comparison pangolin.xml @ 21:81804a978fc0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 35c4813d132f69036addcc447cc6c4ec7da04d92"

20:14ae456b8cc5

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.0.5</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>
    <version_command><![CDATA[pangolin --version]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
      #if $engine.use_assignment_cache and str($db.source) != "download":
        ## This is no good. Better to fail immediately instead of downloading a lot of data first.
        echo "Using the latest assignment cache requires downloading the latest version of pangolin-data." 1>&2; exit 1
      #else:
        ## Sanity chceck was ok, lets do the real thing ...
        #if str($db.source) == "download"

            mkdir datadir &&
            pangolin --update-data --datadir datadir &&
        #else if str($db.source) == "builtin"
            ln -s $db.db_release.fields.path datadir &&
        #end if
        #if $engine.use_assignment_cache:
            ## We need to install also the latest UShER assignment cache data.
            ## Pangolin has functionality to do so, but uses it incorrectly.
            ## We use the pangolin function to install into --datadir here,
            ## then point pangolin to the downloaded file later using
            ## its --assignment-cache parameter

                    <has_n_lines n="35" />
                    <has_n_columns n="16" />
                </assert_contents>
            </output>
        </test>
        <!-- test with extra expanded_lineage column -->
        <test expect_num_outputs="1">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <!-- Test only the default UShER mode for now since the
            pangolearn random forest model uses too much memory

21:81804a978fc0

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy2" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.0.5</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
        <requirement type="package" version="0.3.17">scorpio</requirement>
        <requirement type="package" version="0.23.0">csvtk</requirement>
    </requirements>
    <version_command><![CDATA[pangolin --version]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
      #if $str($engine.analysis_mode) == 'usher' and $engine.use_assignment_cache and str($db.source) != "download":
        ## This is no good. Better to fail immediately instead of downloading a lot of data first.
        echo "Using the latest assignment cache requires downloading the latest version of pangolin-data." 1>&2; exit 1
      #else:
        ## Sanity chceck was ok, lets do the real thing ...
        #if str($db.source) == "download"

            mkdir datadir &&
            pangolin --update-data --datadir datadir &&
        #else if str($db.source) == "builtin"
            ln -s $db.db_release.fields.path datadir &&
        #end if
        #if str($engine.analysis_mode) == 'usher' and $engine.use_assignment_cache:
            ## We need to install also the latest UShER assignment cache data.
            ## Pangolin has functionality to do so, but uses it incorrectly.
            ## We use the pangolin function to install into --datadir here,
            ## then point pangolin to the downloaded file later using
            ## its --assignment-cache parameter

                    <has_n_lines n="35" />
                    <has_n_columns n="16" />
                </assert_contents>
            </output>
        </test>
        <!-- Test that use of latest assignment cache requires downloaded other data -->
        <test expect_failure="true">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <conditional name="engine">
                <param name="use_assignment_cache" value="true" />
            </conditional>
            <conditional name="db">
                <param name="source" value="default" />
            </conditional>
        </test>
        <!-- test with extra expanded_lineage column -->
        <test expect_num_outputs="1">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <!-- Test only the default UShER mode for now since the
            pangolearn random forest model uses too much memory