annotate bcftools_query_list_samples.xml @ 9:de1a3d4cd5a1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools List Samples" id="bcftools_@EXECUTABLE@_list_samples" version="@TOOL_VERSION@">
    <description>in VCF/BCF file</description>
    <macros>
        <token name="@EXECUTABLE@">query</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
bcftools @EXECUTABLE@ --list-samples
## Primary Input/Outputs
@INPUT_FILE@
| tee $output_file | tr '\n' ','
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
    </inputs>
    <outputs>
        <data name="output_file" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="query.vcf" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="C" />
                    <not_has_text text="A" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools List Samples @EXECUTABLE@
=====================================

Lists Samples from a VCF/BCF file

@BCFTOOLS_MANPAGE@#@EXECUTABLE@

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