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author bgruening
date Wed, 15 Jul 2015 12:13:08 -0400
parents 527ecd2fc500
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1:b52872a1755a 2:125da3a296ca
2 <description>an advanced molecular grep program using SMARTS</description> 2 <description>an advanced molecular grep program using SMARTS</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.3.2">openbabel</requirement> 4 <requirement type="package" version="2.3.2">openbabel</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command interpreter="python">
7 <![CDATA[
7 8
8 multi_obgrep.py 9 multi_obgrep.py
9 -i $infile 10 -i $infile
10 --iformat ${infile.ext} 11 --iformat ${infile.ext}
11 -q $query 12 -q $query
13 $invert_matches 14 $invert_matches
14 --n-times $n_times 15 --n-times $n_times
15 $only_name 16 $only_name
16 $full_match 17 $full_match
17 $number_of_matches 18 $number_of_matches
18 --processors 10 19 --processors "\${GALAXY_SLOTS:-12}"
19 20
21 ]]>
20 </command> 22 </command>
21 <inputs> 23 <inputs>
22 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/> 24 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/>
23 <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/> 25 <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
24 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" falsevalue="" checked="false" /> 26 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" falsevalue="" checked="false" />
33 <tests> 35 <tests>
34 <test> 36 <test>
35 </test> 37 </test>
36 </tests> 38 </tests>
37 <help> 39 <help>
40 <![CDATA[
38 41
39 .. class:: infomark 42 .. class:: infomark
40 43
41 **What this tool does** 44 **What this tool does**
42 45
78 81
79 `Open Babel`_ 82 `Open Babel`_
80 83
81 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page 84 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
82 85
86 ]]>
83 </help> 87 </help>
84 </tool> 88 </tool>