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1 <tool id="ctb_remSmall" name="Remove small molecules" version="1.0">
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2 <description></description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 </requirements>
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7 <command>
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8 obabel
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9 -i"${infile.ext}"
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10 "${infile}"
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11 -ocopy
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12 -O "${outfile}"
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13 --filter "atoms > $cutoff"
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14 -e
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15 2>&1
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16 </command>
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17 <inputs>
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18 <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" />
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19 <param name="cutoff" size="3" type="integer" value="5" label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" />
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20 </inputs>
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21 <outputs>
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22 <data format_source="infile" name="outfile" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="infile" ftype="smi" value="3_mol.smi" />
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27 <param name="cutoff" value="5" />
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28 <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" />
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29 </test>
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30 </tests>
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31 <help>
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32
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33 .. class:: infomark
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34
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35 **What this tool does**
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36
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37 Filters a library of compounds and removes small molecules below a predefined input number of atoms.
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38
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39 -----
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40
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41 .. class:: warningmark
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42
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43 **Hint**
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44
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45 Some libraries may contain molecules without a 1D/3D descriptor. These molecules may provoke crashes of any other tool. It is strongly adviced to run this tool before proceeding to any further steps.
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46
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47 -----
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48
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49 .. class:: infomark
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50
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51 **Output**
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52
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53 Same as input format.
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54
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55 -----
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56
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57 .. class:: infomark
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58
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59 **Cite**
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60
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61 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_
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62
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63 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
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64
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65 `Open Babel`_
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66
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67 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
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68
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69 </help>
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70 </tool>
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