| Previous changeset 11:cdc31a261f47 (2017-01-24) Next changeset 13:0e8cbe7d4ff4 (2017-03-31) |
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Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 |
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modified:
deepTools_macros.xml plotCorrelation.xml test-data/bamCompare_result2.bw test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result6.bw test-data/bamPEFragmentSize_histogram_result1.png test-data/bigwigCompare_result1.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/multiBamSummary_result1.npz test-data/multiBamSummary_result2.npz test-data/multiBigwigSummary_result1.npz test-data/plotCorrelation_result1.png test-data/plotCorrelation_result1.tabular test-data/plotCorrelation_result2.png test-data/plotCoverage_result1.png test-data/plotEnrichment_output.png test-data/plotFingerprint_quality_metrics.tabular test-data/plotFingerprint_result1.png test-data/plotFingerprint_result2.png test-data/profiler_result1.png test-data/profiler_result2.png test-data/profiler_result2.tabular tool_dependencies.xml |
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added:
test-data/multiBamSummary_result2b.npz |
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| diff -r cdc31a261f47 -r ed2767cdf4e8 deepTools_macros.xml --- a/deepTools_macros.xml Tue Jan 24 04:57:11 2017 -0500 +++ b/deepTools_macros.xml Fri Mar 31 09:27:20 2017 -0400 |
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| @@ -1,5 +1,17 @@ <macros> + <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> + <token name="@WRAPPER_VERSION@">2.5.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.7.10">python</requirement> + <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement> + <yield /> + </requirements> + <expand macro="stdio" /> + <version_command>@BINARY@ --version</version_command> + </xml> + <xml name="advancedOpt_scaffold"> <conditional name="advancedOpt"> <param name="showAdvancedOpt" type="select" label="Show advanced options" > @@ -97,18 +109,6 @@ </param> </xml> - <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.4.2</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="2.7.10">python</requirement> - <requirement type="package" version="2.4.2">deeptools</requirement> - <yield /> - </requirements> - <expand macro="stdio" /> - <version_command>@BINARY@ --version</version_command> - </xml> - <xml name="smoothLength"> <param argument="--smoothLength" type="integer" value="" optional="True" min="1" label="Smooth values using the following length (in bases)" @@ -181,10 +181,10 @@ <xml name="fragLength"> <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0" label="Minimum fragment length for inclusion." - help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." /> + help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." /> <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0" label="Maximum fragment length for inclusion." - help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." /> + help="A value of 0 (the default) is equivalent to no maximum." /> </xml> <xml name="read_processing_options"> @@ -324,9 +324,7 @@ <xml name="scaleFactor"> <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" - help="When used in combination with --normalizeTo1x or - --normalizeUsingRPKM, the computed scaling factor will - be multiplied by the given scale factor." /> + help="The computed scaling factor will be multiplied by this (default 1)." /> </xml> <xml name="scaleFactors"> @@ -441,19 +439,22 @@ <![CDATA[ #set files=[] #set labels=[] + #import re #if $multibam_conditional.orderMatters == "No": #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): + #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier)) ln -s "${bamfile}" "./${counter}.bam" && ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && #silent $files.append('%s.bam' % $counter) - #silent $labels.append("'%s'" % ($bamfile.display_name)) + #silent $labels.append("'%s'" % identifier) #end for #else: #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): + #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) ln -s "${f.bamfiles}" "./${counter}.bam" && ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" && #silent $files.append('%s.bam' % $counter) - #silent $labels.append("'%s'" % ($f.bamfiles.display_name)) + #silent $labels.append("'%s'" % $identifier) #end for #end if ]]> @@ -463,17 +464,20 @@ <![CDATA[ #set files=[] #set labels=[] + #import re #if $multibigwig_conditional.orderMatters == "No": #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): + #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) ln -s "${bigwig}" "${counter}.bw" && #silent $files.append('%s.bw' % $counter) - #silent $labels.append("'%s'" % ($bigwig.display_name)) + #silent $labels.append("'%s'" % $identifier) #end for #else: #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): + #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) ln -s "${f.bigwigfiles}" "${counter}.bw" && #silent $files.append('%s.bw' % $counter) - #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name)) + #silent $labels.append("'%s'" % $identifier) #end for #end if ]]> |
