annotate freyja_boot.xml @ 4:cd5d77d118f2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06

<tool id="freyja_boot" name="Freyja: Bootstrapping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
      profile="@PROFILE@">
    <description>
        method
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
@RUN_FREYJA_UPDATE_COMMAND@
@PREPROCESS_VCF_INPUT@
@CUSTOM_BARCODES_LINKING@
freyja boot
    @STANDARD_INPUT_FOR_BOOT@
    --nt \${GALAXY_SLOTS:-4}
    #if $nb
        --nb $nb
    #end if
    --output_base 'boot_output'
    @CUSTOM_BARCODES_COMMAND@
    $boxplot_pdf
    ]]></command>
    <inputs>
        <param name="variants_file" type="data" format="tabular" label="Variants file"/>
        <expand macro="demixing_common_options"/>
        <param argument="--nb" type="integer" optional="true" label="Number of bootstraps"/>
        <param name="boxplot_pdf" argument="--boxplot pdf" type="boolean" truevalue="--boxplot pdf"
               falsevalue=""
               checked="false" label="Generate boxplot"/>
    </inputs>
    <outputs>
        <data name="boot_lineages" format="csv" label="${tool.name} on ${on_string}: Lineages"
              from_work_dir="boot_output_lineages.csv"/>
        <data name="boot_summarized" format="csv" label="${tool.name} on ${on_string}: Summarized"
              from_work_dir="boot_output_summarized.csv">
        </data>
        <data name="boot_lineages_plot" format="pdf"
              label="${tool.name} on ${on_string}: Lineages boxplot"
              from_work_dir="boot_output_lineages.pdf">
            <filter>boxplot_pdf</filter>
        </data>
        <data name="boot_summarized_plot" format="pdf"
              label="${tool.name} on ${on_string}: Summarized boxplot"
              from_work_dir="boot_output_summarized.pdf">
            <filter>boxplot_pdf</filter>
        </data>
    </outputs>
    <tests>
        <!-- Test 01: test tsv input files and plots -->
        <test expect_num_outputs="4">
            <conditional name="usher_update_option">
                <param name="choice" value="repo"/>
            </conditional>
            <param name="variants_file" value="variants.tsv"/>
            <param name="depth_file" value="depths.tsv"/>
            <param name="confirmedonly" value="false"/>
            <param name="nb" value="10"/>
            <param name="boxplot_pdf" value="true"/>
            <output name="boot_lineages" ftype="csv">
                <assert_contents>
                    <has_text text="B.1.617.2"/>
                </assert_contents>
            </output>
            <output name="boot_summarized" ftype="csv">
                <assert_contents>
                    <has_text text="Del"/>
                </assert_contents>
            </output>
            <output name="boot_lineages_plot" ftype="pdf">
                <assert_contents>
                    <has_text text="Matplot"/>
                </assert_contents>
            </output>
            <output name="boot_summarized_plot" ftype="pdf">
                <assert_contents>
                    <has_text text="Matplot"/>
                </assert_contents>
            </output>
        </test>

        <!-- Test 02: test VCF input file -->
        <test expect_num_outputs="2">
            <conditional name="usher_update_option">
                <param name="choice" value="repo"/>
            </conditional>
            <param name="variants_file" value="test.vcf"/>
            <param name="depth_file" value="depths.tsv"/>
            <param name="confirmedonly" value="false"/>
            <param name="nb" value="10"/>
            <param name="boxplot_pdf" value="false"/>
            <output name="boot_lineages" ftype="csv">
                <assert_contents>
                    <has_text text="B.1.617.2"/>
                </assert_contents>
            </output>
            <output name="boot_summarized" ftype="csv">
                <assert_contents>
                    <has_text text="Delta"/>
                </assert_contents>
            </output>
        </test>

        <!-- Test 03: Test Custom Usher Barcode file -->
        <test expect_num_outputs="4">
            <conditional name="usher_update_option">
                <param name="choice" value="custom"/>
                <param name="usher_barcodes" location="https://zenodo.org/records/14888005/files/usher_barcodes.csv"/>
            </conditional>
            <param name="variants_file" value="variants.tsv"/>
            <param name="depth_file" value="depths.tsv"/>
            <param name="confirmedonly" value="false"/>
            <param name="nb" value="10"/>
            <param name="boxplot_pdf" value="true"/>
            <output name="boot_lineages" ftype="csv">
                <assert_contents>
                    <has_text text="B.1.617.2"/>
                </assert_contents>
            </output>
            <output name="boot_summarized" ftype="csv">
                <assert_contents>
                    <has_text text="Del"/>
                </assert_contents>
            </output>
            <output name="boot_lineages_plot" ftype="pdf">
                <assert_contents>
                    <has_text text="Matplot"/>
                </assert_contents>
            </output>
            <output name="boot_summarized_plot" ftype="pdf">
                <assert_contents>
                    <has_text text="Matplot"/>
                </assert_contents>
            </output>
        </test>
</tests>
    <help><![CDATA[
@HELP_HEADER@

Information about **freyja boot** method
========================================

A fast bootstrapping method for freyja.

Outputs
=======

Bootstrapping method results:

1. Bootstrap lineages: the 0.025, 0.05,0.25,0.5 (median),0.75, 0.95, and 0.975 percentiles for each lineage;
2. Bootstrap summarized: WHO designated VOI/VOC

    ]]></help>
    <expand macro="citations"/>
</tool>