Mercurial > repos > jdv > b2b_bam2consensus
comparison bam2consensus.xml @ 1:2367d00c5182 draft default tip
"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author | jdv |
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date | Tue, 28 Sep 2021 06:12:40 +0000 |
parents | d32139014ec3 |
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0:d32139014ec3 | 1:2367d00c5182 |
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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 |