annotate strip-it.xml @ 1:b8809b15e1a4 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e

<tool id="ctb_stripit" name="Strip-it" version="1.0.2.1">
    <description>extracts scaffolds from molecules</description>
    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism-->
    <requirements>
        <requirement type="package" version="1.0.2">strip_it</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
        ln -s '$infile' '$infile.${infile.ext}' &&
        strip-it
            --input '$infile.${infile.ext}'
            --output '$outfile'
            --noLog
            $noHeader
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
        <param argument='--noHeader' type='boolean' truevalue='--noHeader' falsevalue=''
            label='Do not print a header in the output file' />

    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="sdf" value="CID_3037.sdf"/>
            <param name="noHeader" value="false"/>
            <output name="outfile" file="Strip-it_on_CID3037.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[


.. class:: infomark

**What this tool does**

Strip-it is a program that extracts scaffolds from organic small molecules, 
based on predefined scaffold types. The scaffold types used by Strip-it include

    - `molecular frameworks`_ as originally described by Bemis and Murcko
    - `molecular frameworks and the reduced molecular frameworks`_ as described by Ansgar Schuffenhauer and coworkers
    - `scaffold topologies`_ as described by Sara Pollock and coworkers

.. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122
.. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
.. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680

-----

.. class:: infomark


**Input**

| - `SDF format`_
| - `SMILES format`_
| - `MOL2 format`_

.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
.. _MOL2 format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf


-----

.. class:: infomark

**Output**

A tabular file with the name and SMILES of the molecule in the first two 
columns; subsequent columns show scaffolds extracted by different methods.

+-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
|     NAME    |            MOLECULE            | RINGS_WITH_LINKERS_1 |  RINGS_WITH_LINKERS_2  |       MURCKO_1       | ... |
+=============+================================+======================+========================+======================+=====+
|  Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1  |   c1ccc(cc1)Nc1ccccc1  |  C1CCC(CC1)CC1CCCCC1 | ... |
+-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
| Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... |
+-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
|     ...     |              ...               |         ...          |           ...          |          ...         | ... |
+-------------+--------------------------------+----------------------+------------------------+----------------------+-----+

-----

.. class:: infomark

**Cite**

`Silicos-it`_ - strip-it

.. _Silicos-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/strip-it/1.0.2/strip-it.html


]]>
    </help>
    <citations>
        <citation type="bibtex">@misc{
            title={Strip-it},
            author={Silicos-it},
            year={2014},

        }</citation>
    </citations>
</tool>