annotate distance_finder.xml @ 0:c066b5accacf draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"

<tool id="openbabel_structure_distance_finder" name="Determine distance to defined points" version="0.1.0">
    <description>- determine the minimum distances between a molecule and a set of 3D points</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <!-- does not run with obabel 2.4.1 -->
        <requirement type="package" version="3.0.0">openbabel</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/distance_finder.py'
            -i '$input'
            -p $points_file
            -o '$output'
    ]]></command>

    <configfiles>
        <configfile name="points_file">$points</configfile>
    </configfiles>

    <inputs>
        <param type="data" name="input" format="sdf" label="Ligands to be analysed" help="Input in SDF format" />
        <param type="text" name="points" area="true" label="3D points to consider" help="Points as X, Y, Z coordinates, one point per line">
            <sanitizer invalid_char="">
                <valid initial="string.printable">
                    <remove value="&apos;" />
                </valid>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data format="sdf" name="output" label="The measured ligands"/>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="sdf" value="ligands.sdf"/>
            <!-- TODO - work out how to specify multi-line text -->
            <param name="points" value="5.655   1.497  18.223" />
            <output name="output" ftype="sdf">
                <assert_contents>
                    <has_text text="distance1" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

This tool reports distances of ligands to reference points provided as atoms in a PDB file.
It is useful for finding out to what extent a ligand occupies an active site.

.. class:: infomark

**Input**

An SD-file containing 3D molecules.

The points parameter contains the points to compare to as X, Y and Z coordinates, one point per line.
An example  is:

5.655   1.497  18.223
1.494  -8.367  18.574
13.034   6.306  25.232

This would encode 3 points.

Each record in the SDF input is read and the closest heavy atom to each of the points is recorded as
properties in the output SDF.

.. class:: infomark

**Output**

The same SD file as the input but with a series of "distance?" properties added where ? is the index of the points
being compared to. In the example there would be properties for distance1, distance2 and distance3.


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