annotate conformers.xml @ 1:a4b1474efada draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"

<tool id="ctb_im_conformers" name="Generate conformers" 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[
        conformers
            -i '$infile'
            -if sdf
            -n '$num'
            -a '$attempts'
            -r '$rmsd'
            #if $conditional_cluster.cluster_method_opts != 'none'
                -c '$conditional_cluster.cluster_method_opts'
                -t '$conditional_cluster.threshold'
            #end if
            -e '$emin'
            -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"/>
        <param name="num" type="integer" label="Number of conformers to generate" value="1"/>
        <param name="rmsd" type="float" value="1.0" min="0" label="RMSD threshold" help="If a conformer is too similar to those already generated (below the RMSD threshold), it is discarded and regenerated."/>
        <param name="attempts" type="integer" value="0" min="0" label="Number of attempts" help="Conformers which are below the RMSD threshold are regenerated. This parameter controls how many times this regeneration should be attempted before giving up. "/>
        <conditional name="conditional_cluster">
            <param name="cluster_method_opts" type="select" label="Cluster method" help="RMSD, TFD (torsion fingerprint deviation) or no clustering.">
                <option value="none" selected="true">None</option>
                <option value="rmsd">RMSD</option>
                <option value="tfd">TFD</option>
            </param>
            <when value="rmsd">
                <param name="threshold" type="float" label="Cluster threshold" value="2.0" min="0" help="Default of 2.0 for RMSD"/>
            </when>
            <when value="tfd">
                <param name="threshold" type="float" label="Cluster threshold" value="0.3" min="0" help="Default of 0.3 for TFD"/>
            </when>
            <when value="none">
            </when>
        </conditional>
        <param name="emin" type="integer" value="0" min="0" label="Energy minimisation iterations" help="Number of EM iterations using the MMFF force field. Default is 0 (i.e. no EM)."/>
    </inputs>
    
    <expand macro="outputs" />
    
    <tests>
        <test>
            <param name="infile" ftype='sdf' value="Kinase_inhibs.sdf"/>
            <param name="num" value="2"/>
            <param name="cluster_method_opts" value="rmsd"/>
            <output name="outfile" ftype="sdf">
            <!-- contents may vary -->
                <assert_contents>
                    <has_text text="ConformerNum"/>
                    <has_size value="207000" delta="10000"/>
                    <has_text_matching expression="^([^\$]+?\$\$\$\$){65,72}?$"/>
                </assert_contents>
            </output>
            <output name="logfile">
                <assert_contents>
                    <has_text text="__InputCount__"/>
                    <has_text text="__OutputCount__"/>
                    <has_n_lines n="40" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What this tool does**

This tool generates conformers for a set of input molecules, using the chemistry toolkit RDKit.


-----

.. class:: infomark

**Input**

| - Molecules in `SDF format`_
| - A number of other parameters can be set; the most important include the number of conformers to generate and the minimum RMSD difference between them.

.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file


-----

.. class:: infomark

 **Output**

SD-file containing generated conformers.

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