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| diff -r cdc31a261f47 -r ed2767cdf4e8 plotCorrelation.xml --- a/plotCorrelation.xml Tue Jan 24 04:57:11 2017 -0500 +++ b/plotCorrelation.xml Fri Mar 31 09:27:20 2017 -0400 |
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| b'@@ -1,142 +1,142 @@\n-<tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">\r\n- <description>Create a heatmap or scatterplot of correlation scores between different samples </description>\r\n- <macros>\r\n- <token name="@BINARY@">plotCorrelation</token>\r\n- <import>deepTools_macros.xml</import>\r\n- </macros>\r\n- <expand macro="requirements"/>\r\n- <command>\r\n-<![CDATA[\r\n- @BINARY@\r\n- --corData "$corData"\r\n- --plotFile "$outFileName"\r\n- --corMethod "$corMethod"\r\n- --whatToPlot "$plotting_type.whatToPlot"\r\n- #if str($plotting_type.whatToPlot) == \'heatmap\':\r\n- @HEATMAP_OPTIONS@\r\n- #else:\r\n- --plotTitle \'$plotting_type.plotTitle\'\r\n- #end if\r\n- $skipZeros\r\n- --plotFileFormat "$outFileFormat"\r\n- $removeOutliers\r\n- #if $outFileCorMatrix:\r\n- --outFileCorMatrix "$matrix"\r\n- #end if\r\n-\r\n-]]>\r\n- </command>\r\n- <inputs>\r\n- <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary tool"/>\r\n- <expand macro="corMethod" />\r\n-\r\n- <conditional name="plotting_type" >\r\n- <param argument="--whatToPlot" type="select" label="Plotting type">\r\n- <option value="heatmap" selected="True">Heatmap</option>\r\n- <option value="scatterplot">Scatterplot</option>\r\n- </param>\r\n- <when value="heatmap">\r\n- <expand macro="heatmap_options" />\r\n- </when>\r\n- <when value="scatterplot">\r\n- <expand macro="plotTitle" />\r\n- </when>\r\n- </conditional>\r\n-\r\n- <expand macro="skipZeros" />\r\n-\r\n- <expand macro="input_image_file_format" />\r\n-\r\n- <param argument="--removeOutliers" type="boolean"\r\n- truevalue="--removeOutliers" falsevalue="" label="Remove regions with very large counts"\r\n- help="If set, bins with very large counts are removed. Bins\r\n- with abnormally high reads counts artificially\r\n- increase pearson correlation; that\'s why, by default,\r\n- plotCorrelation tries to remove outliers using the median\r\n- absolute deviation (MAD) method applying a threshold\r\n- of 200 to only consider extremely large deviations\r\n- from the median. ENCODE blacklist page (https://sites.\r\n- google.com/site/anshulkundaje/projects/blacklists)\r\n- contains useful information about regions with\r\n- unusually high counts."/>\r\n-\r\n- <param name="outFileCorMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>\r\n-\r\n- </inputs>\r\n- <outputs>\r\n- <expand macro="output_image_file_format_not_nested" />\r\n- <data format="tabular" name="matrix" label="${tool.name} on ${on_string}: Correlation matrix">\r\n- <filter>outFileCorMatrix is True</filter>\r\n- </data>\r\n- </outputs>\r\n- <tests>\r\n- <test>\r\n- <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />\r\n- <param name="outFileFormat" value="png" />\r\n- <param name="outFileCorMatrix" value="True" />\r\n- <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />\r\n- <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="300" />\r\n- </test>\r\n- <test>\r\n- <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />\r\n- <param name="outFileFormat" value="png" />\r\n- <param name="whatToPlot" value="scatterplot" />\r\n- <param name="removeOutliers" value="True" />\r\n- <param name="plotTitle" value="Test Plot" />\r\n- '..b' with abnormally high reads counts artificially\n+ increase pearson correlation; that\'s why, by default,\n+ plotCorrelation tries to remove outliers using the median\n+ absolute deviation (MAD) method applying a threshold\n+ of 200 to only consider extremely large deviations\n+ from the median. ENCODE blacklist page (https://sites.\n+ google.com/site/anshulkundaje/projects/blacklists)\n+ contains useful information about regions with\n+ unusually high counts."/>\n+\n+ <param name="outFileCorMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>\n+\n+ </inputs>\n+ <outputs>\n+ <expand macro="output_image_file_format_not_nested" />\n+ <data format="tabular" name="matrix" label="${tool.name} on ${on_string}: Correlation matrix">\n+ <filter>outFileCorMatrix is True</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />\n+ <param name="outFileFormat" value="png" />\n+ <param name="outFileCorMatrix" value="True" />\n+ <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />\n+ <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="300" />\n+ </test>\n+ <test>\n+ <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />\n+ <param name="outFileFormat" value="png" />\n+ <param name="whatToPlot" value="scatterplot" />\n+ <param name="removeOutliers" value="True" />\n+ <param name="plotTitle" value="Test Plot" />\n+ <output name="outFileName" file="plotCorrelation_result2.png" ftype="png" compare="sim_size" delta="300" />\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+What it does\n+------------\n+\n+This tools takes the default output of ``multiBamSummary`` or ``multiBigwigSummary``, and computes the pairwise correlation among samples.