comparison pangolin.xml @ 23:77402759b866 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d7751920c666de56e21cf48ffe19191b2d19d534

22:a2099fb98cdb

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.1.1</token>
        <token name="@PANGOLIN_DATA_VERSION@">1.11</token>
        <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
        <!-- a regex describing the scorpio versions that this wrapper version
        is backwards-compatible with; can be used with the min_scorpio_version
        column of the constellations data table to offer only compatible

    #end if
    ## Report all data package versions that will be used in this run of the tool
    echo "Running pangolin with the following possibly updated data packages:" &&
    pangolin --datadir datadir $use_old_datadir --all-versions | grep -E "pangolin-data|assignment|constellations" &&
#end if
## Finally run the pangolin analysis
pangolin
--threads \${GALAXY_SLOTS:-1}
--tempdir "\${TMPDIR:-.}"
#if str($engine.pangolin_data.source) != 'default' or str($constellations.source) != 'default':

#end if
--outfile report.csv
--max-ambig $max_ambig
--min-length $min_length
$expanded_lineage
'$input1'
&& csvtk csv2tab report.csv
#if not $include_header:
    | tail -n+2
#end if
> '$output1'
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" />
        <conditional name="engine">
            <param argument="--analysis-mode" type="select" label="Analysis mode"
            help="The analysis engine to use for lineage assignment. UShER is considered more accurate, but pangoLEARN is faster">
                <option value="usher">UShER</option>
                <option value="pangolearn">pangoLEARN</option>

23:77402759b866

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.1.2</token>
        <token name="@PANGOLIN_DATA_VERSION@">1.12</token>
        <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
        <!-- a regex describing the scorpio versions that this wrapper version
        is backwards-compatible with; can be used with the min_scorpio_version
        column of the constellations data table to offer only compatible

    #end if
    ## Report all data package versions that will be used in this run of the tool
    echo "Running pangolin with the following possibly updated data packages:" &&
    pangolin --datadir datadir $use_old_datadir --all-versions | grep -E "pangolin-data|assignment|constellations" &&
#end if
## Since v4.0.6 pangolin can handle compressed fasta as input,
## but recognizes file type by suffix.
#if $input1.is_of_type('fasta.gz'):
    #set $query = 'query.fa.gz'
#else:
    #set $query = 'query.fa'
#end if
ln -s '$input1' $query &&
## Finally run the pangolin analysis
pangolin
--threads \${GALAXY_SLOTS:-1}
--tempdir "\${TMPDIR:-.}"
#if str($engine.pangolin_data.source) != 'default' or str($constellations.source) != 'default':

#end if
--outfile report.csv
--max-ambig $max_ambig
--min-length $min_length
$expanded_lineage
$query
&& csvtk csv2tab report.csv
#if not $include_header:
    | tail -n+2
#end if
> '$output1'
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
        <conditional name="engine">
            <param argument="--analysis-mode" type="select" label="Analysis mode"
            help="The analysis engine to use for lineage assignment. UShER is considered more accurate, but pangoLEARN is faster">
                <option value="usher">UShER</option>
                <option value="pangolearn">pangoLEARN</option>