annotate phamer.xml @ 1:724fcc6ee63b draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd

<tool id="phabox_phamer" name="PhaBOX phamer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
    <description>Virus identification</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[
        phabox2 --task phamer
            @GENERAL@
            @PHAMER@
    ]]></command>
    <inputs>
        <expand macro="general"/>
        <expand macro="phamer"/>
    </inputs>
    <outputs>
        <data name="phamer_out" format="tabular" from_work_dir="output/final_prediction/phamer_prediction.tsv"/>
    </outputs>
    <tests>
        <test>
            <param name="dbdir" value="phaboxdb"/>
            <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
            <output name="phamer_out">
                <assert_contents>
                    <has_line line="Accession&#9;Length&#9;Pred&#9;Proportion&#9;PhaMerScore&#9;PhaMerConfidence"/>
                    <has_n_lines n="391"/> <!-- 1 per input sequence-->
                    <has_n_columns n="6"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Identify phage contigs from metagenomics data.

@COMMON_INPUT_DOC@

**Output**:

@COMMON_OUTPUT_DOC@
@PHAMER_OUTPUT_DOC@
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/bib/bbac258</citation>
    </expand>
</tool>