Mercurial > repos > mvdbeek > bam_readtagger
comparison bam_readtagger.xml @ 47:a4e30210fc3d draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit ff53a7c7582a4dfda1bfcc0c8832b4edc223bc5e
| author | mvdbeek |
|---|---|
| date | Mon, 28 Jan 2019 03:26:58 -0500 |
| parents | 4ebfef7b3488 |
| children | 72c9afb724a6 |
comparison
equal
deleted
inserted
replaced
| 46:4ebfef7b3488 | 47:a4e30210fc3d |
|---|---|
| 1 <tool id="bam_readtagger" name="Tag alignment files" version="0.4.15"> | 1 <tool id="bam_readtagger" name="Tag alignment files" version="0.4.16"> |
| 2 <description>from multiple bam files</description> | 2 <description>from multiple bam files</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 7 <requirement type="package" version="0.4.15">readtagger</requirement> | 7 <requirement type="package" version="0.4.16">readtagger</requirement> |
| 8 </requirements> | 8 </requirements> |
| 9 <command detect_errors="aggressive"><![CDATA[ | 9 <command detect_errors="aggressive"><![CDATA[ |
| 10 readtagger -t '$tag_file' -s | 10 readtagger -t '$tag_file' -s |
| 11 #for $element in $alignment_series | 11 #for $element in $alignment_series |
| 12 '$element.annotate_with':$element.r_tag:$element.m_tag | 12 '$element.annotate_with':$element.r_tag:$element.m_tag |
| 21 $discard_proper_pairs | 21 $discard_proper_pairs |
| 22 --cores "\${GALAXY_SLOTS:-2}" | 22 --cores "\${GALAXY_SLOTS:-2}" |
| 23 -o '$tagged_file' | 23 -o '$tagged_file' |
| 24 ]]></command> | 24 ]]></command> |
| 25 <inputs> | 25 <inputs> |
| 26 <param name="tag_file" argument="--tag_file" type="data" format="bam"/> | 26 <param name="tag_file" argument="--tag_file" type="data" format="bam,qname_input_sorted.bam"/> |
| 27 <repeat name="alignment_series" title="Alignments"> | 27 <repeat name="alignment_series" title="Alignments"> |
| 28 <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/> | 28 <param name="annotate_with" argument="--annotate_with" type="data" format="bam,qname_input_sorted.bam"/> |
| 29 <param type="select" name="r_tag" label="First letter to use for read tag" value="A"> | 29 <param type="select" name="r_tag" label="First letter to use for read tag" value="A"> |
| 30 <expand macro="tag_options"/> | 30 <expand macro="tag_options"/> |
| 31 </param> | 31 </param> |
| 32 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B"> | 32 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B"> |
| 33 <expand macro="tag_options"/> | 33 <expand macro="tag_options"/> |