| Previous changeset 0:e1bb51933e7f (2016-01-25) Next changeset 2:5e0a773ab4ee (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:
deepTools_macros.xml plotHeatmap.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 e1bb51933e7f -r 6a247ae015cc deepTools_macros.xml --- a/deepTools_macros.xml Mon Jan 25 20:16:56 2016 -0500 +++ b/deepTools_macros.xml Mon Feb 15 10:26:54 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 e1bb51933e7f -r 6a247ae015cc deepTools_macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml.orig Mon Feb 15 10:26:54 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 e1bb51933e7f -r 6a247ae015cc plotHeatmap.xml --- a/plotHeatmap.xml Mon Jan 25 20:16:56 2016 -0500 +++ b/plotHeatmap.xml Mon Feb 15 10:26:54 2016 -0500 |
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| b'@@ -1,218 +1,258 @@\n-<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0">\r\n- <description>creates a heatmap for a score associated to genomic regions</description>\r\n- <macros>\r\n- <token name="@BINARY@">plotHeatmap</token>\r\n- <import>deepTools_macros.xml</import>\r\n- </macros>\r\n- <expand macro="requirements"/>\r\n- <command>\r\n-<![CDATA[\r\n- @BINARY@\r\n- --matrixFile "$matrixFile"\r\n- --outFileName "$outFileName"\r\n-\r\n- #if $output.showOutputSettings == "yes"\r\n- --plotFileFormat "$output.outFileFormat"\r\n-\r\n- #if $outFileNameMatrix:\r\n- --outFileNameMatrix "$outFileNameMatrix"\r\n- #end if\r\n-\r\n- #if $outFileSortedRegions:\r\n- --outFileSortedRegions "$outFileSortedRegions"\r\n- #end if\r\n- #else\r\n- --plotFileFormat \'png\'\r\n- #end if\r\n-\r\n- #if $advancedOpt.showAdvancedOpt == "yes"\r\n- #if $advancedOpt.sortRegions:\r\n- --sortRegions \'$advancedOpt.sortRegions\'\r\n- #end if\r\n-\r\n- #if $advancedOpt.sortUsing:\r\n- --sortUsing \'$advancedOpt.sortUsing\'\r\n- #end if\r\n-\r\n- #if $advancedOpt.averageTypeSummaryPlot:\r\n- --averageTypeSummaryPlot \'$advancedOpt.averageTypeSummaryPlot\'\r\n- #end if\r\n-\r\n- #if str($advancedOpt.missingDataColor.value) != "None":\r\n- --missingDataColor \'$advancedOpt.missingDataColor\'\r\n- #end if\r\n-\r\n- --colorMap \'$advancedOpt.colorMap\'\r\n-\r\n- #if str($advancedOpt.zMin).strip() != "":\r\n- --zMin $advancedOpt.zMin\r\n- #end if\r\n- #if $advancedOpt.zMax:\r\n- --zMax $advancedOpt.zMax\r\n- #end if\r\n-\r\n- #if str($advancedOpt.yMin).strip() != "":\r\n- --yMin $advancedOpt.yMin\r\n- #end if\r\n- #if $advancedOpt.yMax:\r\n- --yMax $advancedOpt.yMax\r\n- #end if\r\n-\r\n- --xAxisLabel \'$advancedOpt.xAxisLabel\'\r\n- --yAxisLabel \'$advancedOpt.yAxisLabel\'\r\n-\r\n- --heatmapWidth $advancedOpt.heatmapWidth\r\n- --heatmapHeight $advancedOpt.heatmapHeight\r\n-\r\n- --whatToShow \'$advancedOpt.whatToShow\'\r\n-\r\n- --startLabel \'$advancedOpt.startLabel\'\r\n- --endLabel \'$advancedOpt.endLabel\'\r\n- --refPointLabel \'$advancedOpt.referencePointLabel\'\r\n- --regionsLabel \'$advancedOpt.regionsLabel\'\r\n-\r\n- #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":\r\n- --plotTitle \'$advancedOpt.plotTitle\'\r\n- #end if\r\n-\r\n- $advancedOpt.perGroup\r\n-\r\n- @KMEANS_CLUSTERING@\r\n-\r\n- #end if\r\n-]]>\r\n- </command>\r\n- <inputs>\r\n- <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool" help=""/>\r\n-\r\n- <expand macro="input_graphic_output_settings">\r\n- <expand macro="input_image_file_format" />\r\n- <expand macro="input_save_matrix_values" />\r\n- </expand>\r\n-\r\n- <conditional name="advancedOpt" >\r\n- <param name="showAdvancedOpt" type="select" label="Show advanced options" >\r\n- <option value="no" selected="true">no</option>\r\n- <option value="yes">yes</option>\r\n- </param>\r\n- <when value="no" />\r\n- <when value="yes">\r\n- <expand macro="sortRegions" />\r\n- <expand macro="sortUsing" />\r\n- <param argument="--averageTypeSummaryPlot" type="select"\r\n- label="Type of statistic that should be '..b' <expand macro="plotTitle" />\n+ <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""\n+ label="Make one plot per group of regions"\n+ help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>\n+\n+ <expand macro="kmeans_clustering" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <expand macro="output_image_file_format" />\n+ <expand macro="output_graphic_outputs" />\n+ <expand macro="output_save_matrix_values" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />\n+ <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" />\n+ </test>\n+ <test>\n+ <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />\n+ <param name="showAdvancedOpt" value="yes" />\n+ <param name="whatToShow" value="heatmap and colorbar" />\n+ <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" />\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+\n+What it does\n+--------------\n+\n+``plotHeatmap`` visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.