comparison macros.xml @ 1:9758bed53a38 draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd

0:14307de7bbab

<macros>
    <token name="@TOOL_VERSION@">2.1.5</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioadv/vbad101</citation>
            <yield/>

    <xml name="network">
        <section name="network" title="Options for virus-virus connections" help="The options below are used to generate a network for virus-virus connections. The current parameters are optimized for the ICTV 2024 and are highly accurate for grouping genus-level vOTUs. When making changes, make sure you understand what they are.">
            <param argument="--aai" type="float" value="75" min="0" max="100" label="Average amino acids identity"/>
            <param argument="--share" type="float" value="15" min="0" max="100" label="Minimum shared number of proteins"/>
            <param argument="--pcov" type="float" value="80" min="0" max="100" label="Protein-based coverage"/>
            <!-- \-\-draw not recommended top be used according to CLI help -->
        </section>
    </xml>
    <token name="@NETWORK@"><![CDATA[
            --aai $network.aai
            --share $network.share
            --pcov $network.pcov
    ]]></token>

    <xml name="crispr">
        <section name="crispr" title="Options used to predict CRISPRs based on MAGs" help="">
            <param argument="--bfolder" type="data" format="true" optional="true" label="MAGS"/>
            <param argument="--cpident" type="float" value="90" min="90" max="100" label="Alignment identity for CRISPRs"/>
            <param argument="--ccov" type="float" value="90" min="0" max="100" label="Alignment coverage for CRISPRs"/>
            <param argument="--blast" type="select" label="BLAST program for CRISPRs" help="blastn-short will lead to more sensitive results but require more time to execute the program">
                <option value="blastn">blastn</option>
                <option value="blastn-short">blastn-short</option>
            </param>
        </section>
    </xml>
    <token name="@CRISPR_PRE@"><![CDATA[
        #if $crispr.bfolder
            mkdir bfolder &&

    ]]></token>
    <token name="@CRISPR@"><![CDATA[
        #if $crispr.bfolder
            --bfolder bfolder
        #end if
            --cpident $crispr.cpident
            --ccov $crispr.cpident
            --blast $crispr.blast
    ]]></token>

    <xml name="contamination">
        <section name="contamination" title="Options for contamination detection" help="">
            <param argument="--sensitive" type="boolean" truevalue="--sensitive Y" falsevalue="--sensitive N" label="Sensitive search for prokaryotic genes" help="Enabling this will lead to more sensitive results but require more time to execute the program"/>

    <token name="@PHAGCN_OUTPUT_DOC@"><![CDATA[
- Lineage: the predicted taxonomy lineage (NCBI version) of the contigs. Each rank is separated by the ';'.
- PhaGCNScore: the predicted score for each rank in the lineage. Each rank is separated by the ';'.
- Genus: whether the contig has a genus level name ('-' means unknown).
- GenusCluster: if the Genus is '-', the program will assign a genus-level grouping result: group_idx (idx = 1, 2, 3, ...) or singleton. This can be viewed as genus-level OTUs based on the average shared protein identities between sequences.
    ]]></token>
    <token name="@PHATYP_OUTPUT_DOC@"><![CDATA[
- TYPE: virulent or temperate (virus).
- PhaTYPScore: the prediction score given by the deep learning model.
    ]]></token>

1:9758bed53a38

<macros>
    <token name="@TOOL_VERSION@">2.1.11</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioadv/vbad101</citation>
            <yield/>

    <xml name="network">
        <section name="network" title="Options for virus-virus connections" help="The options below are used to generate a network for virus-virus connections. The current parameters are optimized for the ICTV 2024 and are highly accurate for grouping genus-level vOTUs. When making changes, make sure you understand what they are.">
            <param argument="--aai" type="float" value="75" min="0" max="100" label="Average amino acids identity"/>
            <param argument="--share" type="float" value="15" min="0" max="100" label="Minimum shared number of proteins"/>
            <param argument="--pcov" type="float" value="80" min="0" max="100" label="Protein-based coverage"/>
            <!-- \-\-draw not recommended to be used according to CLI help -->
        </section>
    </xml>
    <token name="@NETWORK@"><![CDATA[
            --aai $network.aai
            --share $network.share
            --pcov $network.pcov
    ]]></token>

    <xml name="crispr">
        <section name="crispr" title="Options used to predict CRISPRs based on MAGs" help="">
            <param argument="--bfolder" type="data" format="fasta" optional="true" label="MAGS"/>
            <param argument="--prophage" type="integer" value="1000" min="0" max="100000" label="Minimum alignment length for estimate potential prophage"/>
            <param argument="--cpident" type="float" value="90" min="90" max="100" label="Alignment identity for CRISPRs"/>
            <param argument="--ccov" type="float" value="90" min="0" max="100" label="Alignment coverage for CRISPRs"/>
            <param argument="--blast" type="select" label="BLAST program for CRISPRs" help="blastn-short will lead to more sensitive results but require more time to execute the program">
                <option value="blastn">blastn</option>
                <option value="blastn-short">blastn-short</option>
            </param>
            <param argument="--magonly" type="boolean" truevalue="--magonly Y" falsevalue="--magonly N" label="Only predicting host based on the provided MAGs" help="Default is to predict the host based on the MAGs and the reference database"/>
        </section>
    </xml>
    <token name="@CRISPR_PRE@"><![CDATA[
        #if $crispr.bfolder
            mkdir bfolder &&

    ]]></token>
    <token name="@CRISPR@"><![CDATA[
        #if $crispr.bfolder
            --bfolder bfolder
        #end if
            --prophage $crispr.prophage
            --cpident $crispr.cpident
            --ccov $crispr.ccov
            --blast $crispr.blast
            $magonly
    ]]></token>

    <xml name="contamination">
        <section name="contamination" title="Options for contamination detection" help="">
            <param argument="--sensitive" type="boolean" truevalue="--sensitive Y" falsevalue="--sensitive N" label="Sensitive search for prokaryotic genes" help="Enabling this will lead to more sensitive results but require more time to execute the program"/>

    <token name="@PHAGCN_OUTPUT_DOC@"><![CDATA[
- Lineage: the predicted taxonomy lineage (NCBI version) of the contigs. Each rank is separated by the ';'.
- PhaGCNScore: the predicted score for each rank in the lineage. Each rank is separated by the ';'.
- Genus: whether the contig has a genus level name ('-' means unknown).
- GenusCluster: if the Genus is '-', the program will assign a genus-level grouping result: group_idx (idx = 1, 2, 3, ...) or singleton. This can be viewed as genus-level OTUs based on the average shared protein identities between sequences.
- Prokaryotic virus (Bacteriophages and Archaeal virus): Y/N
    ]]></token>
    <token name="@PHATYP_OUTPUT_DOC@"><![CDATA[
- TYPE: virulent or temperate (virus).
- PhaTYPScore: the prediction score given by the deep learning model.
    ]]></token>