Mercurial > repos > nilesh > rseqc
changeset 52:34e4c586e3c0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
| author | iuc |
|---|---|
| date | Tue, 21 Nov 2017 14:55:32 -0500 |
| parents | 09846d5169fa |
| children | 080fd5739bb4 |
| files | geneBody_coverage.xml junction_annotation.xml read_quality.xml rseqc_macros.xml |
| diffstat | 4 files changed, 60 insertions(+), 23 deletions(-) [+] |
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--- a/geneBody_coverage.xml Tue Mar 14 10:23:21 2017 -0400 +++ b/geneBody_coverage.xml Tue Nov 21 14:55:32 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="@WRAPPER_VERSION@"> +<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="@WRAPPER_VERSION@.1"> <description> Read coverage over gene body. </description> @@ -14,24 +14,42 @@ <version_command><![CDATA[geneBody_coverage.py --version]]></version_command> <command><![CDATA[ - #import re - #set $input_list = [] - #for $i, $input in enumerate($inputs): + #if str($batch_mode.batch_mode_selector) == "merge": + #import re + #set $input_list = [] + #for $i, $input in enumerate($batch_mode.inputs): + #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) + #if $safename in $input_list: + #set $safename = str($safename) + "." + str($i) + #end if + $input_list.append($safename) + ln -sf '${input}' '${safename}.bam' && + ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' && + echo '${safename}.bam' >> 'input_list.txt' && + #end for + geneBody_coverage.py -i 'input_list.txt' -r '${refgene}' --minimum_length ${minimum_length} -o output + #else #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) - #if $safename in $input_list: - #set $safename = str($safename) + "." + str($i) - #end if - $input_list.append($safename) ln -sf '${input}' '${safename}.bam' && ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' && - echo '${safename}.bam' >> 'input_list.txt' && - #end for - geneBody_coverage.py -i 'input_list.txt' -r '${refgene}' --minimum_length ${minimum_length} -o output + geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output + #end if ]]> </command> <inputs> - <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/> + <conditional name="batch_mode"> + <param name="batch_mode_selector" type="select" label="Run each sample separately, or combine mutiple samples into one plot"> + <option value="batch" selected="true">Run each sample separately</option> + <option value="merge">Combine multiple samples into a single plot</option> + </param> + <when value="batch"> + <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/> + </when> + <when value="merge"> + <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/> + </when> + </conditional> <expand macro="refgene_param" /> <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)." /> <expand macro="rscript_output_param" /> @@ -40,7 +58,7 @@ <outputs> <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves pdf)" /> <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap pdf)"> - <filter>len(inputs) >= 3</filter> + <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter> </data> <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" /> <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" /> @@ -49,7 +67,10 @@ <!-- PDF Files contain R version, must avoid checking for diff --> <tests> <test> - <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + <conditional name="batch_mode"> + <param name="batch_mode_selector" value="batch" /> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + </conditional> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> <param name="rscript_output" value="true" /> <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size" /> @@ -57,7 +78,10 @@ <output name="outputtxt" file="output.geneBodyCoverage.txt" /> </test> <test> - <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + <conditional name="batch_mode"> + <param name="batch_mode_selector" value="merge" /> + <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + </conditional> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> <param name="rscript_output" value="true" /> <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size" /> @@ -79,8 +103,8 @@ Coverage skewness was measured by `Pearson’s skewness coefficients <http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_ .. image:: $PATH_TO_IMAGES/geneBody_workflow.png -:width: 800 px -:scale: 80 % + :width: 800 px + :scale: 80 % ## Inputs @@ -94,7 +118,7 @@ Minimum mRNA length Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100). - ## Outputs +## Outputs Text Table that includes the data used to generate the plots @@ -112,9 +136,9 @@ :scale: 80 % .. image:: $PATH_TO_IMAGES/Aug_26.geneBodyCoverage.heatMap.png -:height: 600 px -:width: 600 px -:scale: 80 % + :height: 600 px + :width: 600 px + :scale: 80 % @ABOUT@
--- a/junction_annotation.xml Tue Mar 14 10:23:21 2017 -0400 +++ b/junction_annotation.xml Tue Nov 21 14:55:32 2017 -0500 @@ -5,7 +5,13 @@ <import>rseqc_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <!-- + Required due to conda solver bug: https://github.com/conda/conda/issues/6269 + See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info + --> + <requirement type="package" version="3.4.1">r-base</requirement> + </expand> <expand macro="stdio" />
--- a/read_quality.xml Tue Mar 14 10:23:21 2017 -0400 +++ b/read_quality.xml Tue Nov 21 14:55:32 2017 -0500 @@ -5,7 +5,13 @@ <import>rseqc_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <!-- + Required due to conda solver bug: https://github.com/conda/conda/issues/6269 + See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info + --> + <requirement type="package" version="3.4.1">r-base</requirement> + </expand> <expand macro="stdio" />