comparison pangolin.xml @ 8:3a656a4a43ed draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 5a3f70ab430c70b260dd6e0f5b6c53aed2ca5520"

7:7bb8726be37c

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.7</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($db.source) == "download"
            python '$__tool_directory__/fetch_latest_pangolearn.py' --max_retries=$db.max_retries --timeout=$db.timeout &&
        #else if str($db.source) == "builtin"
            ln -s $db.db_release.fields.path datadir &&
        #end if
        pangolin
        --threads \${GALAXY_SLOTS:-1}

                <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">
                <param name="max_retries" label="Max download retries" help="How many times to retry downloading the pangoLEARN database" type="integer" value="5" />
                <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" />
            </when>
            <when value="builtin">
                <param name="db_release" label="pangoLEARN release" type="select">
                    <options from_data_table="pangolearn">
                        <column name="value" index="0" />

                    <has_text text="USA" />
                    <has_n_lines n="35" />
                </assert_contents>
            </output>
        </test>
        <test expect_failure="true">
            <param name="input1" value="test1.fasta" />
            <conditional name="db">
                <param name="source" value="download" />
                <param name="timeout" value="0.00001" />
                <param name="max_retries" value="1" />
            </conditional>
            <assert_stderr>
                <has_text text="timed out" />
            </assert_stderr>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

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="bibtex">
      @misc{githubpangolin,
        author = {O'Toole, Áine},
        year = {2020},
        title = {pangolin},
        publisher = {GitHub},
        journal = {GitHub repository},
        url = {https://github.com/cov-lineages/pangolin},
      }</citation>
    </citations>
</tool>

8:3a656a4a43ed

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.11</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($db.source) == "download"
            pangolin --update-data --datadir datadir &&
        #else if str($db.source) == "builtin"
            ln -s $db.db_release.fields.path datadir &&
        #end if
        pangolin
        --threads \${GALAXY_SLOTS:-1}

                <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">
                <!-- these are currently not supported by the pangolin downloader -->
                <!-- <param name="max_retries" label="Max download retries" help="How many times to retry downloading the pangoLEARN database" type="integer" value="5" /> -->
                <!-- <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" /> -->
            </when>
            <when value="builtin">
                <param name="db_release" label="pangoLEARN release" type="select">
                    <options from_data_table="pangolearn">
                        <column name="value" index="0" />

                    <has_text text="USA" />
                    <has_n_lines n="35" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

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>