Mercurial > repos > mvdbeek > bam_readtagger
comparison bam_readtagger.xml @ 29:2c62ca47c455 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty
author | mvdbeek |
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date | Tue, 09 May 2017 12:54:10 -0400 |
parents | be95c9c82937 |
children | db5c766503dd |
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28:be95c9c82937 | 29:2c62ca47c455 |
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1 <tool id="bam_readtagger" name="Tag alignment files" version="0.3.22"> | 1 <tool id="bam_readtagger" name="Tag alignment files" version="0.3.23"> |
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="0.3.22">readtagger</requirement> | 7 <requirement type="package" version="0.3.23">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 |
13 #end for | 13 #end for |
14 #if $reference_fasta: | |
15 --reference_fasta '$reference_fasta' | |
16 #end if | |
14 $allow_dovetailing | 17 $allow_dovetailing |
15 $discard_suboptimal | 18 $discard_suboptimal |
16 $discarded | 19 $discarded |
17 $verified | 20 $verified |
18 $discard_proper_pairs | 21 $discard_proper_pairs |
28 </param> | 31 </param> |
29 <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"> |
30 <expand macro="tag_options"/> | 33 <expand macro="tag_options"/> |
31 </param> | 34 </param> |
32 </repeat> | 35 </repeat> |
36 <param argument="--reference_fasta" type="data" format="fasta" label="Reference fasta for realigning clipped reads" optional="True" help="This file is optional. If you provide it, clipped sequences are extracted and aligned against this fasta file."/> | |
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"/> | 37 <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="--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"/> | 38 <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="--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"/> | 39 <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="--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"/> | 40 <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="--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"/> | 41 <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"/> |