Mercurial > repos > iuc > bam_to_scidx
changeset 5:408520e1ae1a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit cadf726e05de4dfc4f2cf708674fcd2828e4c319
| author | iuc |
|---|---|
| date | Mon, 03 Jul 2017 10:09:42 -0400 |
| parents | b737f6d83f48 |
| children | |
| files | bam_to_scidx.xml |
| diffstat | 1 files changed, 17 insertions(+), 15 deletions(-) [+] |
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--- a/bam_to_scidx.xml Fri Jan 13 10:25:43 2017 -0500 +++ b/bam_to_scidx.xml Mon Jul 03 10:09:42 2017 -0400 @@ -3,21 +3,23 @@ <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__/BAMtoscIDX.jar -b localbam.bam -i localbam.bam.bai -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null - ]]> - </command> + <command detect_errors="exit_code"><![CDATA[ +ln -s '${input_bam}' localbam.bam && +ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai && +java -jar '$__tool_directory__/BAMtoscIDX.jar' +-b localbam.bam +-i localbam.bam.bai +-p $require_proper_mate_pairing +-r $read +#if str($min_insert_size): + -m $min_insert_size +#end if +#if str($max_insert_size): + -M $max_insert_size +#end if +-o '$output' +1>/dev/null + ]]></command> <inputs> <param name="input_bam" type="data" format="bam" label="BAM file" /> <param name="require_proper_mate_pairing" type="select" label="Require proper mate-pairing?" help="Required if filtering by insert size for single-end Reqd 1 (below)." >