Mercurial > repos > iuc > pe_histogram
changeset 2:9be99db0304a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
| author | iuc |
|---|---|
| date | Tue, 11 Jul 2017 14:36:59 -0400 |
| parents | b1a427b17e9c |
| children | bd1416eea1f0 |
| files | pe_histogram.xml |
| diffstat | 1 files changed, 16 insertions(+), 25 deletions(-) [+] |
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--- a/pe_histogram.xml Fri Jan 13 10:33:44 2017 -0500 +++ b/pe_histogram.xml Tue Jul 11 14:36:59 2017 -0400 @@ -3,31 +3,22 @@ <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 "$output2" 1>/dev/null - ]]> - </command> + <command detect_errors="aggressive"><![CDATA[ +ln -s '${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."/>