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comparison bcftools_sort.xml @ 0:770db64c4cfc draft

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author greg
date Thu, 01 Nov 2018 10:23:32 -0400
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1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
3 <description>sort VCF/BCF files</description>
4 <macros>
5 <token name="@EXECUTABLE@">sort</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[
10 @PREPARE_ENV@
11 @PREPARE_INPUT_FILE@
12 #set temp_dir = 'tmp'
13 mkdir $temp_dir &&
14 bcftools @EXECUTABLE@
15 @INPUT_FILE@
16 --output-file '$output_file'
17 @OUTPUT_TYPE@
18 --temp-dir '$temp_dir'
19 ]]>
20 </command>
21 <inputs>
22 <expand macro="macro_input"/>
23 <expand macro="macro_select_output_type"/>
24 </inputs>
25 <outputs>
26 <expand macro="macro_vcf_output"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="input_file" value="unsorted.vcf" ftype="vcf"/>
31 <param name="output_type" value="v"/>
32 <output name="output_file" file="sorted.vcf" ftype="vcf"/>
33 </test>
34 </tests>
35 <help><![CDATA[
36 =====================================
37 bcftools @EXECUTABLE@
38 =====================================
39
40 Sort VCF/BCF files.
41
42 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
43
44 @BCFTOOLS_WIKI@
45 ]]>
46 </help>
47 <expand macro="citations"/>
48 </tool>