Mercurial > repos > jdv > b2b_bam2consensus

comparison bam2consensus.xml @ 1:2367d00c5182 draft default tip

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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author jdv
date Tue, 28 Sep 2021 06:12:40 +0000
parents d32139014ec3
children
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0:d32139014ec3 1:2367d00c5182
10 --> 10 -->
11 <requirement type="package" version="7.407">mafft</requirement> 11 <requirement type="package" version="7.407">mafft</requirement>
12 <!-- ncurses needs to be explicitly pulled from conda-forge for samtools to work --> 12 <!-- ncurses needs to be explicitly pulled from conda-forge for samtools to work -->
13 <requirement type="package" version="6.1">ncurses</requirement> 13 <requirement type="package" version="6.1">ncurses</requirement>
14 <requirement type="package" version="1.9">samtools</requirement> 14 <requirement type="package" version="1.9">samtools</requirement>
15 <requirement type="package" version="0.006007">perl-biox-seq</requirement> 15 <requirement type="package" version="0.008002">perl-biox-seq</requirement>
16 <requirement type="package" version="1.23">perl-file-which</requirement>
17 </requirements> 16 </requirements>
18 17
19 <!-- ***************************************************************** --> 18 <!-- ***************************************************************** -->
20 19
21 <version_command>bam2consensus --version | perl -wnE'print "$1\n" for /bam2consensus v(.+)/g'</version_command> 20 <version_command>perl $__tool_directory__/bam2consensus --version | perl -wnE'print "$1\n" for /bam2consensus v(.+)/g'</version_command>
22 21
23 <!-- ***************************************************************** --> 22 <!-- ***************************************************************** -->
24 23
25 <command detect_errors="aggressive"> 24 <command detect_errors="aggressive">
26 <![CDATA[ 25 <![CDATA[
28 ln -s $ref_file ref.tmp; 27 ln -s $ref_file ref.tmp;
29 ln -s $in_bam in.bam; 28 ln -s $in_bam in.bam;
30 samtools faidx ref.tmp; 29 samtools faidx ref.tmp;
31 samtools index in.bam; 30 samtools index in.bam;
32 31
33 bam2consensus 32 perl $__tool_directory__/bam2consensus
34 --ref ref.tmp 33 --ref ref.tmp
35 --bam in.bam 34 --bam in.bam
36 --min_qual $min_qual 35 --min_qual $min_qual
37 --min_depth $min_depth 36 --min_depth $min_depth
38 --trim $trim 37 --trim $trim