Mercurial > repos > iuc > bioext_bam2msa

comparison bam2msa.xml @ 4:a68cb16fa1a0 draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit 0c2133318563cdb508cb5561e95c9066bc17345f"
author iuc
date Sat, 25 Sep 2021 18:52:53 +0000
parents b226e0c805a5
children 27673f5b5343
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3:b226e0c805a5 4:a68cb16fa1a0
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <token name="@VERSION_SUFFIX@">0</token> 6 <token name="@VERSION_SUFFIX@">0</token>
7 </macros> 7 </macros>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 ## avoid bam2msa to create .bai in inputdir
11 ln -s '$input' input_bam &&
12 ln -s '$input.metadata.bam_index' input_bam.bai &&
10 bam2msa 13 bam2msa
11 #if $region_start and $region_end: 14 #if $region_start and $region_end:
12 -r $region_start:$region_end 15 -r $region_start:$region_end
13 #end if 16 #end if
14 '$input' '$output' 17 'input_bam' '$output'
15 ]]></command> 18 ]]></command>
16 <inputs> 19 <inputs>
17 <param name="input" type="data" format="bam,sam" label="Input BAM file"/> 20 <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
18 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> 21 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/>
19 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> 22 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>