comparison medaka_variant.xml @ 3:148f32860445 draft

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

2:ce2bf68a260d

<tool id="medaka_variant_pipeline" name="medaka: Variant pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>via neural networks</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

$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."/>

3:148f32860445

<tool id="medaka_variant_pipeline" name="medaka: Variant pipeline" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>via neural networks</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

$S
## required
-i alignment.bam
-f reference.fa

2>&1 | 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."/>