comparison filter_insertions.xml @ 39:432bb619c079 draft

planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty

38:f6311a04a6c9

    <requirements>
        <requirement type="package" version="0.4.9">readtagger</requirement>
    </requirements>
    <version_command>confirm_insertions --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        confirm_insertions
        --putative_insertions_path '$putative_insertions'
        --all_treatments_path '$all_insertions'
        --all_controls_path '$all_controls'
        --output_path '$output'
        $output_discard
    ]]></command>
    <inputs>
        <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/>
        <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
        <param name="all_controls" label="Path to all unfiltered insertions from control sample" argument="--all_controls_path" type="data" format="gff3"/>
        <param name="output_discard" label="Output discarded records? Thye will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/>
    </inputs>
    <outputs>
        <data name="output" format="gff3"/>
    </outputs>
    <tests>

39:432bb619c079

    <requirements>
        <requirement type="package" version="0.4.9">readtagger</requirement>
    </requirements>
    <version_command>confirm_insertions --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        ln -fs $putative_insertions putative_insertions.gff &&
        ln -fs $all_insertions all_insertions.gff &&
        ln -fs $all_controls all_controls_path.gff &&
        confirm_insertions
        --putative_insertions_path putative_insertions.gff
        --all_treatments_path all_insertions.gff
        --all_controls_path all_controls_path.gff
        --output_path '$output'
        $output_discard
    ]]></command>
    <inputs>
        <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/>
        <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
        <param name="all_controls" label="Path to all unfiltered insertions from control sample" argument="--all_controls_path" type="data" format="gff3"/>
        <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/>
    </inputs>
    <outputs>
        <data name="output" format="gff3"/>
    </outputs>
    <tests>