view standardize.xml @ 1:8ac4f037fdde draft default tip

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

<tool id="ctb_im_standardize" name="Standardize SD-files" 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[
        standardize
            -i '$infile'
            -if sdf
            $fragment_opts
            $neutralize
            --meta
            -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="fragment_opts" type="select" label="Fragment" help="The approach for choosing the largest fragment; alternatively the whole molecule is used.">
            <option value="" selected="true">Use whole molecule</option>
            <option value="--fragment-method hac">Biggest by heavy atom count</option>
            <option value="--fragment-method mw">Biggest by molecular weight</option>
        </param>
        <param name="neutralize" type="boolean" label="Neutralize" truevalue="--neutralize" falsevalue="" help="Remove any charge from the molecule"/>
    </inputs>    
    
    <expand macro="outputs" />
    
    <tests>
        <test>
            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
            <param name="fragment_opts" value="--fragment-method hac"/>
            <output name="outfile" ftype='sdf' file="standardize_output1.sdf"/>
        </test>
        <test>
            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
            <param name="fragment_opts" value="--fragment-method mw"/>
            <param name="neutralize" value="true"/>
            <output name="outfile" ftype='sdf' file="standardize_output2.sdf"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What this tool does**

Standardizes an SD-file using RDKit.

.. class:: infomark

**Input**

| - Input file in `SDF Format`_

.. _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 standardized compounds.

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