annotate end_to_end.xml @ 0:14307de7bbab draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 3c8e23e1dea22f625fb6f77ae61e1f4b605aaae2

<tool id="phabox_end_to_end" name="PhaBOX end to end" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">phabox</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">phabox</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        @CRISPR_PRE@
        phabox2 --task end_to_end
            @GENERAL@
            @PHAMER@
            @NETWORK@
            @CRISPR@
    ]]></command>
    <inputs>
        <expand macro="general"/>
        <expand macro="phamer"/>
        <expand macro="network"/>
        <expand macro="crispr"/>
        <param name="supplements" type="select" optional="true" multiple="true" label="Output supplementary collections">
            <option value="phamer">phamer</option>
            <option value="phagcn">phagcn</option>
            <option value="cherry">cherry</option>
        </param>
    </inputs>
    <outputs>
        <data name="end_to_end_out" format="tabular" from_work_dir="output/final_prediction/final_prediction_summary.tsv"/>
        <expand macro="supp_out" task="phamer"/>
        <expand macro="supp_out" task="phagcn"/>
        <expand macro="supp_out" task="cherry"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="dbdir" value="phaboxdb"/>
            <param name="contigs" value="example_contigs.fa"/>
            <output name="end_to_end_out">
                <assert_contents>
                    <has_n_lines n="11"/>
                    <has_n_columns n="17"/>
                    <has_text text="Accession&#9;Length&#9;Pred&#9;Proportion&#9;PhaMerScore&#9;PhaMerConfidence&#9;Lineage&#9;PhaGCNScore&#9;Genus&#9;GenusCluster&#9;TYPE&#9;PhaTYPScore&#9;Host&#9;CHERRYScore&#9;Method&#9;Host_NCBI_lineage&#9;Host_GTDB_lineage"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

Runs the phabox2 pipeline, i.e. it runs

- phamer: Virus identification
- phagcn: Taxonomic classification
- phatyp: Lifestyle prediction
- cherry: Host prediction

The outputs of the separate tools are joined into one big table.

@COMMON_INPUT_DOC@

**Output**

@COMMON_OUTPUT_DOC@
@PHAMER_OUTPUT_DOC@
@PHAGCN_OUTPUT_DOC@
@PHATYP_OUTPUT_DOC@
@CHERRY_OUTPUT_DOC@
    ]]></help>
    <expand macro="citations"/>
</tool>