Mercurial > repos > greg > call_amr_mutations
comparison call_amr_mutations.xml @ 4:2774bdf30122 draft
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author | greg |
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date | Tue, 21 Mar 2023 19:32:25 +0000 |
parents | 30b17a17c1aa |
children |
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3:30b17a17c1aa | 4:2774bdf30122 |
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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"/> |