comparison guppy_basecaller.xml @ 3:df3f2f852ed5 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit dce10266bcd6c49429740b724d833f109f4e5cad"

2:cfc7ff08ad20

<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.5" python_template_version="3.5">
    <description>A simple wrapper for guppy basecaller that depends on configuration files</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

                         --config *.cfg
                         --num_callers 4
                         --records_per_fastq 0
                         --cpu_threads_per_caller \${GALAXY_SLOTS:-2}
                         --disable_pings
                         --qscore_filtering
###                         --calib_detect
    ]]></command>
    <inputs>
        <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/>
        <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
    </inputs>
    <outputs>
        <data name="guppy_result" format="fastq">
            <discover_datasets directory="out/pass" ext="fastq" pattern=".+\.fastq" visible="true"/>
        </data>
    </outputs>
    <help><![CDATA[
        A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files,
        and a configuration in the form of a tar file.

3:df3f2f852ed5

<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.6" python_template_version="3.5">
    <description>A simple wrapper for guppy basecaller that depends on configuration files</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

                         --config *.cfg
                         --num_callers 4
                         --records_per_fastq 0
                         --cpu_threads_per_caller \${GALAXY_SLOTS:-2}
                         --disable_pings
###                         --qscore_filtering
###                         --calib_detect
        && cat *.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output.fastq
    ]]></command>
    <inputs>
        <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/>
        <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
    </inputs>
    <outputs>
        <data name="output.fastq" format="fastqsanger" />
    </outputs>
    <help><![CDATA[
        A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files,
        and a configuration in the form of a tar file.