annotate gc_derivatization.xml @ 0:600b391827e3 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization commit b757d35278216a1f43bd53ea687a951b005e47df

<tool id="gc_derivatization" name="GC derivatization" version="@TOOL_VERSION@+galaxy0" profile="21.09">
    <description>In silico MeOX and TMS derivatization tool</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">gc-meox-tms</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
    python -m gc_meox_tms -t '${output}' '${input}'
    ]]>
    </command>

    <inputs>
        <param name="input" type="data" format="smi,tabular" help="SMILES list in smi or tabular formats."/>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="input.tabular" ftype="smi"/>
            <output name="output" >
                <assert_contents>
                    <has_text text="CC(N)=O"/>
                    <has_text text="CC(=O)O"/>
                    <has_text text="CC=NOC"/>
                    <has_text text="OC1=CC=CC=C1"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        <![CDATA[
        The tool outputs a table with multiple columns containing the original SMILES as well as with the derivatization group removed.
        The further columns contain all possible derivatized forms of the molecule. See the example output below.

        +----------------+----------------+-------------------------+--------------------+---------------------------------+
        | orig           | deriv. removed | deriv. added            | ...                |                                 |
        +================+================+=========================+====================+=================================+
        | CC(N)=O        | CC(N)=O        | CC(N)=O                 | CC(=O)N[Si](C)(C)C | CC(=O)N([Si](C)(C)C)[Si](C)(C)C |
        +----------------+----------------+-------------------------+--------------------+---------------------------------+
        | OC1=CC=CC=C1   | OC1=CC=CC=C1   | C[Si](C)(C)OC1=CC=CC=C1 | OC1=CC=CC=C1       |                                 |
        +----------------+----------------+-------------------------+--------------------+---------------------------------+
        | CC(=O)O        | CC(=O)O        | CC(=O)O[Si](C)(C)C      | CC(=O)O            |                                 |
        +----------------+----------------+-------------------------+--------------------+---------------------------------+
        | CC=NOC         | CC=O           | CC=NOC                  |                    |                                 |
        +----------------+----------------+-------------------------+--------------------+---------------------------------+
        ]]>
    </help>
    <citations>
        <citation type="doi">https://doi.org/10.1021/acs.analchem.7b01010</citation>
    </citations>     
</tool>