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1 <tool id="ctb_multi_obgrep" name="Multi Compound Search" version="0.1">
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2 <description>an advanced molecular grep program using SMARTS</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.2">openbabel</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7
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8 multi_obgrep.py
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9 -i $infile
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10 --iformat ${infile.ext}
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11 -q $query
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12 -o "${outfile}"
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13 $invert_matches
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14 --n-times $n_times
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15 $only_name
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16 $full_match
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17 $number_of_matches
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18 --processors 10
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19
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20 </command>
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21 <inputs>
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22 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/>
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23 <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
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24 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" falsevalue="" checked="false" />
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25 <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" />
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26 <param name="only_name" type="boolean" label="Only print the name of the molecules (-n)" truevalue="--only-name" falsevalue="" checked="false" />
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27 <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" />
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28 <param name="number_of_matches" type="boolean" label="Print the number of matches (-c)" truevalue="--number-of-matches" falsevalue="" checked="false" />
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29 </inputs>
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30 <outputs>
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31 <data name="outfile" format_source="infile" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 </test>
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36 </tests>
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37 <help>
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38
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39
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40 **What it does**
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41
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42 Providing a query file with SMARTS pattern in each line. These tool will run obgreg in parallel and merges the results.
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43
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44 -----
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45
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46 **Example**
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47
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48
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49
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50 </help>
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51 </tool>
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