comparison consensus.xml @ 2:12c40c8c86db draft

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

1:0632744d5a5f

<tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Assembly polishing via neural networks</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
        ## initialize
        ln -s '${bam}' 'alignment.bam' &&
        ln -s '${bam.metadata.bam_index}' 'alignment.bam.bai' &&

        ## run
        medaka consensus
        ## optional
        --debug ## increase log level
        --threads \${GALAXY_SLOTS:-4}
        --batch_size $batch_size
        #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
            --regions 
            #if $regions_cond.regions_sel == 'custom'
                '$regions_cond.custom'
            #else if $regions_cond.regions_sel == 'bed'
                '$regions_cond.bed'
            #end if
        #end if
        --chunk_len $chunk_len
        --chunk_ovlp $chunk_ovlp
        --model '$model'
        $disable_cudnn
        $check_output
        $save_features
        #if $RG
            --RG '$RG'
        #end if
        #if $tag_name
            --tag_name '$tag_name'
        #end if
        #if $tag_value
            --tag_value $tag_value
        #end if
        $tag_keep_missing
        ## required
        'alignment.bam' ## bam
        'result.hdf' ## output

        |& tee 'log.txt'
    ]]></command>
    <inputs>
        <param argument="bam" type="data" format="bam" label="Select input alignment"/>
        <expand macro="model" argument="--model"/>
        <expand macro="b" argument="--batch_size"/>

            <param name="regions_sel" type="select" label="Specify regions to analyse via">
                <option value="none">None</option>
                <option value="custom">Custom input</option>
                <option value="bed">BED file</option>
            </param>
            <when value="custom">
                <param argument="custom" type="text" value="" optional="true" label="Set genomic regions to analyse"/>
            </when>
            <when value="bed">
                <param argument="bed" type="data" format="bed" optional="true" label="Select file with genomic regions to analyse"/>
            </when>
            <when value="none"/>
        </conditional>
        <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/>
        <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/>
        <param argument="--disable_cudnn" type="boolean" truevalue="--disable_cudnn" falsevalue="" label="Disable use of cuDNN model layers?"/>
        <param argument="--check_output" type="boolean" truevalue="--check_output" falsevalue="" label="Verify integrity of output file after inference?"/>

            <option value="log">Log</option>
        </param>
    </inputs>
    <outputs>
        <!-- standard -->
        <data name="out_result" format="h5" from_work_dir="result.hdf" label="${tool.name} on ${on_string}: Result">
            <filter>'result' in out</filter>
        </data>
        <!-- optional -->
        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
            <filter>'log' in out</filter>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->

2:12c40c8c86db

<tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Assembly polishing via neural networks</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
## initialize
ln -s '${bam}' alignment.bam &&
ln -s '${bam.metadata.bam_index}' alignment.bam.bai &&

## run
medaka consensus
## optional
--debug ## increase log level
--threads \${GALAXY_SLOTS:-4}
--batch_size $batch_size
#if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
    --regions
    #if $regions_cond.regions_sel == 'custom'
        '$regions_cond.custom'
    #else if $regions_cond.regions_sel == 'bed'
        '$regions_cond.bed'
    #end if
#end if
--chunk_len $chunk_len
--chunk_ovlp $chunk_ovlp
--model $model
$disable_cudnn
$check_output
$save_features
#if $RG
    --RG '$RG'
#end if
#if $tag_name
    --tag_name '$tag_name'
#end if
#if str($tag_value):
    --tag_value $tag_value
#end if
$tag_keep_missing
## required
alignment.bam ## bam
'$out_result' ## output

|& tee '$out_log'
    ]]></command>
    <inputs>
        <param argument="bam" type="data" format="bam" label="Select input alignment"/>
        <expand macro="model" argument="--model"/>
        <expand macro="b" argument="--batch_size"/>

            <param name="regions_sel" type="select" label="Specify regions to analyse via">
                <option value="none">None</option>
                <option value="custom">Custom input</option>
                <option value="bed">BED file</option>
            </param>
            <when value="none"/>
            <when value="custom">
                <param argument="custom" type="text" value="" label="Set genomic regions to analyse"/>
            </when>
            <when value="bed">
                <param argument="bed" type="data" format="bed" label="Select file with genomic regions to analyse"/>
            </when>
        </conditional>
        <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/>
        <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/>
        <param argument="--disable_cudnn" type="boolean" truevalue="--disable_cudnn" falsevalue="" label="Disable use of cuDNN model layers?"/>
        <param argument="--check_output" type="boolean" truevalue="--check_output" falsevalue="" label="Verify integrity of output file after inference?"/>

            <option value="log">Log</option>
        </param>
    </inputs>
    <outputs>
        <!-- standard -->
        <data name="out_result" format="h5" label="${tool.name} on ${on_string}: Result">
            <filter>'result' in out</filter>
        </data>
        <!-- optional -->
        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
            <filter>'log' in out</filter>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->