annotate multi_obgrep.xml @ 4:e1e344bd8a84 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c84729ec58f7f52d594066158afed175208d3d66

<tool id="openbabel_multi_obgrep" name="Multi Compound Search" version="@VERSION@.0">
    <description>an advanced molecular grep program using SMARTS</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[

    python $__tool_directory__/multi_obgrep.py
        -i $infile
        --iformat ${infile.ext}
        -q $query
        -o "${outfile}"
        $invert_matches
        --n-times $n_times
        $only_name
        $full_match
        $number_of_matches
        --processors "\${GALAXY_SLOTS:-12}"
]]>
    </command>
    <inputs>
        <expand macro="infile_all_types"/>
        <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
        <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" 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 (-n)" truevalue="--only-name" 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 (-f)" truevalue="--full-match" falsevalue="" checked="false" />
        <param name="number_of_matches" type="boolean" label="Print the number of matches (-c)" truevalue="--number-of-matches" falsevalue="" checked="false" />
    </inputs>
    <outputs>
        <expand macro="output_like_input"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="smi" value="2_mol.smi"/>
            <param name="query" value="pattern.smarts" />
            <output name="outfile" ftype="smi" file="ob_multi_obgrep.smi" />
        </test>
    </tests>
    <help>
<![CDATA[

.. 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.


]]>
    </help>
    <expand macro="citations"/>
</tool>