comparison macros.xml @ 3:16331f8cff98 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859

2:95e88f407e86

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.5.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">freyja</xref>

#end if
#if $meta
    --meta '${meta}'
#end if
$confirmedonly
]]></token>
    <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
#if $usher_update_option.choice == 'custom'
    --barcodes '${usher_update_option.usher_barcodes}'
#end if

               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>

3:16331f8cff98

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.5.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">freyja</xref>

#end if
#if $meta
    --meta '${meta}'
#end if
$confirmedonly
--pathogen '$pathogen'
]]></token>
    <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
#if $usher_update_option.choice == 'custom'
    --barcodes '${usher_update_option.usher_barcodes}'
#end if

               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"/>
        <param argument="--pathogen" type="select" label="Pathogen of interest">
            <option value="SARS-CoV-2" selected="true">SARS-CoV-2</option>
            <option value="MPXV" selected="true">MPXV</option>
            <option value="H5NX" selected="true">H5NX</option>
            <option value="H1N1pdm" selected="true">H1N1pdm</option>
            <option value="FLU-B-VIC" selected="true">FLU-B-VIC</option>
            <option value="MEASLESN450" selected="true">MEASLESN450</option>
            <option value="MEASLES" selected="true">MEASLES</option>
            <option value="RSVa" selected="true">RSVa</option>
            <option value="RSVb" selected="true">RSVb</option>
        </param> 
    </xml>
    <xml name="plot_lineages">
        <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
               checked="false" label="Use lineage specific breakdown"/>
    </xml>