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comparison bam2msa.xml @ 8:a6baa8728699 draft

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit a7729ad7789e8b120055a9a9b53494acb826b371
author iuc
date Mon, 02 Sep 2024 10:14:35 +0000
parents dc7d214d9673
children
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7:f06f478e6b9d 8:a6baa8728699
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 2 <tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>to FASTA multiple sequence alignment</description> 3 <description>to FASTA multiple sequence alignment</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <token name="@VERSION_SUFFIX@">0</token>
7 </macros> 6 </macros>
8 <expand macro="requirements"/> 7 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
10 ## avoid bam2msa to create .bai in inputdir 9 ## avoid bam2msa to create .bai in inputdir
11 ln -s '$input' input_bam && 10 ln -sf '$input' input_bam &&
12 ln -s '$input.metadata.bam_index' input_bam.bai && 11 ln -sf '$input.metadata.bam_index' input_bam.bai &&
13 bam2msa 12 bam2msa
14 #if $region_start and $region_end: 13 #if $region_start and $region_end:
15 -r $region_start:$region_end 14 -r $region_start:$region_end
16 #end if 15 #end if
17 'input_bam' '$output' 16 'input_bam'
17 '$output'
18 ]]></command> 18 ]]></command>
19 <inputs> 19 <inputs>
20 <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"/>
21 <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"/>
22 <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"/>