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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:05:06 +0000
parents 78640d0127ce
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13:274193d6c443 14:985ab0acd514
1 <tool id="openbabel_obgrep" name="Compound search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="openbabel_obgrep" name="Compound search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>- an advanced molecular search program using SMARTS</description> 2 <description>- an advanced molecular search program using SMARTS</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> 3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <token name="@GALAXY_VERSION@">0</token> 6 <token name="@GALAXY_VERSION@">1</token>
7 </macros> 7 </macros>
8 <options sanitize="False"/>
8 <expand macro="requirements"/> 9 <expand macro="requirements"/>
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 12
12 #if $input_type.inp == 'single': 13 #if $input_type.inp == 'single':
57 label="Print a molecule only if the pattern occurs this often inside the molecule" /> 58 label="Print a molecule only if the pattern occurs this often inside the molecule" />
58 <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" /> 59 <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" />
59 <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" /> 60 <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" />
60 <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" /> 61 <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" />
61 </inputs> 62 </inputs>
62 <options sanitize="False"/>
63 <outputs> 63 <outputs>
64 <expand macro="output_like_input"/> 64 <expand macro="output_like_input"/>
65 </outputs> 65 </outputs>
66 <tests> 66 <tests>
67 <test> 67 <test>
90 90
91 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_. 91 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_.
92 92
93 The search query can be submitted either as a single SMARTS pattern or as a file containing multiple SMARTS patterns. 93 The search query can be submitted either as a single SMARTS pattern or as a file containing multiple SMARTS patterns.
94 94
95 .. _Obgrep: http://openbabel.org/wiki/Obgrep 95 .. _Obgrep: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#filtering-molecules-from-a-multimolecule-file
96 .. _here: http://openbabel.org/wiki/SMARTS 96 .. _here: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#smarts-descriptor
97 97
98 ----- 98 -----
99 99
100 .. class:: infomark 100 .. class:: infomark
101 101