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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
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3 <description>sort VCF/BCF files</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">sort</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @PREPARE_ENV@
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11 @PREPARE_INPUT_FILE@
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12 #set temp_dir = 'tmp'
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13 mkdir $temp_dir &&
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14 bcftools @EXECUTABLE@
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15 @INPUT_FILE@
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16 --output-file '$output_file'
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17 @OUTPUT_TYPE@
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18 --temp-dir '$temp_dir'
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19 ]]>
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20 </command>
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21 <inputs>
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22 <expand macro="macro_input"/>
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23 <expand macro="macro_select_output_type"/>
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24 </inputs>
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25 <outputs>
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26 <expand macro="macro_vcf_output"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input_file" value="unsorted.vcf" ftype="vcf"/>
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31 <param name="output_type" value="v"/>
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32 <output name="output_file" file="sorted.vcf" ftype="vcf"/>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 =====================================
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37 bcftools @EXECUTABLE@
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38 =====================================
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39
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40 Sort VCF/BCF files.
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41
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42 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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43
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44 @BCFTOOLS_WIKI@
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45 ]]>
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46 </help>
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47 <expand macro="citations"/>
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48 </tool>
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