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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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4
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8 python '$__tool_directory__/call_amr_mutations.py'
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9 --varscan_raw '$varscan_raw'
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10 --output '$output'
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11 ]]></command>
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12 <inputs>
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13 <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/>
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14 </inputs>
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15 <outputs>
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3
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16 <data name="output" format="vcf"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="varscan_raw" value="input.vcf" ftype="vcf"/>
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21 <output name="output" value="output.vcf" ftype="vcf"/>
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22 </test>
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23 </tests>
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24 <help>
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25 **What it does**
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26
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27 Accepts VarScan mpileup2snps VCF file, filters it, and produces a filtered VCF file.
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28 </help>
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29 <expand macro="citations"/>
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30 </tool>
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