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1 <tool id="call_amr_mutations" name="PIMA: call AMR mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 ## NOTE: This tool provides the functionality of the PIMA filter_varsacn()
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9 ## function here https://github.com/appliedbinf/pima_md/blob/main/pima.py#L3012
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10
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11 python '$__tool_directory__/filter_varscan.py'
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12 --varscan_raw '$varscan_raw'
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13 --output '$output'
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14 ]]></command>
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15 <inputs>
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16 <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/>
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="vcf"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="varscan_raw" value="input.vcf" ftype="vcf"/>
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24 <output name="output" value="output.vcf" ftype="vcf"/>
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25 </test>
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26 </tests>
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27 <help>
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28 **What it does**
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29
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30 Accepts VarScan mpileup2snps VCF file, filters it, and produces a filtered VCF file.
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31 </help>
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32 <expand macro="citations"/>
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33 </tool>
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