Mon Dec 05 08:09:05 2016 -0500 |
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| @@ -0,0 +1,3 @@ +bin labels -0.0Kb 0.0Kb +bins 1 2 +file_0 genes 2477942.34473 2610259.65234 |
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| diff -r 000000000000 -r 1638c02b28b5 tool-data/deepTools_seqs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/deepTools_seqs.loc.sample Mon Dec 05 08:09:05 2016 -0500 |
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| @@ -0,0 +1,27 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of 2bit genome files for use with deepTools. You will +#need to supply these files and then create a deepTools_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The deepTools_seqs.loc +#file has this format: +# +#<unique_build_id> <display_name> <file_path> +# +#So, for example, if your deepTools_seqs.loc began like this: +# +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +# +#then your /depot/data2/galaxy/twobit/ directory +#would need to contain the following 2bit files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit +# +#Your deepTools_seqs.loc file should include an entry per line for +#each file you have stored that you want to be available. Note that +#your files should all have the extension '2bit'. +# +#Please note that the <unique_build_id> is also used as "Species name abbreviation". |
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| diff -r 000000000000 -r 1638c02b28b5 tool-data/lastz_seqs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/lastz_seqs.loc.sample Mon Dec 05 08:09:05 2016 -0500 |
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| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of 2bit genome files for use with deepTools. +#This file is named lastz_seqs.loc file to make use of an already existing loc +#file from the lastz tool that is created by the twobit data-manager. +#You will need to supply these files and then create a lastz_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The lastz_seqs.loc +#file has this format: +# +#<unique_build_id> <display_name> <file_path> +# +#So, for example, if your lastz_seqs.loc began like this: +# +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +# +#then your /depot/data2/galaxy/twobit/ directory +#would need to contain the following 2bit files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit +# +#Your lastz_seqs.loc file should include an entry per line for +#each file you have stored that you want to be available. Note that +#your files should all have the extension '2bit'. +# +#Please note that the <unique_build_id> is also used as "Species name abbreviation". |
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| diff -r 000000000000 -r 1638c02b28b5 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Dec 05 08:09:05 2016 -0500 |
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| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of 2bit sequence files for use in Lastz --> + <table name="lastz_seqs" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 1638c02b28b5 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Dec 05 08:09:05 2016 -0500 |
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| @@ -0,0 +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" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="deeptools" version="2.4.1"> + <repository changeset_revision="e9855a43ac53" name="package_python_2_7_deeptools_2_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
