annotate screen.xml @ 0:2c11d1f9e00b draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"

<tool id="ctb_im_screen" name="Screen" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>a compound against a library using RDKit</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        screen
            #if $comparator.comparator_opts == 'str':
                --qsmiles '${comparator.input}'
            #else:
                --qmolfile ${comparator.input}
            #end if

            -i '$infile'
            -if sdf
            #if $comparator.comparator_opts == 'mol'
                --isMol
            #end if
            #if $fragment_opts
                -f '$fragment_opts'
            #end if
            --simmin '$sim_min'
            --simmax '$sim_max'
            -d '$descriptor_opts'
            -m '$metric_opts'
            #if $hac_min != ''
                --hacmin '$hac_min'
            #end if
            #if $hac_max != ''
                --hacmax '$hac_max'
            #end if
            #if $mw_min != ''
                --mwmin '$mw_min'
            #end if
            #if $mw_max != ''
                --mwmax '$mw_max'
            #end if
            --meta
            -o outp &>> $logfile &&  ## the script does not exit 0
        cat outp_metrics.txt &>> $logfile &&
        gzip -d outp.sdf.gz
    ]]></command>
    <inputs>
        <conditional name="comparator">
            <param name='comparator_opts' type='select' label="Input type" help="Enter SMILES string or Mol file.">
                <option value='file'>Mol/SDF file</option>
                <option value='str'>SMILES string</option>
            </param>
            <when value='str'>
                <param name="input" type="text" label="SMILES input" help="Enter SMILES for a compound.">
                    <validator type='length' min='5'/>
                </param>
            </when>
            <when value='file'>
                <param name="input" type="data" format="sdf,mol" label="Input" help="Input file in mol/sdf format"/>
            </when>
        </conditional>
        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF or JSON format, for comparison"/>
        <param name="sim_min" type="float" label="Similarity lower cutoff" value="0.7" min="0" max="1" help="(1.0 means identical)"/>
        <param name="sim_max" type="float" label="Similarity upper cutoff" value="1.0" min="0" max="1" help="(1.0 means identical)"/>
        <param name="descriptor_opts" type="select" label="Type of descriptor or fingerprint" help="Default is rdkit">
            <option value="rdkit" selected="true">rdkit</option>
            <option value="maccs">maccs</option>
            <option value="morgan2">morgan2</option>
            <option value="morgan3">morgan3</option>
        </param>
        <param name="metric_opts" type="select" label="Similarity metric" help="Default is the Tanimoto coefficient">
            <option value="tanimoto" selected="true">tanimoto</option>
            <option value="asymmetric">asymmetric</option>
            <option value="braunblanquet">braunblanquet</option>
            <option value="cosine">cosine</option>
            <option value="dice">dice</option>
            <option value="kulczynski">kulczynski</option>
            <option value="mcconnaughey">mcconnaughey</option>
            <option value="rogotgoldberg">rogotgoldberg</option>
            <option value="russel">russel</option>
            <option value="sokal">sokal</option>
        </param>
        <param name="fragment_opts" type="select" optional="true" label="Find single fragment" help="Find single fragment if more than one (hac = biggest by heavy atom count, mw = biggest by mol weight )">
            <option value="hac">Biggest by heavy atom count</option>
            <option value="mw">Biggest by molecular weight</option>
        </param>
        <param name="hac_min" type="integer" optional="true" label="Minimum heavy atom count" help="Minimum number of heavy atoms for a candidate to pass screening"/>
        <param name="hac_max" type="integer" optional="true" label="Maximum heavy atom count" help="Maximum number of heavy atoms for a candidate to pass screening"/>
        <param name="mw_min" type="float" optional="true" label="Minimum molecular weight" help="Minimum molecular weight for a candidate to pass screening"/>
        <param name="mw_max" type="float" optional="true" label="Maximum molecular weight" help="Maximum molecular weight for a candidate to pass screening"/>
    </inputs>
    
    <expand macro="outputs" />
    
    <tests>
        <test>
            <param name='comparator_opts' value="str"/>
            <param name="input" value="C1N=C(C2=CC=CC=C2)C2=CC=CC=C2C2=C1C=NC(NC1=CC=CC=C1)=N2"/>
            <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/>
            <param name="descriptor_opts" value="rdkit" />
            <param name="metric_opts" value="tanimoto" />
            <param name="sim_min" value="0.45" />
            <param name="sim_max" value="1.0" />
            <output name="outfile" ftype='sdf' file="screen_output1.sdf"/>
        </test>
        <test>
            <param name='comparator_opts' value="file"/>
            <param name="input" value="pyrimethamine.mol" ftype="mol"/>
            <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/>
            <param name="descriptor_opts" value="rdkit" />
            <param name="metric_opts" value="tanimoto" />
            <param name="sim_min" value="0.7" />
            <param name="sim_max" value="0.8" />
            <output name="outfile" ftype='sdf' file="screen_output2.sdf"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What this tool does**

Screen a library against a compound, filtering by fingerprint similarity and a number of other properties.

.. class:: infomark

**Input**

| - Compound library in `SDF Format`_
| - Compound to screen against in `SMILES`_ or `SDF Format`_
| - Type of fingerprint
| - Required molecular weight and heavy atom count

.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

-----

.. class:: infomark

 **Output**

SD-file of screened compounds, with new 'Similarity' property.

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