annotate pbf_ev.xml @ 0:38b8e1d2bb78 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"

<tool id="ctb_im_pbf_ev" name="Calculate plane of best fit for molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>using RDKit</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        pbf_ev
            -i '$infile'
            -if sdf
            --meta
            -of sdf
            -o outp &>> $logfile &&
        ##cat outp_metrics.txt &>> $logfile &&
        gzip -d outp.sdf.gz
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
    </inputs>

    <expand macro="outputs" />

    <tests>
        <test>
            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
            <output name="logfile">
                <assert_contents>
                    <has_text text="Handled 36 molecules, resulting in 36 outputs"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What this tool does**

Calculate plane of best fit for molecules.

.. class:: infomark

**Input**

| - Input file in `SDF Format`_

.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

-----

.. class:: infomark

 **Output**

SD-file with plane of best fit.

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