comparison bcftools_sort.xml @ 0:1d4c51dcbbbe draft

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author greg
date Wed, 19 Dec 2018 08:58:27 -0500
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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 #set temp_dir = 'tmp'
12 mkdir $temp_dir &&
13 bcftools @EXECUTABLE@
14 $input_file
15 --output-file '$output_file'
16 @OUTPUT_TYPE@
17 --temp-dir '$temp_dir'
18 ]]>
19 </command>
20 <inputs>
21 <expand macro="macro_input"/>
22 <expand macro="macro_select_output_type"/>
23 </inputs>
24 <outputs>
25 <expand macro="macro_vcf_output"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="input_file" value="unsorted.vcf" ftype="vcf"/>
30 <param name="output_type" value="v"/>
31 <output name="output_file" file="sorted.vcf" ftype="vcf"/>
32 </test>
33 </tests>
34 <help><![CDATA[
35 =====================================
36 bcftools @EXECUTABLE@
37 =====================================
38
39 Sort VCF/BCF files.
40
41 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
42
43 @BCFTOOLS_WIKI@
44 ]]>
45 </help>
46 <expand macro="citations"/>
47 </tool>