\n+Results can be visualized as **scatterplots** or as a **heatmap** of correlation coefficients (see below for examples).\n+\n+Theoretical Background\n+----------------------\n+\n+The result of the correlation computation is a **table of correlation coefficients** that indicates how "strong" the relationship between two samples is and it will consist of numbers between -1 and 1. (-1 indicates perfect anti-correlation, 1 perfect correlation.)\n+\n+We offer two different functions for the correlation computation: *Pearson* or *Spearman*.\n+\n+The *Pearson method* measures the **metric differences** between samples and is therefore influenced by outliers.\n+The *Spearman method* is based on **rankings**.\n+\n+Output\n+------\n+\n+The default output is a **diagnostic plot** -- either a scatterplot or a clustered heatmap displaying the values for each pair-wise correlation (see below for example plots).\n+\n+Optionally, you can also obtain a table of the pairwise correlation coefficients.\n+\n+.. image:: $PATH_TO_IMAGES/plotCorrelation_output.png\n+ :width: 600\n+ :height: 271\n+\n+Example plots\n+-------------\n+\n+The following is the output of ``plotCorrelation`` with our test ChIP-Seq datasets (to be found under "Shared Data" --> "Data Library").\n+\n+Average coverages were computed over 10 kb bins for chromosome X,\n+from bigWig files using ``multiBigwigSummary``. This was then used with ``plotCorrelation`` to make a heatmap of Spearman correlation coefficients.\n+\n+.. image:: $PATH_TO_IMAGES/plotCorrelation_galaxy_bw_heatmap_output.png\n+ :width: 600\n+ :height: 518\n+\n+The scatterplot could look like this:\n+\n+.. image:: $PATH_TO_IMAGES/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png\n+ :width: 600\n+ :height: 600\n+\n+-----\n+\n+@REFERENCES@\n+]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r cdc31a261f47 -r ed2767cdf4e8 test-data/computeMatrixOperations.txt --- a/test-data/computeMatrixOperations.txt Tue Jan 24 04:57:11 2017 -0500 +++ b/test-data/computeMatrixOperations.txt Fri Mar 31 09:27:20 2017 -0400 |
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| @@ -1,4 +1,4 @@ Groups: genes Samples: - file_0 + bamCoverage_result4_bw_0 |
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| diff -r cdc31a261f47 -r ed2767cdf4e8 test-data/plotCorrelation_result1.tabular --- a/test-data/plotCorrelation_result1.tabular Tue Jan 24 04:57:11 2017 -0500 +++ b/test-data/plotCorrelation_result1.tabular Fri Mar 31 09:27:20 2017 -0400 |
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| @@ -1,3 +1,3 @@ - 'bowtie2-test1.bam' 'bowtie2-test1.bam' -'bowtie2-test1.bam' 1.0000 1.0000 -'bowtie2-test1.bam' 1.0000 1.0000 + 'bowtie2 test1.bam' 'bowtie2 test1.bam' +'bowtie2 test1.bam' 1.0000 1.0000 +'bowtie2 test1.bam' 1.0000 1.0000 |
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| diff -r cdc31a261f47 -r ed2767cdf4e8 test-data/plotFingerprint_quality_metrics.tabular --- a/test-data/plotFingerprint_quality_metrics.tabular Tue Jan 24 04:57:11 2017 -0500 +++ b/test-data/plotFingerprint_quality_metrics.tabular Fri Mar 31 09:27:20 2017 -0400 |
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| @@ -1,3 +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 +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA |
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| diff -r cdc31a261f47 -r ed2767cdf4e8 test-data/profiler_result2.tabular --- a/test-data/profiler_result2.tabular Tue Jan 24 04:57:11 2017 -0500 +++ b/test-data/profiler_result2.tabular Fri Mar 31 09:27:20 2017 -0400 |
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| @@ -1,3 +1,3 @@ bin labels -0.0Kb 0.0Kb bins 1 2 -file_0 genes 2477942.34473 2610259.65234 +bamCoverage_result4_bw_0 genes 2477942.875 2610260.125 |
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| diff -r cdc31a261f47 -r ed2767cdf4e8 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 24 04:57:11 2017 -0500 +++ b/tool_dependencies.xml Fri Mar 31 09:27:20 2017 -0400 |
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| @@ -1,7 +1,7 @@ <?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" /> + <repository changeset_revision="bd7165ea6526" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="deeptools" version="2.4.2"> <repository changeset_revision="efc55c226f11" name="package_python_2_7_deeptools_2_4_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> |
