comparison filter_insertions.xml @ 52:b03c6d8c37c1 draft

planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 45d0337e2a0d35e9a83d9c87c005c876c45ee054

51:08656cd6c989

<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.19">
    <description>based on softclips in control files</description>
    <requirements>
        <requirement type="package" version="0.4.19">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 &&

        #end for
        --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 one or more control samples" argument="--all_controls_path" multiple="True" 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>

52:b03c6d8c37c1

<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.0">
    <description>based on softclips in control files</description>
    <requirements>
        <requirement type="package" version="0.5.0">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 &&

        #end for
        --output_path '$output'
        $output_discard
    ]]></command>
    <inputs>
        <param name="putative_insertions" label="Select dataset with filtered putative insertions" argument="--putative_insertions_path" type="data" format="gff3"/>
        <param name="all_insertions" label="Select datasets with all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
        <param name="all_controls" label="Select datasets with all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" 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>