annotate ob_genProp.xml @ 12:a72ae2711a97 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"

<tool id="openbabel_genProp" name="Compute physico-chemical properties" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>for a set of molecules</description>
    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[
    python '$__tool_directory__/ob_genProp.py'
      -i '${infile}'
      --iformat '${infile.ext}'
      --oformat '${output_opts.output_format_types}'
      #if $output_opts.output_format_types == 'table':
            --header $output_opts.header
      #end if
      -o '${outfile}'
]]>
    </command>
    <inputs>
        <expand macro="infile_all_types"/>
        <conditional name="output_opts">
            <param name="output_format_types" type="select" label="Specify output format file">
                <option value="table">Tabular format</option>
                <option value="sdf" selected="True">sdf</option>
            </param>
            <when value="table">
                <param name="header" type="boolean" checked="False" label="Print the headers of the table as the first row of the table"/>
            </when>
            <when value="sdf" />
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="outfile" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="output_opts.output_format_types" value="sdf" format="sdf"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
            <param name="output_format_types" value="sdf" />
            <output name="outfile" ftype="sdf" file="ob_genprop_on_CID2244.sdf" lines_diff="2" />
        </test>
        <test>
            <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
            <param name="output_format_types" value="table" />
            <param name="header" value="true" />
            <output name="outfile" ftype="tabular" file="ob_genprop_on_CID2244.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Computes several physico-chemical properties for a set of molecules.

The following physico-chemical properties and descriptors are computed for each molecule:

	- number of hydrogen-bond donor and acceptor groups

	- number of rotatable bonds

	- logP

	- number of rings

	- number of heavy atoms

	- molecular weight

	- total Polar Surface Area

	- molecular refractivity

	- Canonical SMILES

	- InChI string

	- InChI-Key

	- Spectrophores(TM)

-----

.. class:: infomark

**Input**

- SDF_
- MOL2_

.. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
.. _MOL2: http://www.tripos.com/index.php?family=modules,SimplePage,Mol2_File_Format2009

3D coordinates of the molecules have to be provided.

-----

.. class:: warningmark

**Hint** the generation of Spectrophores(TM) requires the previous addition of explicit hydrogen atoms and the proper definition of 3D coordinates. The user is directed towards the corresponding tools if accurate Spectrophores(TM) descriptors are required.

-----

.. class:: infomark

**Output**

Either a SD-file containing several computed physico-chemical properties stored as metadata or a tabular file with the metadata stored in columns.

-----

.. class:: infomark

**Cite**

N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_

Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel.

.. |Spectrophores (TM)| unicode:: Spectrophores U+2122

`Open Babel`_

.. _Open Babel: http://openbabel.org/wiki/Main_Page
.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
.. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html


]]>
    </help>
    <expand macro="citations">
        <citation type="doi">10.1186/1752-153X-2-5</citation>
    </expand>
</tool>