Mercurial > repos > mvdbeek > bam_readtagger
diff bam_readtagger.xml @ 43:6f9b1b81b593 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 7ee4c1dd4e13a4d634b0e80efdd2309289a29a1c
author | mvdbeek |
---|---|
date | Fri, 26 Oct 2018 06:11:17 -0400 |
parents | 4fdf606153df |
children | 4870f1d6f037 |
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--- a/bam_readtagger.xml Thu May 24 11:51:27 2018 -0400 +++ b/bam_readtagger.xml Fri Oct 26 06:11:17 2018 -0400 @@ -1,31 +1,31 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.11"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.4.12"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.11">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ - readtagger -t '$tag_file' -s - #for $element in $alignment_series - '$element.annotate_with':$element.r_tag:$element.m_tag - #end for - #if $reference_fasta: - --reference_fasta '$reference_fasta' - #end if - $allow_dovetailing - $discard_suboptimal - $discarded - $verified - $discard_proper_pairs - --cores "\${GALAXY_SLOTS:-2}" - -o '$tagged_file' +readtagger -t '$tag_file' -s +#for $element in $alignment_series + '$element.annotate_with':$element.r_tag:$element.m_tag +#end for +#if $reference_fasta: + --reference_fasta '$reference_fasta' +#end if +$allow_dovetailing +$discard_suboptimal +$discarded +$verified +$discard_proper_pairs +--cores "\${GALAXY_SLOTS:-2}" +-o '$tagged_file' ]]></command> <inputs> - <param name="tag_file" argument="--tag_file" type="data" format="bam"/> + <param name="tag_file" argument="--tag_file" type="data" format="qname_sorted.bam,bam"/> <repeat name="alignment_series" title="Alignments"> - <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/> + <param name="annotate_with" argument="--annotate_with" type="data" format="qname_sorted.bam,bam"/> <param type="select" name="r_tag" label="First letter to use for read tag" value="A"> <expand macro="tag_options"/> </param>