Mercurial > repos > bgruening > deeptools_plot_fingerprint
changeset 10:314348664620 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
| author | bgruening |
|---|---|
| date | Mon, 05 Dec 2016 08:06:43 -0500 |
| parents | ef2bcce0be62 |
| children | 716ce4890b52 |
| files | deepTools_macros.xml plotFingerprint.xml test-data/bamCompare_result1.bg 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/bigwigCompare_result2.bg test-data/computeGCBias_result1.tabular test-data/computeMatrixOperations.txt test-data/computeMatrixOperations_result2.mat.gz test-data/correctGCBias_result1.bam test-data/plotFingerprint_quality_metrics.tabular test-data/plotFingerprint_result2.tabular test-data/sequence.2bit tool_dependencies.xml |
| diffstat | 18 files changed, 876 insertions(+), 780 deletions(-) [+] |
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--- a/deepTools_macros.xml Tue Oct 25 19:05:49 2016 -0400 +++ b/deepTools_macros.xml Mon Dec 05 08:06:43 2016 -0500 @@ -98,11 +98,11 @@ </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.3.6</token> + <token name="@WRAPPER_VERSION@">2.4.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> - <requirement type="package" version="2.3.6">deepTools</requirement> + <requirement type="package" version="2.4.1">deeptools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -285,11 +285,21 @@ </param> </xml> + <xml name="sortRegionsComputeMatrix"> + <param argument="--sortRegions" type="select" label="Sort regions" + help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> + <option value="no">no ordering</option> + <option value="keep" selected="true">maintain the same ordering as the input files</option> + <option value="descend">descending order</option> + <option value="ascend">ascending order</option> + </param> + </xml> + <xml name="sortRegions"> <param argument="--sortRegions" type="select" label="Sort regions" help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> <option value="no">no ordering</option> - <option value="descend" selected="true">descending order</option> + <option value="descend">descending order</option> <option value="ascend">ascending order</option> </param> </xml> @@ -362,21 +372,62 @@ </xml> <xml name="multiple_input_bams"> - <param argument="--bamfiles" type="data" format="bam" min="1" - label="Bam file" multiple="true" - help=""/> + <conditional name="multibam_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bamfiles" type="data" format="bam" min="1" + label="Bam file" multiple="true" + help=""/> + </when> + <when value="Yes"> + <repeat name="multibam_repeats" min="1" title="BAM Files"> + <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> + </repeat> + </when> + </conditional> </xml> <xml name="multiple_input_bams_min2"> - <param argument="--bamfiles" type="data" format="bam" min="2" - label="Bam file" multiple="true" - help=""/> + <conditional name="multibam_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples +is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bamfiles" type="data" format="bam" min="2" + label="Bam file" multiple="true" + help=""/> + </when> + <when value="Yes"> + <repeat name="multibam_repeats" min="2" title="BAM Files"> + <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> + </repeat> + </when> + </conditional> </xml> <xml name="multiple_input_bigwigs"> - <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" - label="Bigwig file" - help="A Bigwig file."/> + <conditional name="multibigwig_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples +is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" + label="Bigwig file" + help="A Bigwig file."/> + </when> + <when value="Yes"> + <repeat name="multibigwig_repeats" min="2" title="BigWig files"> + <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/> + </repeat> + </when> + </conditional> </xml> <xml name="plotTitle"> @@ -390,12 +441,21 @@ <![CDATA[ #set files=[] #set labels=[] - #for $counter, $bamfile in enumerate($bamfiles): - 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)) - #end for + #if $multibam_conditional.orderMatters == "No": + #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): + 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)) + #end for + #else: + #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): + ln -s "${f.bamfile}" "./${counter}.bam" && + ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" && + #silent $files.append('%s.bam' % $counter) + #silent $labels.append("'%s'" % ($f.bamfile.display_name)) + #end for + #end if ]]> </token> @@ -403,11 +463,19 @@ <![CDATA[ #set files=[] #set labels=[] - #for $counter, $bigwig in enumerate($bigwigfiles): - ln -s "${bigwig}" "${counter}.bw" && - #silent $files.append('%s.bw' % $counter) - #silent $labels.append("'%s'" % ($bigwig.display_name)) - #end for + #if $multibigwig_conditional.orderMatters == "No": + #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): + ln -s "${bigwig}" "${counter}.bw" && + #silent $files.append('%s.bw' % $counter) + #silent $labels.append("'%s'" % ($bigwig.display_name)) + #end for + #else: + #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): + ln -s "${f.bigwig}" "${counter}.bw" && + #silent $files.append('%s.bw' % $counter) + #silent $labels.append("'%s'" % ($f.bigwig.display_name)) + #end for + #end if ]]> </token>
