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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 08:34:39 -0400
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1 <tool id="_obgrep" name="Compound Search" version="@VERSION@.0">
2 <description>an advanced molecular grep program using SMARTS</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command>
9 <![CDATA[
10 obgrep
11 $invert_matches
12 #if $n_times:
13 -t $n_times
14 #end if
15 $only_name
16 $full_match
17 $number_of_matches
18 -i "${infile.ext}"
19 "${smarts_pattern}"
20 "${infile}"
21 > "${outfile}"
22 ]]>
23 </command>
24 <inputs>
25 <expand macro="infile_all_types"/>
26 <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
27 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" />
28 <param name="n_times" type="integer" value="" min="1" optional="True"
29 label="Print a molecule only if the pattern occurs # times inside the molecule" />
30 <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" />
31 <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" />
32 <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" />
33 </inputs>
34 <options sanitize="False"/>
35 <outputs>
36 <expand macro="output_like_input"/>
37 </outputs>
38 <tests>
39 <test>
40 <param name="infile" ftype="smi" value="8_mol.smi"/>
41 <param name="smarts_pattern" value="CO"/>
42 <param name="invert_matches" value="False" />
43 <param name="only_name" value="False" />
44 <param name="full_match" value="False" />
45 <param name="number_of_matches" value="False" />
46 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
47 </test>
48 </tests>
49 <help>
50 <![CDATA[
51
52 .. class:: infomark
53
54 **What this tool does**
55
56 Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
57 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
58
59
60 .. _Obgrep: http://openbabel.org/wiki/Obgrep
61 .. _here: http://openbabel.org/wiki/SMARTS
62
63 -----
64
65 .. class:: infomark
66
67 **Input**
68
69 | - `SD-Format`_
70 | - `SMILES Format`_
71
72 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
73 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
74
75 -----
76
77 .. class:: infomark
78
79 **Output**
80
81 Same as input format.
82
83 ]]>
84 </help>
85 <expand macro="citations"/>
86 </tool>