comparison ob_grep.xml @ 14:985ab0acd514 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf

13:274193d6c443

<tool id="openbabel_obgrep" name="Compound search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>- an advanced molecular search program using SMARTS</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>
<![CDATA[

        #if $input_type.inp == 'single':

            label="Print a molecule only if the pattern occurs this often 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" help="Print matching molecules only when the number of heavy atoms equals 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>
        <expand macro="output_like_input"/>
    </outputs>
    <tests>
        <test>

Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files. Not all SMARTS features from the original implementation in the Daylight Toolkit are supported by OpenBabel; please have a look here_.

The search query can be submitted either as a single SMARTS pattern or as a file containing multiple SMARTS patterns.

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

-----

.. class:: infomark

14:985ab0acd514

<tool id="openbabel_obgrep" name="Compound search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>- an advanced molecular search program using SMARTS</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@">1</token>
    </macros>
    <options sanitize="False"/>
    <expand macro="requirements"/>
    <command>
<![CDATA[

        #if $input_type.inp == 'single':

            label="Print a molecule only if the pattern occurs this often 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" help="Print matching molecules only when the number of heavy atoms equals 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>
    <outputs>
        <expand macro="output_like_input"/>
    </outputs>
    <tests>
        <test>

Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files. Not all SMARTS features from the original implementation in the Daylight Toolkit are supported by OpenBabel; please have a look here_.

The search query can be submitted either as a single SMARTS pattern or as a file containing multiple SMARTS patterns.

.. _Obgrep: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#filtering-molecules-from-a-multimolecule-file
.. _here: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#smarts-descriptor

-----

.. class:: infomark