comparison filter_insertions.xml @ 64:190d64e5e32b draft

"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit be63fdf98ea1aaa5009136c6b0f8c1311e53bb8e"

63:e675e6d349bd

<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.10">
    <description>based on softclips in control files</description>
    <requirements>
        <requirement type="package" version="0.5.10">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 &&

        #for i, p in enumerate($all_controls)
            --all_controls_paths all_controls_${i}.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>
    <tests>

64:190d64e5e32b

<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.11">
    <description>based on softclips in control files</description>
    <requirements>
        <requirement type="package" version="0.5.11">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 &&

        #for i, p in enumerate($all_controls)
            --all_controls_paths all_controls_${i}.gff
        #end for
        --output_path '$output'
        $output_discard
        --min_length $min_length
    ]]></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"/>
        <param argument="--min_length" label="Minimum length necessary to match clip patterns" help="If too low will create false matches, if too high will not find legitimate matches." value="4" min="1" type="integer"/>
    </inputs>
    <outputs>
        <data name="output" format="gff3"/>
    </outputs>
    <tests>