--- a/plotFingerprint.xml Tue Oct 25 19:05:49 2016 -0400 +++ b/plotFingerprint.xml Mon Dec 05 08:06:43 2016 -0500 @@ -19,6 +19,15 @@ #if $output.saveRawCounts: --outRawCounts '$outFileRawCounts' #end if + #if $output.saveQualityMetrics: + --outQualityMetrics '$outFileQualityMetrics' + #if $output.JSDsample: + #if "'{}'".format($output.JSDsample.display_name) in $labels: + #set JSDidx = $labels.index("'{}'".format($output.JSDsample.display_name)) + --JSDsample "./${JSDidx}.bam" + #end if + #end if + #end if #else --plotFileFormat 'png' #end if @@ -34,10 +43,6 @@ $advancedOpt.ignoreDuplicates $advancedOpt.skipZeros - #if $advancedOpt.minMappingQuality: - --minMappingQuality '$advancedOpt.minMappingQuality' - #end if - #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": --plotTitle '$advancedOpt.plotTitle' #end if @@ -80,6 +85,11 @@ <when value="yes"> <expand macro="input_image_file_format" /> <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/> + <param name="saveQualityMetrics" type="boolean" label="Save quality metrics" + help="The file will have one row per input BAM file and columns containing a variety of QC metrics. For the full description of all metrics and their interpretation, please see our online documentation: http://deeptools.readthedocs.io/en/latest/content/feature/plotFingerprint_QC_metrics.html. (--outQualityMetrics)"/> + <param name="JSDsample" type="data" format="bam" + label="Jensen-Shannon distance reference sample" + help="If output metrics should be saved, then use this sample as the reference for computing the Jensen-Shannon distance and CHANCE metrics of all other samples. Normally this is an input sample. If you don't specify this, then these metrics will not be computed. This is only applicable if quality metrics are being saved. (--JSDsample)" /> </when> </conditional> </inputs> @@ -93,6 +103,14 @@ )) </filter> </data> + <data format="tabular" name="outFileQualityMetrics" label="${tool.name} on ${on_string}: quality metrics"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveQualityMetrics'] is True + )) + </filter> + </data> </outputs> <tests> <test> @@ -106,9 +124,12 @@ <param name="showAdvancedOpt" value="yes" /> <param name="showOutputSettings" value="yes" /> <param name="saveRawCounts" value="True" /> + <param name="saveQualityMetrics" value="True" /> <param name="plotTitle" value="Test Fingerprint Plot" /> + <param name="JSDsample" value="bowtie2 test1.bam" ftype="bam" /> <output name="outFileName" file="plotFingerprint_result2.png" ftype="png" compare="sim_size" /> <output name="outFileRawCounts" file="plotFingerprint_result2.tabular" ftype="tabular" /> + <output name="outFileQualityMetrics" file="plotFingerprint_quality_metrics.tabular" ftype="tabular" /> </test> </tests> <help> @@ -127,7 +148,7 @@ The default output is a diagnostic plot (see below for an example and further down for some background information). -Optionally, you can obtain the table of raw counts that was used to generate the plot. +Optionally, you can obtain the table of raw values that were used to generate the plot. .. image:: $PATH_TO_IMAGES/plotFingerprint_output.png :width: 600 @@ -149,10 +170,10 @@ Theoretical Background ---------------------- -The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the specified length. -These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank) -and the cumulative sum of read counts are plotted. An ideal input (control) with a uniform distribution of reads alignments -result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion +The tool first samples indexed BAM files and sums the per-base coverage of reads/fragments overlapping a window (bin) of the specified length. +These values are then sorted according to their rank (the bin with the highest number of reads has the highest rank) +and the cumulative sum plotted. An ideal input (control) with a uniform distribution of reads alignments +and infinite sequencing depth will result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are most commonly seen with transcription factors.
--- a/test-data/bamCompare_result1.bg Tue Oct 25 19:05:49 2016 -0400 +++ b/test-data/bamCompare_result1.bg Mon Dec 05 08:06:43 2016 -0500 @@ -1,1 +1,1 @@ -chrM 0 16569 1.00 +chrM 0 16569 1
--- a/test-data/bamCoverage_result3.bg Tue Oct 25 19:05:49 2016 -0400 +++ b/test-data/bamCoverage_result3.bg Mon Dec 05 08:06:43 2016 -0500 @@ -1,7 +1,7 @@ -chrM 0 210 9768764.94 -chrM 210 220 9560918.88 -chrM 220 230 7690304.31 -chrM 230 240 5196151.56 -chrM 240 250 3325537.00 -chrM 250 260 623538.19 -chrM 260 16569 0.00 +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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrixOperations.txt Mon Dec 05 08:06:43 2016 -0500 @@ -0,0 +1,4 @@ +Groups: + genes +Samples: + file_0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotFingerprint_quality_metrics.tabular Mon Dec 05 08:06:43 2016 -0500 @@ -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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--- a/tool_dependencies.xml Tue Oct 25 19:05:49 2016 -0400 +++ b/tool_dependencies.xml Mon Dec 05 08:06:43 2016 -0500 @@ -3,7 +3,7 @@ <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="2.3.6"> - <repository changeset_revision="05f46fef1ea5" name="package_python_2_7_deeptools_2_3_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <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>