comparison metaeuk_easy_predict.xml @ 3:860f8836c936 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit 412a084cda6aeca8dfe0b0dbfff9c3426aec7707

2:be6bbdeafcb8

<tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy0">
    <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description>
    <xrefs>
        <xref type="bio.tools">MetaEuk</xref>
    </xrefs>
    <macros>
        <token name="@TOOL_VERSION@">5.34c21f2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        mkdir -p ./tmp &&
        metaeuk easy-predict 
            '$contigs'
            '$query'
            output.fasta
            "./tmp/metaeuk_working"
            --threads \${GALAXY_SLOTS:-1}
            --min-length '${min_length}'
            -e '${segment_eval}'
            --metaeuk-eval '${metaeuk_eval}'
            --metaeuk-tcov '${metaeuk_tcov}'
        #if $adv.adv_options == "yes"

    ]]></command>
    <inputs>
        <param name="contigs" type="data" format="fasta" label="Contigs to search again" />
        <param name="query" type="data" format="fasta" label="Proteins to search against contigs" />
        <param argument="-e" name="segment_eval" type="float" value="100" label="Maximum e-value of individual match segment" />
        <param argument="--min-length" name="min_length" type="integer" value="15" label="Minimum number of codons in predicted open reading frame" />
        <param argument="--metaeuk-eval" name="metaeuk_eval" type="float" value="0.001" label="Maximum e-value of combined exon set" />
        <param argument="--metaeuk-tcov" name="metaeuk_tcov" type="float" value="0.5" label="Minimum length ratio of combined exon set to target" />
        <conditional name="adv">
            <param type="select"  name="adv_options" label="Show advanced options">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param argument="--max-intron" name="max_intron" value="10000" type="integer" label="Maximum intron size" />
                <param argument="--min-intron" name="min_intron" value="15" type="integer" label="Minimum intron size" />
            </when>
            <when value="no">
            </when>
        </conditional>
        <param name="write_frag_coords" type="select" value="0" label="Write the contig coords of the stop-to-stop fragment in which putative exon lies" help="The fragment coordinates in square brackets refer to the original fragment in which the exon was found." >
            <option value="0">Yes</option>
            <option value="1">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="fasta" />
        <data name="gff_output" format="gff" />
    </outputs>

    <tests>
        <test>
            <param name="contigs" ftype="fasta" value="contigs.fna" />

3:860f8836c936

<tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy1" profile="23.0">
    <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description>
    <macros>
        <token name="@TOOL_VERSION@">7.bba0d80</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">MetaEuk</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        mkdir -p ./tmp &&
        metaeuk easy-predict 
            '$contigs'
            '$query'
            output.fasta
            "./tmp/metaeuk_working"
            --threads "\${GALAXY_SLOTS:-1}"
            --min-length '${min_length}'
            -e '${segment_eval}'
            --metaeuk-eval '${metaeuk_eval}'
            --metaeuk-tcov '${metaeuk_tcov}'
        #if $adv.adv_options == "yes"

    ]]></command>
    <inputs>
        <param name="contigs" type="data" format="fasta" label="Contigs to search again" />
        <param name="query" type="data" format="fasta" label="Proteins to search against contigs" />
        <param argument="-e" name="segment_eval" type="float" value="100" label="Maximum e-value of individual match segment" />
        <param argument="--min-length" type="integer" value="15" label="Minimum number of codons in predicted open reading frame" />
        <param argument="--metaeuk-eval" type="float" value="0.001" label="Maximum e-value of combined exon set" />
        <param argument="--metaeuk-tcov" type="float" value="0.5" label="Minimum length ratio of combined exon set to target" />
        <conditional name="adv">
            <param type="select"  name="adv_options" label="Show advanced options">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param argument="--max-intron" value="10000" type="integer" label="Maximum intron size" />
                <param argument="--min-intron" value="15" type="integer" label="Minimum intron size" />
            </when>
            <when value="no">
            </when>
        </conditional>
        <param name="write_frag_coords" type="select" value="0" label="Write the contig coords of the stop-to-stop fragment in which putative exon lies" help="The fragment coordinates in square brackets refer to the original fragment in which the exon was found." >
            <option value="0">Yes</option>
            <option value="1">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
        <data name="gff_output" format="gff" label="${tool.name} on ${on_string}: GFF" />
    </outputs>

    <tests>
        <test>
            <param name="contigs" ftype="fasta" value="contigs.fna" />