| Previous changeset 1:b7d7ae3963aa (2017-01-13) Next changeset 3:580e8bcb6413 (2019-12-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce |
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modified:
tag_pileup_frequency.xml |
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| diff -r b7d7ae3963aa -r 6432735cdb22 tag_pileup_frequency.xml --- a/tag_pileup_frequency.xml Fri Jan 13 10:35:07 2017 -0500 +++ b/tag_pileup_frequency.xml Fri Jun 16 14:13:32 2017 -0400 |
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| @@ -3,31 +3,29 @@ <requirements> <requirement type="package" version="8.0.112">openjdk</requirement> </requirements> - <command> - <![CDATA[ - mkdir -p output && - ln -f -s "${input1.metadata.bam_index}" "${input1}.bai" && - java -jar $__tool_directory__/TagPileup.jar - -b "$input1" - -i "${input1}.bai" - -c "$input2" - -s $tag_shift - -n $bin_size - -e $tags_equal - -r $reads - -p $proper_pe - -a $combine_strands - -t "\${GALAXY_SLOTS:-4}" - -w $composite_smoothing_window - -m "true" - -x "$output1" - -h $output_heatmap - #if str($output_heatmap) == "true": - -o output - #end if - 1>/dev/null - ]]> - </command> + <command detect_errors="exit_code"><![CDATA[ +mkdir -p output && +ln -f -s '${input1.metadata.bam_index}' '${input1}.bai' && +java -jar '$__tool_directory__/TagPileup.jar' +-b '$input1' +-i '${input1}.bai' +-c '$input2' +-s $tag_shift +-n $bin_size +-e $tags_equal +-r $reads +-p $proper_pe +-a $combine_strands +-t "\${GALAXY_SLOTS:-4}" +-w $composite_smoothing_window +-m true +-x '$output1' +-h $output_heatmap +#if str($output_heatmap) == "true": + -o output +#end if +1>/dev/null + ]]></command> <inputs> <param name="input1" type="data" format="bam" label="BAM file" /> <param name="input2" type="data" format="bed" label="Bed file" /> |