annotate filter/ob_grep.xml @ 1:b52872a1755a draft

update cheminfolib dependency

<tool id="ctb_obgrep" name="Compound Search" version="0.1">
    <description>an advanced molecular grep program using SMARTS</description>
    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command>
        ## The command is a Cheetah template which allows some Python based syntax.
        ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
        obgrep

        $invert_matches
        #if $n_times != 0:
            -t $n_times
        #end if

        $only_name
        $full_match
        $number_of_matches
        -i ${infile.ext}
        "${smarts_pattern}"
        "${infile}"
        > "${outfile}" 2>&#38;1
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format."/>
        <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
        <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" />
        <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" />
        <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" />
        <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern" truevalue="-f" falsevalue="" checked="false" />
        <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" />
    </inputs>
    <options sanitize="False"/>
    <outputs>
        <data name="outfile" format_source="infile" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
    <test>
        <param name="infile" ftype="smi" value="8_mol.smi"/>
        <param name="smarts_pattern" value="CO"/>
        <param name="invert_matches" value="" />
        <param name="n_times" value="0"/>
        <param name="only_name" value="" />
        <param name="full_match" value="" />
        <param name="number_of_matches" value="" />
        <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
    </test>
    </tests>
    <help>

.. class:: infomark

**What this tool does**

Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.


.. _Obgrep: http://openbabel.org/wiki/Obgrep
.. _here: http://openbabel.org/wiki/SMARTS

-----

.. class:: infomark

**Input**

| - `SD-Format`_
| - `SMILES Format`_

.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

-----

.. class:: infomark

**Output**

Same as input format.

-----

.. class:: infomark

**Cite**

N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_

.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33

`Open Babel`_

.. _`Open Babel`: http://openbabel.org/wiki/Main_Page

    </help>
</tool>