Mercurial > repos > bgruening > openbabel
comparison subsearch/subsearch.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 |
|---|---|
| 2 <description>of fingerprint data sets</description> | 2 <description>of fingerprint data sets</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 subsearch.py | 9 subsearch.py |
| 9 -i $query | 10 -i $query |
| 10 --iformat "${query.ext}" | 11 --iformat "${query.ext}" |
| 11 --fastsearch-index "${os.path.join($fastsearch.extra_files_path,'molecule.fs')}" | 12 --fastsearch-index "${os.path.join($fastsearch.files_path,'molecule.fs')}" |
| 12 -o "${outfile}" | 13 -o "${outfile}" |
| 13 --oformat $oformat | 14 --oformat $oformat |
| 14 --max-candidates $max_candidates | 15 --max-candidates $max_candidates |
| 15 --processors 10 | 16 --processors "\${GALAXY_SLOTS:-12}" |
| 16 | 17 |
| 18 ]]> | |
| 17 </command> | 19 </command> |
| 18 <inputs> | 20 <inputs> |
| 19 <param name="query" type='data' format="tabular,smi,sdf,inchi,text" label="query"/> | 21 <param name="query" type='data' format="tabular,smi,sdf,inchi,text" label="query"/> |
| 20 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/> | 22 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/> |
| 21 <param name="max_candidates" size="6" type="integer" value="4000" label="The maximum number of candidates"/> | 23 <param name="max_candidates" size="6" type="integer" value="4000" label="The maximum number of candidates"/> |
| 40 <tests> | 42 <tests> |
| 41 <test> | 43 <test> |
| 42 </test> | 44 </test> |
| 43 </tests> | 45 </tests> |
| 44 <help> | 46 <help> |
| 47 <![CDATA[ | |
| 45 | 48 |
| 46 .. class:: infomark | 49 .. class:: infomark |
| 47 | 50 |
| 48 **What this tool does** | 51 **What this tool does** |
| 49 | 52 |
| 67 | 70 |
| 68 `Open Babel`_ | 71 `Open Babel`_ |
| 69 | 72 |
| 70 .. _Open Babel: http://openbabel.org/wiki/Main_Page | 73 .. _Open Babel: http://openbabel.org/wiki/Main_Page |
| 71 | 74 |
| 75 ]]> | |
| 72 </help> | 76 </help> |
| 73 </tool> | 77 </tool> |