\n+Like ``plotProfile``, it requires that computeMatrix was run first to calculate the values.\n+\n+We have implemented a number of optional parameters to optimize the visual output and we encourage you to play around with the min/max values\n+displayed in the heatmap as well as with the different coloring options.\n+\n+**TIP:** *If your data is rather sparse and the resulting heatmap is too black, change the "Missing data color" to white (via "Advanced options").*\n+\n+The most powerful option is probably the **k-means/hierarchical clustering** where you can sort your regions into groups of regions with similar score distributions.\n+\n+**NOTE:** *The clustering will only work if you supplied a single BED file to computeMatrix. plotHeatmap cannot cluster regions within pre-defined groups. Moreover, k-means will be much faster than hierarchical clustering.*\n+\n+Output\n+--------------\n+\n+This is a heatmap based on two bigWig files generated with default settings and k-means clustering.\n+\n+.. image:: $PATH_TO_IMAGES/plotHeatmap_example.png\n+ :width: 600\n+ :height: 694\n+\n+.. image:: $PATH_TO_IMAGES/plotHeatmap_example02.png\n+ :width: 600\n+ :height: 694\n+\n+In addition to the image, ``plotHeatmap`` can also generate the values underlying both the heatmap.\n+\n+See the following table for the optional output options:\n+\n++-----------------------------------+--------------------+-----------------+-----------------+\n+| **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** |\n++-----------------------------------+--------------------+-----------------+-----------------+\n+| values underlying the heatmap | yes | yes | no |\n++-----------------------------------+--------------------+-----------------+-----------------+\n+| values underlying the profile | no | no | yes |\n++-----------------------------------+--------------------+-----------------+-----------------+\n+| sorted and/or filtered regions | yes | yes | yes |\n++-----------------------------------+--------------------+-----------------+-----------------+\n+\n+**More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_.\n+\n+-----\n+\n+@REFERENCES@\n+]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r e1bb51933e7f -r 6a247ae015cc test-data/bamCoverage_result2.bw |
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| Binary file test-data/bamCoverage_result2.bw has changed |
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| diff -r e1bb51933e7f -r 6a247ae015cc test-data/bamCoverage_result4.bw |
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| Binary file test-data/bamCoverage_result4.bw has changed |
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| diff -r e1bb51933e7f -r 6a247ae015cc test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Mon Jan 25 20:16:56 2016 -0500 +++ b/test-data/bamPEFragmentSize_result1.txt Mon Feb 15 10:26:54 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 e1bb51933e7f -r 6a247ae015cc test-data/bigwigCompare_result1.bw |
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| Binary file test-data/bigwigCompare_result1.bw has changed |
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| diff -r e1bb51933e7f -r 6a247ae015cc test-data/correctGCBias_result1.bam |
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| Binary file test-data/correctGCBias_result1.bam has changed |
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| diff -r e1bb51933e7f -r 6a247ae015cc test-data/plotCoverage_result1.png |
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| Binary file test-data/plotCoverage_result1.png has changed |
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| diff -r e1bb51933e7f -r 6a247ae015cc test-data/plotCoverage_result1.tabular --- a/test-data/plotCoverage_result1.tabular Mon Jan 25 20:16:56 2016 -0500 +++ b/test-data/plotCoverage_result1.tabular Mon Feb 15 10:26:54 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 e1bb51933e7f -r 6a247ae015cc tool_dependencies.xml --- a/tool_dependencies.xml Mon Jan 25 20:16:56 2016 -0500 +++ b/tool_dependencies.xml Mon Feb 15 10:26:54 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 e1bb51933e7f -r 6a247ae015cc tool_dependencies.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml.orig Mon Feb 15 10:26:54 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> |
