galaxytools/chemicaltoolbox/lirasearch/lirasearch.xml at 666e74483afe78286415d37e873c42f7bb5c565b · simonbray/galaxytools · GitHub

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<tool id="lirasearch" name="Identify similar conformers" version="@TOOL_VERSION@" profile="20.01">
    <description>using LiraSearch spherical harmonic descriptors</description>
    <macros>
        <token name="@TOOL_VERSION@">0.1.0</token>
    </macros>
    <requirements>
        <container type="docker">sb17/lirasearch:@TOOL_VERSION@</container>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
            export HOME=`pwd` &&
            #if $ligand.ext == 'pdb':
                ln -s $ligand ligand.pdb &&
            #else
                python /opt/scripts/convert_sdf_to_pdb.py $ligand ligand.pdb &&
            #end if
            python -m esp_dnn.predict -m ligand -i . -o . &&
            esp-surface-generator ligand.pdb.pqr ligand.pdb.tmesh &&
            sh-coeff-calculator . &&
            micromamba run -n lirasearch python /opt/scripts/lira_search_sdf.py --in_file rid_coeffs.csv --out_file output --out_keys keys.txt --database ${database_select.fields.path}/rid_coeffs.csv --num_results $num_results &&
	    mkdir search_results && rocksdb_to_sdf ${database_select.fields.path} keys.txt search_results &&
	    micromamba run -n lirasearch python /opt/scripts/lira_super.py --target ligand.pdb --folder search_results &&
            cat search_results/*rotated.sdf >> '$output_sdf'
            ]]>
    </command>
    <inputs>
        <param name="ligand" type="data" format="pdb,sdf" label="Ligand file" help="Query for searching database" />
        <param name="database_select" type="select" label="Select database to search">
	    <options from_data_table="lirasearch">
                <filter type="sort_by" column="2" />
                <validator type="no_options" message="No databases are available!" />
	    </options>
        </param>
        <param name="num_results" type="integer" value="50" label="Number of results to return" />
    </inputs>
    <outputs>
        <data name="output_sdf" format="sdf" label="SDF with LiraSearch query results" />
    </outputs>
    <tests>
        <test>
	    <param name="ligand" value="ligand.pdb" ftype="pdb" />
	    <param name="database_select" value="test"/>
            <param name="num_results" value="2" />
            <output name="output_sdf" value="lirasearch_output.sdf"/>
        </test>
        <test>
            <param name="ligand" value="ligand.sdf"/>
	    <param name="database_select" value="test"/>
            <param name="num_results" value="2" />
            <output name="output_sdf" value="lirasearch_output.sdf"/>
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Identify similar conformers to an input ligand, based on predicting the electrostatic potential (ESP) using a deep neural network and computing spherical harmonic coefficients.
]]>
    </help>
    <citations>
        <citation type="doi">10.1101/2022.01.19.476747</citation>
        <citation type="doi">10.1021/acs.jmedchem.9b01129</citation>
    </citations>
</tool>