Mercurial > repos > nilesh > rseqc
diff geneBody_coverage.xml @ 49:6b33e31bda10 draft
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
| author | lparsons |
|---|---|
| date | Thu, 16 Jul 2015 17:43:43 -0400 |
| parents | 2e6190c29c54 |
| children | f242ee103277 |
line wrap: on
line diff
--- a/geneBody_coverage.xml Tue Apr 21 10:27:06 2015 -0400 +++ b/geneBody_coverage.xml Thu Jul 16 17:43:43 2015 -0400 @@ -1,40 +1,49 @@ -<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="2.4"> +<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="2.4galaxy1"> <description> Read coverage over gene body. </description> + + <macros> + <import>rseqc_macros.xml</import> + </macros> + <requirements> - <requirement type="package" version="3.0.3">R</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="2.4">rseqc</requirement> + <expand macro="requirement_package_r" /> + <expand macro="requirement_package_numpy" /> + <expand macro="requirement_package_rseqc" /> </requirements> - <command> + + <expand macro="stdio" /> + + <version_command><![CDATA[geneBody_coverage.py --version]]></version_command> + + <command><![CDATA[ #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name) #set $fname = "d1_" + str($safename) + ".bam" - ln -s '${input}' '${fname}' && - ln -s '${input.metadata.bam_index}' '${fname}.bai' && - echo '${fname}' > input_list.txt && + ln -s '${input}' '${fname}' && + ln -s '${input.metadata.bam_index}' '${fname}.bai' && + echo '${fname}' > input_list.txt && #for $i, $additional_input in enumerate($additionalinputs): #set $index = $i+2 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $additional_input.file.display_name) #set $fname = 'd' + str($index) + '_' + str($safename) + ".bam" - ln -s '$additional_input.file' '${fname}' && - ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' && - echo '${fname}' >> input_list.txt && + ln -s '$additional_input.file' '${fname}' && + ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' && + echo '${fname}' >> input_list.txt && #end for geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output + ]]> </command> - <stdio> - <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> - <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> - </stdio> + <inputs> - <param name="input" type="data" label="Additional input .bam files" format="bam" /> - <repeat name="additionalinputs" title="Input .bam file"> - <param name="file" type="data" label="Input .bam file" format="bam" /> + <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/> + <repeat name="additionalinputs" title="Additional input .bam files"> + <param name="file" type="data" label="Additional input .bam file" format="bam" /> </repeat> - <param name="refgene" type="data" label="Reference Genome" format="bed" /> - <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length" help="Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100)." /> + <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/> + <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length in bp (default: 100)" help="mRNA that are shorter than this value will be skipped (--minimum_length)." /> </inputs> + <outputs> <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves PDF)" /> <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap PDF)"> @@ -43,7 +52,29 @@ <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage.r" label="${tool.name} on ${on_string} (R Script)" /> <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" /> </outputs> - <help> + + <tests> + <test> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/> + <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf"/> + <output name="outputr" file="output.geneBodyCoverage.r"/> + <output name="outputtxt" file="output.geneBodyCoverage.txt"/> + </test> + <test> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <param name="file_0" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <param name="file_1" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/> + <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf"/> + <output name="outputcurvespdf" file="output2.geneBodyCoverage.heatMap.pdf"/> + <output name="outputr" file="output2.geneBodycoverage.r"/> + <output name="outputtxt" file="output2.geneBodyCoverage.txt"/> + </test> + + </tests> + + <help><![CDATA[ geneBody_coverage.py ++++++++++++++++++++ @@ -52,7 +83,12 @@ If 3 or more BAM files were provided. This program generates a lineGraph and a heatmap. If fewer than 3 BAM files were provided, only lineGraph is generated. See below for examples. When heatmap is generated, samples are ranked by the "skewness" of the coverage: Sample with best (worst) coverage will be displayed at the top (bottom) of the heatmap. -Coverage skewness was measured by `Pearson’s skewness coefficients <http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_ +Coverage skewness was measured by `Pearson’s skewness coefficients <http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_ + + .. image:: http://rseqc.sourceforge.net/_images/geneBody_workflow.png + :width: 800 px + :scale: 80 % + Inputs ++++++++++++++ @@ -100,8 +136,9 @@ .. image:: http://rseqc.sourceforge.net/_static/logo.png .. _RSeQC: http://rseqc.sourceforge.net/ - - +]]> + </help> - </help> + <expand macro="citations" /> + </tool>