comparison pangolin.xml @ 16:ca0d8cf80567 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"

15:36912871ccdc

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.17</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
        <requirement type="package" version="0.23.0">csvtk</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($db.source) == "download"
            pangolin --update-data --datadir datadir &&

        <param argument="--min-length" type="integer" label="Minimum query length allowed" 
            value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
        <param name="include_header" type="boolean" label="Include header line in output file" 
            truevalue="true" falsevalue="false" />
        <conditional name="db">
            <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database">
                <option value="download">Download latest from web</option>
                <option value="builtin">Use database from Galaxy server</option>
                <option value="default">Use default database built in to pangolin (not recommended)</option>
            </param>
            <when value="download">

assignment, and the default option for this tool is to download the latest version of the model before the pangolin
tool runs. A pangoLEARN data manager exists so that the Galaxy admin can download specific versions of the pangoLEARN
model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the
default model rapidly becomes out of date.

    ]]></help>
    <citations>
      <citation type="doi">10.1093/ve/veab064</citation>
    </citations>
</tool>

16:ca0d8cf80567

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.17</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
        <requirement type="package" version="0.3.16">scorpio</requirement>
        <requirement type="package" version="0.23.0">csvtk</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($db.source) == "download"
            pangolin --update-data --datadir datadir &&

        <param argument="--min-length" type="integer" label="Minimum query length allowed" 
            value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
        <param name="include_header" type="boolean" label="Include header line in output file" 
            truevalue="true" falsevalue="false" />
        <conditional name="db">
            <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database. While 'Download latest from web' is recommended, if errors occur see the warning in the main help text below.">
                <option value="download">Download latest from web</option>
                <option value="builtin">Use database from Galaxy server</option>
                <option value="default">Use default database built in to pangolin (not recommended)</option>
            </param>
            <when value="download">

assignment, and the default option for this tool is to download the latest version of the model before the pangolin
tool runs. A pangoLEARN data manager exists so that the Galaxy admin can download specific versions of the pangoLEARN
model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the
default model rapidly becomes out of date.

.. class:: warningmark

	The "Download latest from web" updates the pangolin database but not the pangolin (and scorpio) software. If
	the database format changes this can cause the pangolin job and the tool to fail. The solution to this kind of
	failure is to update the pangolin tool installed in the Galaxy server.
    ]]></help>
    <citations>
      <citation type="doi">10.1093/ve/veab064</citation>
    </citations>
</tool>