| Previous changeset 11:4ae546bddd00 (2017-01-24) Next changeset 13:b8431744eab3 (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 plotCoverage.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 4ae546bddd00 -r 94b05ea80203 deepTools_macros.xml --- a/deepTools_macros.xml Tue Jan 24 04:56:34 2017 -0500 +++ b/deepTools_macros.xml Fri Mar 31 09:26:58 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'" % $identifier) #end for #end if ]]> |
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| diff -r 4ae546bddd00 -r 94b05ea80203 plotCoverage.xml --- a/plotCoverage.xml Tue Jan 24 04:56:34 2017 -0500 +++ b/plotCoverage.xml Fri Mar 31 09:26:58 2017 -0400 |
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| b'@@ -1,124 +1,124 @@\n-<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">\r\n- <description>assesses the sequencing depth of BAM files </description>\r\n- <macros>\r\n- <token name="@BINARY@">plotCoverage</token>\r\n- <import>deepTools_macros.xml</import>\r\n- </macros>\r\n- <expand macro="requirements"/>\r\n- <command>\r\n-<![CDATA[\r\n- #set files=[]\r\n- #set labels=[]\r\n-\r\n- @multiple_input_bams@\r\n-\r\n- @BINARY@\r\n-\r\n- @THREADS@\r\n-\r\n- --plotFile \'$outFileName\'\r\n- --bamfiles #echo " ".join($files)#\r\n- --labels #echo " ".join($labels)#\r\n- --plotFileFormat "$outFileFormat"\r\n-\r\n- #if $outRawCounts:\r\n- --outRawCounts \'$outFileRawCounts\'\r\n- #end if\r\n-\r\n- #if $advancedOpt.showAdvancedOpt == "yes":\r\n- --numberOfSamples \'$advancedOpt.numberOfSamples\'\r\n- $advancedOpt.skipZeros\r\n-\r\n- #if str($advancedOpt.region).strip() != \'\':\r\n- --region \'$advancedOpt.region\'\r\n- #end if\r\n- --numberOfSamples $advancedOpt.numberOfSamples\r\n-\r\n- #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":\r\n- --plotTitle \'$advancedOpt.plotTitle\'\r\n- #end if\r\n- @ADVANCED_OPTS_READ_PROCESSING@\r\n- @blacklist@\r\n- #end if\r\n-\r\n-]]>\r\n- </command>\r\n- <inputs>\r\n-\r\n- <expand macro="multiple_input_bams" />\r\n-\r\n- <conditional name="advancedOpt">\r\n- <param name="showAdvancedOpt" type="select" label="Show advanced options" >\r\n- <option value="no" selected="true">no</option>\r\n- <option value="yes">yes</option>\r\n- </param>\r\n- <when value="no" />\r\n- <when value="yes">\r\n- <param argument="--numberOfSamples" type="integer" value="100000" min="1"\r\n- label="Number of samples"\r\n- help="Number of samples taken from the genome to compute the scaling factors."/>\r\n- <expand macro="region_limit_operation" />\r\n- <expand macro="read_processing_options" />\r\n- <expand macro="skipZeros" />\r\n- <expand macro="plotTitle" />\r\n- <expand macro="blacklist" />\r\n- </when>\r\n- </conditional>\r\n-\r\n- <expand macro="input_image_file_format" />\r\n- <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>\r\n-\r\n-\r\n- </inputs>\r\n- <outputs>\r\n- <expand macro="output_image_file_format_not_nested" />\r\n- <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">\r\n- <filter>outRawCounts is True</filter>\r\n- </data>\r\n- </outputs>\r\n- <tests>\r\n- <test>\r\n- <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />\r\n- <!--param name="outFileFormat" value="png" /-->\r\n- <param name="showAdvancedOpt" value="yes" />\r\n- <param name="plotTitle" value="Test Title from Galaxy" />\r\n- <param name="outRawCounts" value="True" />\r\n- <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />\r\n- <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />\r\n- </test>\r\n- </tests>\r\n- <help>\r\n-<![CDATA[\r\n-What it does\r\n--------------\r\n-\r\n-This tool is useful to **assess the sequencing depth** of a given sample.\r\n-It samples 1 million bp, counts the number of overlapping reads and reports\r\n-a coverage histogram that tells you how many bases are covered how many times.\r\n-\r\n-**Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly.