annotate rxn_maker.xml @ 1:8ef5428fb809 draft default tip

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

<tool id="ctb_im_rxn_maker" name="Reaction maker" 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[
        rxn_maker
            -i '$infile'
            -if sdf
            $multi
            -r '$reagent_opts'
            -rl '$reagent_file'
            -rlf 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="multi" type="boolean" label="Multi mode" truevalue="--multi" falsevalue="" help="Output one file for each reaction, in a Galaxy collection"/>
        <param name="reagent_opts" type="select" label="Reagent options" help="Name of reaction to be run">
            <option value="Amides" selected="true">Amides</option>
            <option value="SNAr">Nucleophilic aromatic substitution (SNAr mechanism)</option>
            <option value="Urea">Urea</option>
            <option value="Suzuki_Coupling">Suzuki coupling</option>
            <option value="Sulfonamide">Sulfonamide</option>
            <option value="Reductive_Amination">Reductive amination</option>
            <option value="N-Alkylation">N-alkylation</option>
            <option value="Ether_Coupling">Ether coupling</option>
            <option value="Ester_Coupling">Ester coupling</option>
            <option value="Benzimidazole">Benzimidazole</option>
            <option value="Triazole">Triazole</option>
            <option value="Benzoxazole">Benzoxazole</option>
            <option value="Sarah_Cu">Sarah Cu</option>
            <option value="Sarah_Quat_Am">Sarah Quat Am</option>
        </param>
        <param name="reagent_file" type="data" format="sdf" label="Reagent file" help="File in SDF format containing reagents for a reaction"/>

    </inputs>
    
    <outputs>
        <data name="outfile" format="sdf" label="SDF output for ${tool.name}" from_work_dir="outp.sdf"/>
        <data name="logfile" format="txt" label="Logfile for ${tool.name}"/>
        <collection name="output_list" type="list">
            <filter>multi</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sdf$" ext="sdf" />
        </collection>
    </outputs>

    <tests>
        <test>
            <param name="infile" value="sulfonyl_chloride.sdf" ftype="sdf"/>
            <param name="reagent_file" value="sdf-aliphatic-primary-amines-175.sdf" ftype="sdf"/>
            <param name="reagent_opts" value="Sulfonamide" />
            <output name="logfile">
                <assert_contents>
                    <has_text text="Created 1707 molecules from a total of  1 input molecules"/>
                </assert_contents>
            </output>
            <output name="outfile" ftype='sdf' file="rxn_maker_output1.sdf"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What this tool does**

Provides the output of reactions between input molecules and a list of reagents (both in SDF format).

.. class:: infomark

**Input**

| - Input file in `SDF Format`_
| - Reagent file in `SDF Format`_

In addition, a list of reaction types needs to be specified.

.. _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 with reaction products.

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