Mercurial > repos > bgruening > deeptools_plot_fingerprint
changeset 14:801ca6971efc draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
| author | bgruening |
|---|---|
| date | Sun, 14 May 2017 17:59:21 -0400 |
| parents | c224e8aa3f36 |
| children | f8fc4e5aff9d |
| files | deepTools_macros.xml plotFingerprint.xml repository_dependencies.xml test-data/bamPEFragmentSize_result1.txt test-data/plotFingerprint_quality_metrics.tabular tool_dependencies.xml |
| diffstat | 6 files changed, 36 insertions(+), 51 deletions(-) [+] |
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--- a/deepTools_macros.xml Fri Mar 31 17:44:40 2017 -0400 +++ b/deepTools_macros.xml Sun May 14 17:59:21 2017 -0400 @@ -1,10 +1,9 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.5.0</token> + <token name="@WRAPPER_VERSION@">2.5.1.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.7.10">python</requirement> <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement> <yield /> </requirements> @@ -25,6 +24,21 @@ </conditional> </xml> + <token name="@PLOTWIDTHHEIGHT@"> + --plotWidth '$advancedOpt.plotWidth' + --plotHeight '$advancedOpt.plotHeight' + </token> + + <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT"> + <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0" + label="Plot height" + help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." /> + + <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0" + label="Plot width" + help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." /> + </xml> + <token name="@ADVANCED_OPTS_READ_PROCESSING@"> #if $advancedOpt.doExtendCustom.doExtend == 'custom': --extendReads $advancedOpt.doExtendCustom.extendReadsValue @@ -369,46 +383,26 @@ </citations> </xml> - <xml name="multiple_input_bams"> + <xml name="multiple_input_bams" tokens="MIN"> <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" + <param argument="--bamfiles" type="data" format="bam" min="@MIN@" label="Bam file" multiple="true" help=""/> </when> <when value="Yes"> - <repeat name="multibam_repeats" min="1" title="BAM Files"> + <repeat name="multibam_repeats" min="@MIN@" title="BAM Files"> <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> </repeat> </when> </conditional> </xml> - <xml name="multiple_input_bams_min2"> - <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"> + <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE"> <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."> @@ -416,13 +410,13 @@ <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."/> + <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@" + label="@LABEL@" + help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/> </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 name="multibigwig_repeats" min="@MIN@" title="@TITLE@"> + <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/> </repeat> </when> </conditional> @@ -467,16 +461,16 @@ #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' % $counter) + #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) + ln -f -s "${bigwig}" "${identifier}_${counter}.bw" && + #silent $files.append('%s_%s.bw' % ($identifier, $counter)) #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' % $counter) + ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" && + #silent $files.append('%s_%s.bw' % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for #end if
--- a/plotFingerprint.xml Fri Mar 31 17:44:40 2017 -0400 +++ b/plotFingerprint.xml Sun May 14 17:59:21 2017 -0400 @@ -24,7 +24,7 @@ #if $output.JSDsample: #if "'{}'".format($output.JSDsample.display_name) in $labels: #set JSDidx = $labels.index("'{}'".format($output.JSDsample.display_name)) - --JSDsample "./${JSDidx}.bam" + --JSDsample "${JSDidx}.bam" #end if #end if #end if @@ -53,7 +53,7 @@ </command> <inputs> - <expand macro="multiple_input_bams" /> + <expand macro="multiple_input_bams" MIN="1"/> <expand macro="region_limit_operation" /> <conditional name="advancedOpt"> @@ -87,7 +87,7 @@ <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" + <param name="JSDsample" type="data" format="bam" optional="true" 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>
--- a/repository_dependencies.xml Fri Mar 31 17:44:40 2017 -0400 +++ b/repository_dependencies.xml Sun May 14 17:59:21 2017 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories> - <repository changeset_revision="df883cc67fbd" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9946bc39c834" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories>
--- a/test-data/bamPEFragmentSize_result1.txt Fri Mar 31 17:44:40 2017 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Sun May 14 17:59:21 2017 -0400 @@ -1,6 +1,6 @@ -BAM file : 0.bam +Sample label: bowtie2 test1.bam Sample size: 3 Fragment lengths:
--- a/test-data/plotFingerprint_quality_metrics.tabular Fri Mar 31 17:44:40 2017 -0400 +++ b/test-data/plotFingerprint_quality_metrics.tabular Sun May 14 17:59:21 2017 -0400 @@ -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 0.269004498068 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 +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 0.0 0.269004498068 0 0 0
--- a/tool_dependencies.xml Fri Mar 31 17:44:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="python" version="2.7.10"> - <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="2.5.0"> - <repository changeset_revision="72856dd1f9a5" name="package_python_2_7_deeptools_2_5_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>