Mercurial > repos > bgruening > deeptools_plot_coverage
changeset 25:4e12ea27f788 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83
| author | bgruening |
|---|---|
| date | Wed, 29 May 2019 09:43:57 -0400 |
| parents | 3b9d990a0a0e |
| children | 56bce3c82278 |
| files | deepTools_macros.xml plotCoverage.xml test-data/plotCoverage.metrics test-data/plotCoverage_result1.png |
| diffstat | 4 files changed, 62 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/deepTools_macros.xml Tue Apr 02 08:13:59 2019 -0400 +++ b/deepTools_macros.xml Wed May 29 09:43:57 2019 -0400 @@ -1,10 +1,10 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">3.2.1.0</token> + <token name="@WRAPPER_VERSION@">3.3.0.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.2.1">deeptools</requirement> + <requirement type="package" version="3.3.0">deeptools</requirement> <requirement type="package" version="1.9">samtools</requirement> </requirements> <expand macro="stdio" />
--- a/plotCoverage.xml Tue Apr 02 08:13:59 2019 -0400 +++ b/plotCoverage.xml Wed May 29 09:43:57 2019 -0400 @@ -25,6 +25,23 @@ --outRawCounts '$outFileRawCounts' #end if + #if ' '.join(map(str, $BED)) != 'None': + #set bedFileLList=[] + #for $f in $BED: + #silent $bedFileList.append("'%s'" % $f) + #end for + #if $bedFileList != ["'None'"]: + --BED #echo ' '.join($bedFileList)# + #end if + #end if + + #if $coverageOpt.showCoverageOpt == "yes": + --outCoverageMetrics '$outFileCoverageMetrics' + #for $t in $coverageOpt.thresholds: + -ct $t.coverageThreshold + #end for + #end if + #if $advancedOpt.showAdvancedOpt == "yes": --numberOfSamples '$advancedOpt.numberOfSamples' $advancedOpt.skipZeros @@ -48,11 +65,28 @@ <expand macro="multiple_input_bams" MIN="1"/> <expand macro="custom_sample_labels" /> + <param argument="--BED" type="data" format="bed,gtf" multiple="true" optional="true" min="0" + label="Regions of interest" + help="Limits the coverage analysis to the regions specified in these files. This overrides --numberOfSamples. It is inadvisable to combine this with saving the raw counts." /> + + <conditional name="coverageOpt"> + <param name="showCoverageOpt" type="select" label="Show coverage metrics options"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param argument="--outCoverageMetrics" type="boolean" label="Save per-threshold coverage metrics?"/> + <repeat name="thresholds" title="Coverage Thresholds"> + <param argument="--coverageThreshold" type="integer" min="0" label="Coverage Threshold" value="0"/> + </repeat> + </when> + </conditional> <conditional name="advancedOpt"> <param name="showAdvancedOpt" type="select" label="Show advanced options" > - <option value="no" selected="true">no</option> - <option value="yes">yes</option> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> </param> <when value="no" /> <when value="yes"> @@ -78,6 +112,9 @@ <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> <filter>outRawCounts is True</filter> </data> + <data format="tabular" name="outFileCoverageMetrics" label="${tool.name} on ${on_string}: Threshold Metrics"> + <filter>coverageOpt.outCoverageMetrics is True</filter> + </data> </outputs> <tests> <test> @@ -89,6 +126,18 @@ <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" /> <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" /> </test> + <test> + <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> + <param name="showAdvancedOpt" value="yes" /> + <param name="plotTitle" value="Test Title from Galaxy" /> + <param name="showCoverageOpt" value="yes" /> + <param name="coverageThreshold" value="0" /> + <param name="coverageThreshold" value="5" /> + <param name="coverageThreshold" value="10" /> + <param name="coverageThreshold" value="20" /> + <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" /> + <output name="outFileCoverageMetrics" file="plotCoverage.metrics" ftype="tabular" /> + </test> </tests> <help> <![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotCoverage.metrics Wed May 29 09:43:57 2019 -0400 @@ -0,0 +1,9 @@ +Sample Threshold Percent +bowtie2 test1.bam 0 100.000 +bowtie2 test1.bam 0 100.000 +bowtie2 test1.bam 5 1.509 +bowtie2 test1.bam 5 1.509 +bowtie2 test1.bam 10 1.461 +bowtie2 test1.bam 10 1.461 +bowtie2 test1.bam 20 1.406 +bowtie2 test1.bam 20 1.406