comparison bam2msa.xml @ 0:12729213b4ae draft

planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
author iuc
date Wed, 16 May 2018 17:34:58 -0400
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children 0a4ad829d87a
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-1:000000000000 0:12729213b4ae
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>