annotate mordred_descriptors.xml @ 2:d074b0c2b54f draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"

<tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="1.2.0">
    <description>with Mordred</description>
    <requirements>
        <requirement type="package" version="1.2.0">mordred</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/mordred_descriptors.py'
            -i '${input}'
            --iformat '${input.ext}' 
            -o '${output}'
            $header
            $use_3d
            $smi_col
    ]]></command>
    <inputs>
        <param name="input" format="smi,sdf,inchi" type="data" label="Molecule data"
            help="SDF, SMILES or InChi format"/>
        <param name='header' type='boolean' truevalue='--header' falsevalue=''
            label='Include a header line' help='Include names of the descriptors as the first line in the output file'/>
        <param name='use_3d' type='boolean' truevalue='--3d' falsevalue=''
            label='Calculate 3D descriptors' help='Include 3D as well as 2D descriptors - only valid if an SD-file is selected'/>
        <param name='smi_col' type='boolean' truevalue='--smiles' falsevalue=''
            label='Add column with SMILES' help='Add a column to the output file containing SMILES of all compounds'/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype='sdf' value="10mol.sdf" />
            <param name="header" value="True" />
            <param name="use_3d" value="True" />
            <param name="smi_col" value="False" />
            <output name="output" ftype='tabular' file="10sdf.tab" />
        </test>
        <test>
            <param name="input" ftype='smi' value="8mol.smi" />
            <param name="header" value="True" />
            <param name="use_3d" value="False" />
            <param name="smi_col" value="True" />
            <output name="output" ftype='tabular' file="8smi.tab" />
        </test>
    </tests>

    <help><![CDATA[
Calculates up to 1825 molecular descriptors using the Mordred package. A list of all
descriptors is located here_.

.. _here: https://github.com/simonbray/mordred-descriptors

.. class:: infomark

**Input**

A file containing multiples chemical structures, either in SMILES, InChi or SDF format.

-----

.. class:: infomark

**Output**

A tabular file, in which each column represents a molecular descriptor (1613 in total,
or 1825 if 3D descriptors are included). Each row describes a single molecule. Empty
cells indicate that a descriptor could not be calculated for that molecule. Rows which
are entirely empty most likely indicate a wrongly encoded molecule.

    ]]></help>
    <citations>
        <citation type="doi">10.1186/s13321-018-0258-y</citation>
    </citations>
</tool>