comparison sygma.xml @ 1:0e330829de40 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sygma commit 5b2d7437ba0875c0913630fd2165c82ed933422c"

0:a2369e86bc48

<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"/>

.. 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>

1:0e330829de40

<tool id="sygma" name="Generate possible metabolites with SyGMa" version="@VERSION@+galaxy1">
    <description>by performing common reactions on one or more parent molecule(s)</description>
    <macros>
        <token name="@VERSION@">1.1.1</token>
    </macros>
    <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'
            #if $detailed
              --detailed
            #end if
    ]]></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."/>
        <param type="boolean" name="detailed" label="Include more detailed information" help="Will return detailed information including molecular formula of the chemical structure and transformation pathway involved."/>
    </inputs>
    <outputs>
        <data name="output" format="tsv"/>
    </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.smi" ftype="smi"/>
            <param name="phase1" value="1"/>
            <param name="phase2" value="1"/>
            <param name="detailed" value="true"/>
            <output name="output" file="o_detailed.smi"/>
        </test>
        <test>
            <param name="input" value="i.sdf" ftype="sdf"/>
            <param name="phase1" value="2"/>
            <param name="phase2" value="0"/>

.. 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**

A tab-separated values (tsv) file for each molecule in the input file.
Columns contain a generated ID code (compound_id), SMILES strings of the
metabolite outputs (smiles) and an empirical probability score (sygma_score).
Calculated score value corresponds to an estimated probability that a product is
actually metabolically produced in humans). The first line is always the parent
molecule itself.

+----------------------------------+-------------+-------------+
| smiles                           | compound_id | sygma_score |
+----------------------------------+-------------+-------------+
| Oc1ccccc1                        | SYGMA0MOL0  | 1.0         |
+----------------------------------+-------------+-------------+
| O=C(O)C1OC(Oc2ccccc2)C(O)C(O)C1O | SYGMA0MOL1  | 0.25        |
+----------------------------------+-------------+-------------+

If option for more detailed output is selected, additional columns include
molecular formula (molecular_formula) of the chemical structure, number of
reactions (sygma_n) and transformation pathway (sygma_pathway) involved.

+----------------------------------+-------------+--------------+-------------------+----------+---------------------------------------+
| smiles                           | compound_id | sygma_score  | molecular_formula | sygma_n  | sygma_pathway                         |
+----------------------------------+-------------+--------------+-------------------+----------+---------------------------------------+
| Oc1ccccc1                        | SYGMA0MOL0  | 1.0          | C6H6O             | 1        | parent                                |
+----------------------------------+-------------+--------------+-------------------+----------+---------------------------------------+
| O=C(O)C1OC(Oc2ccccc2)C(O)C(O)C1O | SYGMA0MOL1  | 0.25         | C12H14O7          | 2        | O-glucuronidation_(aromatic_hydroxyl) |
+----------------------------------+-------------+--------------+-------------------+----------+---------------------------------------+

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