view mordred_descriptors.xml @ 3:cc0f89287ecf draft default tip

"planemo upload for repository commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:31:30 -0400
parents d074b0c2b54f
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<tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
        <token name="@TOOL_VERSION@">1.2.0</token>
        <token name="@GALAXY_VERSION@">0</token>
    <description>with Mordred</description>
        <requirement type="package" version="@TOOL_VERSION@">mordred</requirement>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/'
            -i '${input}'
            --iformat '${input.ext}' 
            -o '${output}'
        <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'/>
        <data name="output" format="tabular" />
            <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="" lines_diff="2"/>
            <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="" lines_diff="2"/>

Calculates up to 1825 molecular descriptors using the Mordred package. A list of all
descriptors is located here_.

.. _here:

.. class:: infomark


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


.. class:: infomark


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.

        <citation type="doi">10.1186/s13321-018-0258-y</citation>