Mercurial > repos > bgruening > openbabel_subsearch

comparison subsearch.xml @ 7:ab2b9d87b067 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:34:19 -0400
parents 98e12cc1f3a8
children 171c94786a56
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6:9a83f24376b0 7:ab2b9d87b067
17 --processors "\${GALAXY_SLOTS:-12}" 17 --processors "\${GALAXY_SLOTS:-12}"
18 18
19 ]]> 19 ]]>
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <param name="query" type='data' format="tabular,smi,sdf,inchi,txt" label="query"/> 22 <param name="query" type='data' format="tabular,smi,sdf,inchi,txt" label="Query"/>
23 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index" help="The OpenBabel fastsearch index can be created with the convert tool."/> 23 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index" help="The OpenBabel fastsearch index can be created with the compound conversion tool."/>
24 <param name="max_candidates" type="integer" value="4000" label="The maximum number of candidates"/> 24 <param name="max_candidates" type="integer" value="4000" label="Maximum number of candidates"/>
25 <param name='oformat' type='select' format='text' label="Output format."> 25 <param name='oformat' type='select' format='text' label="Output format">
26 <option value='smi'>SMILES</option> 26 <option value='smi'>SMILES</option>
27 <option value='inchi'>InChI</option> 27 <option value='inchi'>InChI</option>
28 <option value='sdf'>SD-Files</option> 28 <option value='sdf'>SD-Files</option>
29 <option value='mol2'>mol2</option> 29 <option value='mol2'>mol2</option>
30 <option value='names'>Return the molecule names only</option> 30 <option value='names'>Return the molecule names only</option>
42 </outputs> 42 </outputs>
43 <tests> 43 <tests>
44 <test> 44 <test>
45 <param name="query" ftype="sdf" value="CID_2244.sdf"/> 45 <param name="query" ftype="sdf" value="CID_2244.sdf"/>
46 <param name="fastsearch" value="ob_convert_on_CID2244_obfs.txt" ftype="obfs" > 46 <param name="fastsearch" value="ob_convert_on_CID2244_obfs.txt" ftype="obfs" >
47 <composite_data value='molecule.sdf' ftype="sdf"/> 47 <composite_data value='molecule.sdf' />
48 <composite_data value='molecule.fs'/> 48 <composite_data value='molecule.fs'/>
49 </param> 49 </param>
50 <param name="oformat" value="names" /> 50 <param name="oformat" value="names" />
51 <output name="outfile" ftype="tabular" file="ob_subsearch_with_CID2244.tabular" /> 51 <output name="outfile" ftype="tabular" file="ob_subsearch_with_CID2244.tabular" />
52 </test> 52 </test>