annotate variant.xml @ 1:43388fc8ad0b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"

<?xml version="1.0"?>
<tool id="medaka_variant" name="medaka: Variant" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Probability decoding</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
## initialize
@REF_FASTA@

## run
medaka variant
## optional
--debug
#if $region
    --region '${region}'
#end if
$verbose
## required
reference.fa
#for $current in $inputs
    '$current'
#end for
'$out_result' ## output

|& tee '$out_log'
    ]]></command>
    <inputs>
        <param argument="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
        <expand macro="reference"/>
        <param argument="--region" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','."/>
        <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
        <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
            <option value="result" selected="true">Result</option>
            <option value="log">Log</option>
        </param>
    </inputs>
    <outputs>
        <!-- standard -->
        <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result">
            <filter>'result' in out</filter>
        </data>
        <!-- optional -->
        <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
            <filter>'log' in out</filter>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->
        <test expect_num_outputs="1">
            <conditional name="reference_source">
                <param name="reference_source_selector" value="cached"/>
                <param name="ref_file" value="bwa-mem-mt-genome"/>
            </conditional>
            <param name="inputs" value="consensus.hdf"/>
            <output name="out_result">
                <assert_contents>
                    <has_n_lines n="6"/>
                    <has_line line="##fileformat=VCFv4.1"/>
                </assert_contents>
            </output>
        </test>
        <!-- #2 -->
        <test expect_num_outputs="2">
            <conditional name="reference_source">
                <param name="reference_source_selector" value="cached"/>
                <param name="ref_file" value="bwa-mem-mt-genome"/>
            </conditional>
            <param name="inputs" value="consensus.hdf"/>
            <param name="verbose" value="true"/>
            <param name="out" value="result,log"/>
            <output name="out_result">
                <assert_contents>
                    <has_n_lines n="13"/>
                    <has_line line="##fileformat=VCFv4.1"/>
                </assert_contents>
            </output>
            <output name="out_log">
                <assert_contents>
                    <has_n_lines n="17"/>
                    <has_text_matching expression=".+Loaded.+"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

@WID@

The module *variant* decodes probabilities.

**Input**

- reference sequence (FASTA)
- (several) consensus files (H5/HDF)

**Output**

- decoded probabilities (VCF)

**References**

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