view quickmege.xml @ 0:1582fc3aa9d1 draft default tip

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"

<tool id="quickmerge" name="quickmerge" version="@VERSION@">
    <description> improves contiguity of genome assemblies based on long molecule sequences</description>
    <macros>
        <token name="@VERSION@">0.3</token>
    </macros>
    <requirement type="package" version="@VERSION@">quickmerge</requirement>
    <version_command><![CDATA[ echo @VERSION@]]></version_command>

    <command detect_errors="exit_code"><![CDATA[
        merge_wrapper.py
        -hco $hco
        -c $c_params
        -l $length_cutoff
        $no_nucmer
        $no_delta
        $stop_after_nucmer
        $stop_after_df
        -ml $merging_length_cutoff
        -t \${GALAXY_SLOTS:-1}
        $version4
        $clean_only
        $hybrid_assembly
        $self_assembly
    ]]>    </command>

    <inputs>
        <param name="hybrid_assembly" type="data" format="fasta.fasta.gz" label="Hybrid assembly"/>
        <param name="self_assembly" type="data" format="fasta.fasta.gz" label="Self assembly"/>
        <param name="hco" type="float" min="0" value="0.5" label="Quickmerge hco parameter" />
        <param name="c_params" type="float" min="0" value="1.5" label="Quickmerge c parameter" />
        <param name="length_cutoff" type="integer" min="0" value="0" label="Minimum seed contig length to be merged" />
        <param name="no_nucmer" type="boolean" truevalue="--no_nucmer" falsevalue="" checked="false" label="Skip the nucmer step" />
        <param name="no_delta" type="boolean" truevalue="--no_delta" falsevalue="" checked="false" label="Skip the nucmer and delta-filter steps" />
        <param name="stop_after_nucmer" type="boolean" truevalue="--stop_after_nucmer" falsevalue="" checked="false" label="Do not perform the delta-filter and merger steps" />
        <param name="stop_after_df" type="boolean" truevalue="--stop_after_df" falsevalue="" checked="false" label="Do not perform the merger step" />
        <param name="merging_length_cutoff" type="integer" min="0" value="5000" label="set the merging length cutoff necessary for use in quickmerge" />
        <param name="version4" type="boolean" truevalue="--version4" falsevalue="" checked="false" label="Do not perform the merger step" />
        <param name="clean_only" type="boolean" truevalue="--clean_only" falsevalue="" checked="false" label="Generate safe FASTA files for merging, but do not merge" />
    </inputs>

    <outputs>
        <data name="merged_qm" format="fasta" label="${tool.name} on ${on_string}: merged" from_work_dir="merged_qm.fasta"/>
        <data name="hybrid_oneline" format="fasta" label="${tool.name} on ${on_string}: hybrid_oneline" from_work_dir="hybrid_oneline.fa"/>
        <data name="self_oneline" format="fasta" label="${tool.name} on ${on_string}: self_oneline" from_work_dir="self_oneline.fa"/>
        <data name="param_summary" format="tsv" label="${tool.name} on ${on_string}: param summary" from_work_dir="param_summary_qm.txt"/>
        <data name="anchor_summary_qm" format="tsv" label="${tool.name} on ${on_string}: anchor summary" from_work_dir="anchor_summary_qm.txt"/>
        <data name="aln_summary_qm" format="tsv" label="${tool.name} on ${on_string}: anchor summary" from_work_dir="aln_summary_qm.tsv"/>
    </outputs>
    <help><![CDATA[
    ]]>    </help>
    <citations>
        <citation type="doi">10.1093/nar/gkw654</citation>
    </citations>
</tool>