Mercurial > repos > mvdbeek > bam_readtagger

comparison bam_readtagger.xml @ 29:4be52149b343 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba
author mvdbeek
date Tue, 09 May 2017 10:37:52 -0400
parents 41f2c4537540
children 9f0af01ad389
comparison
equal deleted inserted replaced
28:41f2c4537540 29:4be52149b343
1 <tool id="bam_readtagger" name="Tag alignment files" version="0.3.21"> 1 <tool id="bam_readtagger" name="Tag alignment files" version="0.3.22">
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="0.3.21">readtagger</requirement> 7 <requirement type="package" version="0.3.22">readtagger</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 readtagger -t '$tag_file' -a 10 readtagger -t '$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
13 #end for 13 #end for
14 $allow_dovetailing 14 $allow_dovetailing
15 $keep_suboptimal 15 $discard_suboptimal
16 $discarded 16 $discarded
17 $verified 17 $verified
18 $discard_proper_pairs 18 $discard_proper_pairs
19 --cores "\${GALAXY_SLOTS:-2}" 19 --cores "\${GALAXY_SLOTS:-2}"
20 -o '$tagged_file' 20 -o '$tagged_file'
28 </param> 28 </param>
29 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B"> 29 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B">
30 <expand macro="tag_options"/> 30 <expand macro="tag_options"/>
31 </param> 31 </param>
32 </repeat> 32 </repeat>
33 <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"/> 33 <param argument="--allow_dovetailing" type="boolean" truevalue="--allow_dovetailing" falsevalue="--no_allow_dovetailing" checked="True" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
34 <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"/> 34 <param argument="--discard_suboptimal_alternate_tags" name="discard_suboptimal" type="boolean" checked="True" truevalue="--discard_suboptimal_alternate_tags" falsevalue="--no_discard_suboptimal" label="Discard suboptimal alternative tags" help="Check this to discard alternative tags that cannot explain the current read cigar"/>
35 <param argument="-dp" name="discard_proper_pairs" type="boolean" truevalue="-dp" falsevalue="" label="Discard alternative tags for proper pairs" help="Check this to discard alternative tags for reads in proper pairs"/> 35 <param argument="--discard_if_proper_pair" name="discard_proper_pairs" type="boolean" truevalue="--discard_if_proper_pair" falsevalue="--no_discard_if_proper_pair" label="Discard alternative tags for proper pairs" checked="True" help="Check this to discard alternative tags for reads in proper pairs"/>
36 <param argument="-wd" name="discarded" type="boolean" truevalue="-wd discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/> 36 <param argument="--discarded_path" name="discarded" type="boolean" truevalue="--discarded_path discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/>
37 <param argument="-wv" name="verified" type="boolean" truevalue="-wv verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/> 37 <param argument="--verified_path" name="verified" type="boolean" truevalue="--verified_path verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/>
38 </inputs> 38 </inputs>
39 <outputs> 39 <outputs>
40 <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/> 40 <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
41 <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string"> 41 <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string">
42 <filter>verified is True</filter> 42 <filter>verified is True</filter>