Mercurial > repos > bgruening > openbabel_multi_obgrep

comparison multi_obgrep.xml @ 0:69fdca56b2cd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author bgruening
date Sat, 20 May 2017 08:33:11 -0400
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1 <tool id="openbabel_multi_obgrep" name="Multi Compound Search" version="@VERSION@.0">
2 <description>an advanced molecular grep program using SMARTS</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="aggressive">
8 <![CDATA[
9
10 python $__tool_directory__/multi_obgrep.py
11 -i $infile
12 --iformat ${infile.ext}
13 -q $query
14 -o "${outfile}"
15 $invert_matches
16 --n-times $n_times
17 $only_name
18 $full_match
19 $number_of_matches
20 --processors "\${GALAXY_SLOTS:-12}"
21 ]]>
22 </command>
23 <inputs>
24 <expand macro="infile_all_types"/>
25 <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
26 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" falsevalue="" checked="false" />
27 <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" />
28 <param name="only_name" type="boolean" label="Only print the name of the molecules (-n)" truevalue="--only-name" falsevalue="" checked="false" />
29 <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" />
30 <param name="number_of_matches" type="boolean" label="Print the number of matches (-c)" truevalue="--number-of-matches" falsevalue="" checked="false" />
31 </inputs>
32 <outputs>
33 <expand macro="output_like_input"/>
34 </outputs>
35 <tests>
36 <test>
37 <param name="infile" ftype="smi" value="2_mol.smi"/>
38 <param name="query" value="pattern.smarts" />
39 <output name="outfile" ftype="smi" file="ob_multi_obgrep.smi" />
40 </test>
41 </tests>
42 <help>
43 <![CDATA[
44
45 .. class:: infomark
46
47 **What this tool does**
48
49 Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
50 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
51
52 .. _Obgrep: http://openbabel.org/wiki/Obgrep
53 .. _here: http://openbabel.org/wiki/SMARTS
54
55 -----
56
57 .. class:: infomark
58
59 **Input**
60
61 | - `SD-Format`_
62 | - `SMILES Format`_
63
64 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
65 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
66
67 -----
68
69 .. class:: infomark
70
71 **Output**
72
73 Same as input format.
74
75
76 ]]>
77 </help>
78 <expand macro="citations"/>
79 </tool>