Mercurial > repos > mvdbeek > bam_readtagger
diff bam_readtagger.xml @ 28:be95c9c82937 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
author | mvdbeek |
---|---|
date | Tue, 09 May 2017 10:38:06 -0400 |
parents | 9f7737be4732 |
children | 2c62ca47c455 |
line wrap: on
line diff
--- a/bam_readtagger.xml Fri Apr 28 02:16:42 2017 -0400 +++ b/bam_readtagger.xml Tue May 09 10:38:06 2017 -0400 @@ -1,18 +1,18 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.21"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.22"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.21">readtagger</requirement> + <requirement type="package" version="0.3.22">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ - readtagger -t '$tag_file' -a + readtagger -t '$tag_file' -s #for $element in $alignment_series '$element.annotate_with':$element.r_tag:$element.m_tag #end for $allow_dovetailing - $keep_suboptimal + $discard_suboptimal $discarded $verified $discard_proper_pairs @@ -30,11 +30,11 @@ <expand macro="tag_options"/> </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"/> - <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"/> - <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"/> - <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"/> + <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"/> + <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"/> + <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"/> + <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"/> + <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"/> </inputs> <outputs> <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>