Mercurial > repos > iuc > bioext_bam2msa
view bam2msa.xml @ 3:b226e0c805a5 draft
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
author | iuc |
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date | Fri, 20 Aug 2021 21:03:56 +0000 |
parents | 0a4ad829d87a |
children | a68cb16fa1a0 |
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<?xml version="1.0"?> <tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>to FASTA multiple sequence alignment</description> <macros> <import>macros.xml</import> <token name="@VERSION_SUFFIX@">0</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ bam2msa #if $region_start and $region_end: -r $region_start:$region_end #end if '$input' '$output' ]]></command> <inputs> <param name="input" type="data" format="bam,sam" label="Input BAM file"/> <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> </inputs> <outputs> <data name="output" format="fasta"/> </outputs> <tests> <test> <param name="input" ftype="bam" value="bam2msa-in1.bam"/> <output name="output" file="bam2msa-out1.fa"/> </test> <test> <param name="input" ftype="bam" value="bam2msa-in2.bam"/> <output name="output" file="bam2msa-out2.fa"/> </test> </tests> <help>Extract MSA from a BAM file</help> <expand macro="citations"/> </tool>