view variant.xml @ 3:e86fcef8ed91 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"

<?xml version="1.0"?>
<tool id="medaka_variant" name="medaka: Variant" version="@TOOL_VERSION@+galaxy1" 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

2>&1 | tee '$out_log'

#if $out_annotated
    && python '$__tool_directory__/annotateVCF.py' '$out_result' '$in_mpileup' '$out_annotated'
#end if
    ]]></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 ','.">
            <sanitizer invalid_char="">
                <valid initial="string.ascii_letters,string.digits">
                    <add value="_"/>
                    <add value=","/>
                    <add value="."/>
                </valid>
            </sanitizer>
        </param>
        <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>

        <conditional name="output_annotated">
            <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires pileup file)">
                <option value="true" selected="true">Output annotated VCF</option>
                <option value="false">Don't output annotated VCF</option>
            </param>
            <when value="true">
                <param name="in_mpileup" type = "data" format="pileup" optional="false" label="Mpileup to annotate the VCF"/>
            </when>
        </conditional>
        <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
    </inputs>
    <outputs>
        <!-- standard -->
        <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result"/>
        <!-- optional -->
        <data name="out_annotated" format="vcf" label="${tool.name} on ${on_string}: Annotated">
            <filter>output_annotated_select</filter>
        </data>
        <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
            <filter>output_log_bool</filter>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->
        <test expect_num_outputs="3">
            <param name="inputs" value="medaka_test.hdf"/>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="ref.fasta"/>
            </conditional>
            <conditional name="output_annotated">
                <param name="output_annotated_select" value="true"/>
                <param name="in_mpileup" value="annotate_vcf_test.pileup"/>
            </conditional>
            <param name="output_log_bool" value="true"/>
            
            <output name="out_result">
                <assert_contents>
                    <has_n_lines n="9"/>
                    <has_line line="##fileformat=VCFv4.1" />
                    <has_line line="##medaka_version=1.0.3" />
                </assert_contents>
            </output>
            <output name="out_annotated">
                <assert_contents>
                    <has_n_lines n="16"/>
                    <has_line line="##fileformat=VCFv4.1" />
                    <has_line line="##medaka_version=1.0.3" />
                    <has_line line="##annotateVCFVersion=0.1" />
                </assert_contents>
            </output>
            <output name="out_log">
                <assert_contents>
                    <has_n_lines n="8" />
                </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>