annotate bcftools_sort.xml @ 1:bb0f975d69b4 draft default tip

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<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
    <description>sort VCF/BCF files</description>
    <macros>
        <token name="@EXECUTABLE@">sort</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
@PREPARE_ENV@
#set temp_dir = 'tmp'
mkdir $temp_dir &&
bcftools @EXECUTABLE@
$input_file
--output-file '$output_file'
@OUTPUT_TYPE@
--temp-dir '$temp_dir'
]]>
    </command>
    <inputs>
        <expand macro="macro_input"/>
        <expand macro="macro_select_output_type"/>
    </inputs>
    <outputs>
        <expand macro="macro_vcf_output"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="unsorted.vcf" ftype="vcf"/>
            <param name="output_type" value="v"/>
            <output name="output_file" file="sorted.vcf" ftype="vcf"/>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================

Sort VCF/BCF files.

@BCFTOOLS_MANPAGE@#@EXECUTABLE@

@BCFTOOLS_WIKI@
]]>
    </help>
    <expand macro="citations"/>
</tool>