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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 37b1832f15c9960e02c6cae831b1f9f717818af8
author | iuc |
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date | Fri, 13 Jan 2017 10:33:44 -0500 |
parents | 2f6c7f82ad4a |
children | 9be99db0304a |
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<tool id="pe_histogram" name="Paired-end histogram" version="1.0.1"> <description>of insert size frequency</description> <requirements> <requirement type="package" version="8.0.112">openjdk</requirement> </requirements> <stdio> <!-- Anything other than zero is an error --> <exit_code range=":-1" /> <exit_code range="1:" /> <!-- Check stderr in case the return code has not been set --> <regex match="Error:" /> <regex match="Exception:" /> </stdio> <command> <![CDATA[ ln -s "${input_bam}" "localbam.bam" && ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" && java -jar $__tool_directory__/PEHistogram.jar -B "localbam.bam" -I "localbam.bam.bai" #if str($lower_limit) != '': -l $lower_limit #end if #if str($upper_limit) != '': -u $upper_limit #end if -p "$output1" -t "$output2" 1>/dev/null ]]> </command> <inputs> <param name="input_bam" type="data" format="bam" label="BAM file" /> <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/> <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." /> </inputs> <outputs> <data name="output1" format="png" /> <data name="output2" format="tabular" /> </outputs> <tests> <test> <param name="input_bam" value="input.bam" ftype="bam" /> <output name="output1" file="output1.png" ftype="png" compare="sim_size" /> <output name="output2" file="output1.tabular" ftype="tabular" compare="contains" /> </test> <test> <param name="input_bam" value="input.bam" ftype="bam" /> <param name="lower_limit" value="200" /> <param name="upper_limit" value="300" /> <output name="output1" file="output2.png" ftype="png" compare="sim_size" /> <output name="output2" file="output2.tabular" ftype="tabular" compare="contains" /> </test> </tests> <help> **What it does** Produces an insert size histogram and basic statistics for a paired-end BAM file. Two outputs are produced: - a png image consisting of the histogram of the insert size frequency - a tabular file containing the alignment statistics ----- **Options** * **Lower bp limit** - the lower bp limit on insert size for calculating the histogram. * **Upper bp limit** - the upper bp limit on insert size for calculating the histogram. </help> <citations> <citation type="bibtex"> @unpublished{None, author = {Lai, William}, title = {None}, year = {None}, eprint = {None}, url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} }</citation> </citations> </tool>