comparison pangolin.xml @ 11:073de3fb84a0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 593540812c77e419c093a423e3598270a49b5e45"

10:fe3e8506112c

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.14</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 &&

                    <has_text text="Consensus_EB232-crude-prep_S297" />
                    <has_n_lines n="2" />
                </assert_contents>
            </output>
        </test>
        <!-- testing with builtin data is too large -->
        <!-- <test expect_num_outputs="1">
            <param name="input1" value="test1.fasta"/>
            <conditional name="db">
                <param name="source" value="builtin" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text text="Consensus_EB232-crude-prep_S297" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test> 
        <test expect_num_outputs="1">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <conditional name="db">
                <param name="source" value="builtin" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text text="Serbia" />
                    <has_text text="Poland" />
                    <has_text text="USA" />
                    <has_n_lines n="34" />
                </assert_contents>
            </output>
        </test> -->
        <!-- test include-header option -->
        <test expect_num_outputs="1">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <param name="include_header" value="true" />
            <conditional name="db">

11:073de3fb84a0

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.14</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
	<!-- the scorpio requirement is because pangolin got an update to use scorpio 0.3.13 (to detect AY.4.2 better) 
             while still using the pangolin 3.1.14 code. when pangolin gets updated past 3.1.14 this requirement can
             be removed -->
	<requirement type="package" version="0.3.13">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 &&

                    <has_text text="Consensus_EB232-crude-prep_S297" />
                    <has_n_lines n="2" />
                </assert_contents>
            </output>
        </test>
        <!-- test include-header option -->
        <test expect_num_outputs="1">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <param name="include_header" value="true" />
            <conditional name="db">