annotate target_screen.xml @ 0:d4c2d5bc0524 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/misc commit 94322884bede7ddb9f2a9166952dd0115bdb4e49

<tool id="target_screen" name="MS target screening" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>Extract peaks from recetox-aplcms tables using a list of target ions</description>
    <macros>
        <token name="@TOOL_VERSION@">0.1.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>

    <requirements>
        <requirement type="package" version="2.2.3">pandas</requirement>
        <requirement type="package" version="17.0.0">pyarrow</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        python3 '${__tool_directory__}/target_screen.py' --peaks '$peaks' --markers '$markers' --output '$hits' --ppm $ppm --rt_tol $rt
    ]]></command>

    <inputs>
        <param name="peaks" type="data" format="parquet"/>
        <param name="markers" type="data" format="tabular"/>
        <param name="ppm" type="integer" min="0" max="1000" value="10" label="ppm" help="Tolerance for peak filtering in ppm." />
        <param name="rt" type="integer" min="0" max="100" value="10" label="rt tolerance" help="Toelrance regarding retention time to filter out peaks" />
    </inputs>

    <outputs>
        <data name="hits" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>

    <tests>
        <test>
            <param name="peaks" value="target_screen/peaks.parquet"/>
            <param name="markers" value="target_screen/markers.tsv"/>
            <output name="hits" value="target_screen/out.tsv"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool pulls out peaks from a table given a list of markers.
The markers are matched based on m/z values with a specified ppm tolerance and matched based on retention time with a tolerance in units of retention time.
    ]]></help>
    <citations>
        <citation type="doi">10.25080/Majora-92bf1922-00a</citation>
    </citations>
</tool>