Mercurial > repos > bgruening > openbabel
comparison filter/ob_remSmall.xml @ 2:125da3a296ca draft default tip
Uploaded
| author | bgruening |
|---|---|
| date | Wed, 15 Jul 2015 12:13:08 -0400 |
| parents | 527ecd2fc500 |
| children |
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| 1:b52872a1755a | 2:125da3a296ca |
|---|---|
| 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> | 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="2.3.2">openbabel</requirement> | 5 <requirement type="package" version="2.3.2">openbabel</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <command> | 7 <command> |
| 8 <![CDATA[ | |
| 8 obabel | 9 obabel |
| 9 -i"${infile.ext}" | 10 -i"${infile.ext}" |
| 10 "${infile}" | 11 "${infile}" |
| 11 -ocopy | 12 -ocopy |
| 12 -O "${outfile}" | 13 -O "${outfile}" |
| 13 --filter "atoms > $cutoff" | 14 --filter "atoms > $cutoff" |
| 14 -e | 15 -e |
| 15 2>&1 | 16 2>&1 |
| 17 ]]> | |
| 16 </command> | 18 </command> |
| 17 <inputs> | 19 <inputs> |
| 18 <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" /> | 20 <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" /> |
| 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)" /> | 21 <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)" /> |
| 20 </inputs> | 22 </inputs> |
| 27 <param name="cutoff" value="5" /> | 29 <param name="cutoff" value="5" /> |
| 28 <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" /> | 30 <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" /> |
| 29 </test> | 31 </test> |
| 30 </tests> | 32 </tests> |
| 31 <help> | 33 <help> |
| 34 <![CDATA[ | |
| 32 | 35 |
| 33 .. class:: infomark | 36 .. class:: infomark |
| 34 | 37 |
| 35 **What this tool does** | 38 **What this tool does** |
| 36 | 39 |
| 64 | 67 |
| 65 `Open Babel`_ | 68 `Open Babel`_ |
| 66 | 69 |
| 67 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page | 70 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page |
| 68 | 71 |
| 72 ]]> | |
| 69 </help> | 73 </help> |
| 70 </tool> | 74 </tool> |