Mercurial > repos > greg > call_amr_mutations

comparison call_amr_mutations.xml @ 4:2774bdf30122 draft

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author greg
date Tue, 21 Mar 2023 19:32:25 +0000
parents 30b17a17c1aa
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3:30b17a17c1aa 4:2774bdf30122
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ## NOTE: This tool provides the functionality of the PIMA filter_varsacn() 8 python '$__tool_directory__/call_amr_mutations.py'
9 ## function here https://github.com/appliedbinf/pima_md/blob/main/pima.py#L3012
10
11 python '$__tool_directory__/filter_varscan.py'
12 --varscan_raw '$varscan_raw' 9 --varscan_raw '$varscan_raw'
13 --output '$output' 10 --output '$output'
14 ]]></command> 11 ]]></command>
15 <inputs> 12 <inputs>
16 <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/> 13 <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/>