\r\n-\r\n-Output\r\n----------\r\n-\r\n-The default output i'..b'bamfiles #echo " ".join($files)#\n+ --labels #echo " ".join($labels)#\n+ --plotFileFormat "$outFileFormat"\n+\n+ #if $outRawCounts:\n+ --outRawCounts \'$outFileRawCounts\'\n+ #end if\n+\n+ #if $advancedOpt.showAdvancedOpt == "yes":\n+ --numberOfSamples \'$advancedOpt.numberOfSamples\'\n+ $advancedOpt.skipZeros\n+\n+ #if str($advancedOpt.region).strip() != \'\':\n+ --region \'$advancedOpt.region\'\n+ #end if\n+ --numberOfSamples $advancedOpt.numberOfSamples\n+\n+ #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":\n+ --plotTitle \'$advancedOpt.plotTitle\'\n+ #end if\n+ @ADVANCED_OPTS_READ_PROCESSING@\n+ @blacklist@\n+ #end if\n+\n+]]>\n+ </command>\n+ <inputs>\n+\n+ <expand macro="multiple_input_bams" />\n+\n+ <conditional name="advancedOpt">\n+ <param name="showAdvancedOpt" type="select" label="Show advanced options" >\n+ <option value="no" selected="true">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <param argument="--numberOfSamples" type="integer" value="100000" min="1"\n+ label="Number of samples"\n+ help="Number of samples taken from the genome to compute the scaling factors."/>\n+ <expand macro="region_limit_operation" />\n+ <expand macro="read_processing_options" />\n+ <expand macro="skipZeros" />\n+ <expand macro="plotTitle" />\n+ <expand macro="blacklist" />\n+ </when>\n+ </conditional>\n+\n+ <expand macro="input_image_file_format" />\n+ <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>\n+\n+\n+ </inputs>\n+ <outputs>\n+ <expand macro="output_image_file_format_not_nested" />\n+ <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">\n+ <filter>outRawCounts is True</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />\n+ <!--param name="outFileFormat" value="png" /-->\n+ <param name="showAdvancedOpt" value="yes" />\n+ <param name="plotTitle" value="Test Title from Galaxy" />\n+ <param name="outRawCounts" value="True" />\n+ <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />\n+ <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+What it does\n+-------------\n+\n+This tool is useful to **assess the sequencing depth** of a given sample.\n+It samples 1 million bp, counts the number of overlapping reads and reports\n+a coverage histogram that tells you how many bases are covered how many times.\n+\n+**Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly.\n+\n+Output\n+---------\n+\n+The default output is a **panel of two plots** (see below for an example): One is a density plot visualizing the frequencies of read coverages, the other one lets you estimate what fraction of the genome has a depth of sequencing of, for example, 2 overlapping reads or more.\n+\n+The optional output is a table where each row represents the number of reads overlapping with a sampled bp.\n+\n+.. image:: $PATH_TO_IMAGES/plotCoverage_output.png\n+ :width: 600\n+ :height: 345\n+\n+Example plot\n+-----------------\n+\n+.. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png\n+ :width: 600\n+ :height: 291\n+\n+\n+@REFERENCES@\n+]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 4ae546bddd00 -r 94b05ea80203 test-data/computeMatrixOperations.txt --- a/test-data/computeMatrixOperations.txt Tue Jan 24 04:56:34 2017 -0500 +++ b/test-data/computeMatrixOperations.txt Fri Mar 31 09:26:58 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 4ae546bddd00 -r 94b05ea80203 test-data/plotCorrelation_result1.tabular --- a/test-data/plotCorrelation_result1.tabular Tue Jan 24 04:56:34 2017 -0500 +++ b/test-data/plotCorrelation_result1.tabular Fri Mar 31 09:26:58 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 4ae546bddd00 -r 94b05ea80203 test-data/plotFingerprint_quality_metrics.tabular --- a/test-data/plotFingerprint_quality_metrics.tabular Tue Jan 24 04:56:34 2017 -0500 +++ b/test-data/plotFingerprint_quality_metrics.tabular Fri Mar 31 09:26:58 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 4ae546bddd00 -r 94b05ea80203 test-data/profiler_result2.tabular --- a/test-data/profiler_result2.tabular Tue Jan 24 04:56:34 2017 -0500 +++ b/test-data/profiler_result2.tabular Fri Mar 31 09:26:58 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 4ae546bddd00 -r 94b05ea80203 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 24 04:56:34 2017 -0500 +++ b/tool_dependencies.xml Fri Mar 31 09:26:58 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" /> |
