comparison medaka_variant.xml @ 1:92cdc29a8620 draft

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

0:711d4deb7bdf

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
        ## initialize
        @REF_FASTA@  
        ## link doesn't work
        cp '${i}' 'alignment.bam' &&
        cp '${i.metadata.bam_index}' 'alignment.bam.bai' &&

        ## run
        medaka_variant
        ## optional
        #if str($r) != ''
            -r '$r'
        #end if
        -o 'results'
        -s '$s'
        -m '$m'
        -t \${GALAXY_SLOTS:-4}
        -b $b
        -N $N
        -P $P
        $U
        $S
        ## required
        -i 'alignment.bam'
        -f 'reference.fa'

        |& tee 'log.txt'
    ]]></command>
    <inputs>
        <param argument="-i" type="data" format="bam" label="Select input reads" help="Read groups are currently ignored, so the bam should only contain reads from a single sample."/>
        <expand macro="reference"/>
        <param argument="-r" type="text" value="" optional="true" label="Set region string(s)" help="If not provided, will process all contigs."/>

            <filter>'round_1_hap_2_probs_hdf' in out</filter>
        </data>
        <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
            <filter>'round_1_unfiltered_vcf' in out</filter>
        </data>
        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
            <filter>'log' in out</filter>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->

1:92cdc29a8620

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
## initialize
@REF_FASTA@
## link doesn't work
cp '${i}' alignment.bam &&
cp '${i.metadata.bam_index}' alignment.bam.bai &&

## run
medaka_variant
## optional
#if $r:
    -r '$r'
#end if
-o results
-s $s
-m $m
-t \${GALAXY_SLOTS:-4}
-b $b
-N $N
-P $P
$U
$S
## required
-i alignment.bam
-f reference.fa

|& tee '$out_log'
    ]]></command>
    <inputs>
        <param argument="-i" type="data" format="bam" label="Select input reads" help="Read groups are currently ignored, so the bam should only contain reads from a single sample."/>
        <expand macro="reference"/>
        <param argument="-r" type="text" value="" optional="true" label="Set region string(s)" help="If not provided, will process all contigs."/>

            <filter>'round_1_hap_2_probs_hdf' in out</filter>
        </data>
        <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
            <filter>'round_1_unfiltered_vcf' in out</filter>
        </data>
        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
            <filter>'log' in out</filter>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->