comparison variant.xml @ 1:43388fc8ad0b draft

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

0:3cde72a6e37c

        <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
        'result.vcf' ## output

        |& tee log.txt
        ]]></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?"/>

            <option value="log">Log</option>
        </param>
    </inputs>
    <outputs>
        <!-- standard -->
        <data name="out_result" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result">
            <filter>'result' in out</filter>
        </data>
        <!-- optional -->
        <data name="out_log" format="tabular" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
            <filter>'log' in out</filter>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->

1:43388fc8ad0b

        <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?"/>

            <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 -->