Mercurial > repos > mvdbeek > bam_tag_reads
changeset 2:d05f883765ba draft
planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit deb166021688193b84e799315b08d31518009583
| author | mvdbeek |
|---|---|
| date | Fri, 10 Feb 2017 13:00:43 -0500 |
| parents | 8138277ea0e5 |
| children | 10346efa8867 |
| files | bam_tag_reads.xml test-data/test.bam test-data/test.out test-data/test2.bam |
| diffstat | 4 files changed, 4 insertions(+), 2 deletions(-) [+] |
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--- a/bam_tag_reads.xml Wed Feb 08 03:36:05 2017 -0500 +++ b/bam_tag_reads.xml Fri Feb 10 13:00:43 2017 -0500 @@ -1,10 +1,10 @@ -<tool id="bam_tag_reads" name="Tag alignment files" version="0.1.3"> +<tool id="bam_tag_reads" name="Tag alignment files" version="0.1.4"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.1.3">tag_reads</requirement> + <requirement type="package" version="0.1.4">tag_reads</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ tag_reads -t '$tag_file' -a @@ -12,6 +12,7 @@ '$element.annotate_with':$element.r_tag:$element.m_tag #end for $allow_dovetailing + $keep_suboptimal -o '$tagged_file' ]]></command> <inputs> @@ -26,6 +27,7 @@ </param> </repeat> <param argument="--allow_dovetailing" type="boolean" truevalue="-d" falsevalue="" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/> + <param argument="-k" name="keep_suboptimal" type="boolean" truevalue="-k" falsevalue="" label="Keep suboptimal alternative tags" help="Check this to also keep alternative tags that cannot explain the current read cigar"/> </inputs> <outputs> <data name="tagged_file" format="bam"/>