comparison macros.xml @ 1:1f467ed22412 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5

0:08c2d81e7942

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.3.8</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">freyja</xref>

]]></token>
    <token name="@DASH_COMMAND@"><![CDATA[
echo '${plot_format.plot_title}' > plot_title.txt &&
echo '${plot_format.plot_intro}' > plot_intro.txt &&
freyja dash
    #if $need_aggregation.choice == 'no'
        '$tsv_aggregated'
    #else
        'aggregated.tsv'
    #end if

    plot_intro.txt
    --output abundances_dashboard.html
]]></token>
    <token name="@PLOT_COMMAND@"><![CDATA[
freyja plot
    #if $need_aggregation.choice == 'no'
        '$tsv_aggregated'
    #else
        'aggregated.tsv'
    #end if

    <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
#if $plot_format.choice == 'dash'
    @DASH_COMMAND@
#else if $plot_format.choice == 'plot'
    freyja plot
    #if $need_aggregation.choice == 'no'
        $tsv_aggregated
    #else
        aggregated.tsv
    #end if

               help="e.g. 0.0001."/>
        <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
               checked="false"
               label="Remove unconfirmed lineages from the analysis"
               help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
    </xml>
    <token name="@HELP_HEADER@"><![CDATA[
What it does
============

Freyja is intended as a post-processing step after primer trimming and variant calling in iVar (Grubaugh and Gangavaparu et al., 2019). From measurements of SNV freqency and sequencing depth at each position in the genome, Freyja returns an estimate of the true lineage abundances in the sample.
]]></token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.5281/zenodo.6585067</citation>
        </citations>
    </xml>
</macros>

1:1f467ed22412

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.4.4</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">freyja</xref>

]]></token>
    <token name="@DASH_COMMAND@"><![CDATA[
echo '${plot_format.plot_title}' > plot_title.txt &&
echo '${plot_format.plot_intro}' > plot_intro.txt &&
freyja dash
    --mincov $plot_format.mincov
    #if $need_aggregation.choice == 'no'
        '$tsv_aggregated'
    #else
        'aggregated.tsv'
    #end if

    plot_intro.txt
    --output abundances_dashboard.html
]]></token>
    <token name="@PLOT_COMMAND@"><![CDATA[
freyja plot
    $plot_format.lineages
    --mincov $plot_format.mincov
    #if $need_aggregation.choice == 'no'
        '$tsv_aggregated'
    #else
        'aggregated.tsv'
    #end if

    <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
#if $plot_format.choice == 'dash'
    @DASH_COMMAND@
#else if $plot_format.choice == 'plot'
    freyja plot
    $plot_format.lineages
    --mincov $plot_format.mincov
    #if $need_aggregation.choice == 'no'
        $tsv_aggregated
    #else
        aggregated.tsv
    #end if

               help="e.g. 0.0001."/>
        <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
               checked="false"
               label="Remove unconfirmed lineages from the analysis"
               help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
        <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue=""
               checked="false"
               label="Use larger library with non-public lineages"
               help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
    </xml>
    <xml name="plot_lineages">
        <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
               checked="false" label="Use lineage specific breakdown"/>
    </xml>
    <xml name="plot_mincov">
        <param argument="--mincov" type="float" min="0" max="100" value="60"
               label="Minimum genome coverage"
               help="Include in the plot only samples where the 'coverage' value is greater than the specified --mincov parameter. It excludes samples with coverage values below the minimum coverage threshold. By default, the minimum genome coverage is set at 60 percent."/>
    </xml>
    <token name="@HELP_HEADER@"><![CDATA[
What it does
============

Freyja is intended as a post-processing step after primer trimming and variant calling in iVar (Grubaugh and Gangavaparu et al., 2019). From measurements of SNV freqency and sequencing depth at each position in the genome, Freyja returns an estimate of the true lineage abundances in the sample.
]]></token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41586-022-05049-6</citation>
        </citations>
    </xml>
</macros>