view sygma.xml @ 0:a2369e86bc48 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sygma commit 2bf5c0cc96e8768a36219297eab1e6cf3766651e"

<tool id="sygma" name="Generate possible metabolites with SyGMa" version="@VERSION@">
    <macros>
        <token name="@VERSION@">1.1.1</token>
    </macros>
    <description>by performing common reactions on one or more parent molecule(s)</description>
    <requirements>
        <requirement type="package" version="@VERSION@">sygma</requirement>
        <requirement type="package" version="2019.03.4">rdkit</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/sygma_metabolites.py' 
            -i '$input' 
            --iformat '$input.ext' 
            -o '$output' 
            --phase1 '$phase1' 
            --phase2 '$phase2'
    ]]></command>
    <inputs>
        <param type="data" name="input" format="smi,sdf" label="Parent molecule(s)" help="Upload an SDF or SMILES file."/>
        <param type="integer" name="phase1" value="1" min="0" label="Number of reaction cycles to apply for phase 1" help="Phase 1 metabolism rules include different types of oxidation, reduction, hydrolysis and condensation reactions."/>
        <param type="integer" name="phase2" value="1" min="0" label="Number of reaction cycles to apply for phase 2" help="Phase 2 metabolism rules include several conjugation reactions, e.g. with glucuronyl, sulfate, methyl or acetyl."/>
    </inputs>
    <outputs>
        <data name="output" format="smi"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="i.smi" ftype="smi"/>
            <param name="phase1" value="1"/>
            <param name="phase2" value="1"/>
            <output name="output" file="o.smi"/>
        </test>
        <test>
            <param name="input" value="i.sdf" ftype="sdf"/>
            <param name="phase1" value="2"/>
            <param name="phase2" value="0"/>
            <output name="output" file="o2.smi"/>
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

SyGMa (Systematic Generation of potential Metabolites) is a tool to generate 
possible metabolic products of an input parent structure. The tool provides 
two rulesets to cover both phase 1 and 2 metabolism.

-----

.. class:: infomark

**Input**

A file in SMILES or SDF format. Files may contain multiple molecule 
entries; in this case outputs are distinguished by the code included in the 
output file (e.g. SYGMA0MOL0 vs SYGMA1MOL0).

The number of reaction cycles to be performed for both phase 1 and phase 2 
metabolism should also be specified.

-----

.. class:: infomark

 **Output**

For each molecule in the input file, a SMILES file is produced containing 
SMILES strings of the metabolite outputs, a generated ID code, and an empirical 
probability score (corresponding to an estimated probability that a product is 
actually metabolically produced in humans). The first line is always the parent
molecule itself::

    Oc1ccccc1   SYGMA0MOL0    1.0
    O=C(O)C1OC(Oc2ccccc2)C(O)C(O)C1O    SYGMA0MOL1 0.25
    O=S(=O)(O)Oc1ccccc1 SYGMA0MOL2  0.119
    Oc1ccc(O)cc1    SYGMA0MOL3 0.056
    COc1ccccc1  SYGMA0MOL4   0.054
    Oc1ccccc1O  SYGMA0MOL5   0.032
    O=C(O)C1OC(Oc2ccc(O)cc2)C(O)C(O)C1O SYGMA0MOL6  0.014
    O=C(O)C1OC(Oc2ccccc2O)C(O)C(O)C1O   SYGMA0MOL7    0.008
    O=S(=O)(O)Oc1ccc(O)cc1  SYGMA0MOL8   0.00666
    O=S(=O)(O)Oc1ccccc1O    SYGMA0MOL9 0.00381
    COc1ccc(O)cc1   SYGMA0MOL10   0.00302
    COc1ccccc1O SYGMA0MOL11 0.00173


    ]]></help>
    <citations>
        <citation type="doi">10.1002/cmdc.200700312</citation>
    </citations>
</tool>