Mercurial > repos > iuc > bioext_bam2msa
comparison bam2msa.xml @ 0:12729213b4ae draft
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
author | iuc |
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date | Wed, 16 May 2018 17:34:58 -0400 |
parents | |
children | 0a4ad829d87a |
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-1:000000000000 | 0:12729213b4ae |
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1 <?xml version="1.0"?> | |
2 <tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0"> | |
3 <description>to FASTA multiple sequence alignment</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 bam2msa | |
10 #if $region_start and $region_end: | |
11 -r $region_start:$region_end | |
12 #end if | |
13 '$input' '$output' | |
14 ]]></command> | |
15 <inputs> | |
16 <param name="input" type="data" format="bam,sam" label="Input BAM file"/> | |
17 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> | |
18 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> | |
19 </inputs> | |
20 <outputs> | |
21 <data name="output" format="fasta"/> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="input" ftype="bam" value="bealign-out1.bam"/> | |
26 <output name="output" file="bam2msa-out1.fa"/> | |
27 </test> | |
28 <test> | |
29 <param name="input" ftype="bam" value="bealign-out2.bam"/> | |
30 <output name="output" file="bam2msa-out2.fa"/> | |
31 </test> | |
32 </tests> | |
33 <help>Extract MSA from a BAM file</help> | |
34 <expand macro="citations"/> | |
35 </tool> |