annotate PaDEL.xml @ 1:a84bcb007b09 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit 7fb96a3844b4771084f18de2346ed6d5e241d839"

<tool id="padel" name="PaDEL descriptor" version="@TOOL_VERSION@">
    <description>calculator</description>
    <macros>
        <token name="@TOOL_VERSION@">2.21</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">padel</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
    ln -s '$input' ./molecule.${input.ext} &&

    padel 
        $coordinate2d
        $detectaromaticity
        $removesalt
        $standardizenitro
        $convert3d
        $retain3d
        $coordinate3d
        $fingerprint
        -retainorder true
        -file ./out.csv
        -maxruntime 600000
        -dir ./molecule.${input.ext}
    &&
    
    cat ./out.csv | tr "," "\\t" > '$descriptor'

]]></command>
    <inputs>
        <param format="sdf,smi" name="input" type="data" label="SDF or SMILES file" optional= "false"/>
        
        <param name="detectaromaticity" type="boolean" label="Detect aromaticity"
               truevalue="-detectaromaticity" falsevalue="" checked="true" help="Remove existing aromaticity information in the molecule before calculation of descriptors."/>

        <param name="removesalt" type="boolean" label="Remove salt"
               truevalue="-removesalt" falsevalue="" checked="true" help="Remove salt from molecule(s). Choose No if you have already removed salt from the molecule yourself (recommended)."/>

        <param name="standardizenitro" type="boolean" label="Standardize nitro groups"
               truevalue="-standardizenitro" falsevalue="" checked="true" help="Standardize nitro groups to N(:O):O."/>

        <param name="convert3d" type="boolean" label="Convert to 3D"
               truevalue="-convert3d" falsevalue="" checked="false" help="Convert molecule to 3D representation."/>

        <param name="coordinate2d" type="boolean" label="Calculate 2d descriptors"
               truevalue="-2d" falsevalue="" checked="true" help="Calculate 1D and 2D descriptors."/>

        <param name="retain3d" type="boolean" label="Retain 3D coordinates"
               truevalue="-retain3d" falsevalue="" checked="false" help="Retain 3D coordinates when standardizing structure."/>

        <param name="coordinate3d" type="boolean" label="Calculate 3d descriptors"
               truevalue="-3d" falsevalue="" checked="false" help="Calculate 3D descriptors. To calculate 3D descriptors, the convert molecule to 3D option should be selected."/>

        <param name="fingerprint" type="boolean" label="Calculate fingerprints"
               truevalue="-fingerprints" falsevalue="" checked="true" help="Calculate molecular fingerprints."/>

    </inputs>
    <outputs>
        <data format="csv" name="descriptor" label="PaDEL descriptor file for $input.name "/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="test.sdf" ftype="sdf"/>
            <param name="detectaromaticity" value="-detectaromaticity" />
            <param name="removesalt" value="-removesalt" />
            <param name="standardizenitro" value="-standardizenitro" />
            <param name="convert3d" value="" />
            <param name="retain3d" value="" />
            <param name="maxruntime" value="600000" />
            <param name="coordinate2d" value="-2d" />
            <param name="coordinate3d" value="" />
            <param name="fingerprint" value="" />
            <param name="retainorder" value="-retainorder" />
            <output name="descriptor">
               <assert_contents>
                    <has_n_columns n="1445" />
                    <has_text text="3.735268" />
                    <has_text text="13.148254" />
                    <has_text text="0.38897" />
                    <has_text text="-0.00131" />
               </assert_contents>
           </output>
        </test>
        <test>
            <param name="input" value="test.sdf" ftype="sdf"/>
            <param name="detectaromaticity" value="-detectaromaticity" />
            <param name="removesalt" value="-removesalt" />
            <param name="standardizenitro" value="-standardizenitro" />
            <param name="convert3d" value="" />
            <param name="retain3d" value="" />
            <param name="maxruntime" value="600000" />
            <param name="coordinate2d" value="-2d" />
            <param name="coordinate3d" value="" />
            <param name="fingerprint" value="-fingerprints" />
            <param name="retainorder" value="-retainorder" />
            <output name="descriptor">
               <assert_contents>
                    <has_n_columns n="2326" />
                    <has_text text="1.17828" />
                    <has_text text="2.77182" />
                    <has_text text="-1.06144" />
                    <has_text text="-5.91478" />
               </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="test.sdf" ftype="sdf"/>
            <param name="detectaromaticity" value="" />
            <param name="removesalt" value="-removesalt" />
            <param name="standardizenitro" value="-standardizenitro" />
            <param name="convert3d" value="" />
            <param name="retain3d" value="" />
            <param name="maxruntime" value="600000" />
            <param name="coordinate2d" value="-2d" />
            <param name="coordinate3d" value="" />
            <param name="fingerprint" value="-fingerprints" />
            <param name="retainorder" value="-retainorder" />
            <output name="descriptor">
               <assert_contents>
                    <has_n_columns n="2326" />
                    <has_text text="0.93896" />
                    <has_text text="2.85714" />
                    <has_text text="-33.59391" />
                    <has_text text="11.62754" />
               </assert_contents>
            </output>
        </test>
     </tests>
     <help><![CDATA[

The PaDEL descriptor tool calculates different kinds of molecular descriptors and fingerprints, using the Chemistry Development Kit (CDK). Descriptors include atom type, electrotopological state descriptors, Crippen's logP and MR, extended topochemical atom (ETA) descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, binary fingerprints and count of chemical substructures. For more details, please consult the cited publication.

-----

.. class:: infomark

**Input**

    - SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
    - SMILES Format: http://www.molecular-networks.com/products/corina

-----

.. class:: infomark

**Output**
    - Tabular file, where each descriptor (value) is shown in a separate column.
    
    ]]></help>
    <citations>
        <citation type="bibtex">
            @article{rdkit,
                author = {Chun Wei Yap},
                title = {PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints},
                url ={https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21707}
            }</citation>
    </citations>
</tool>