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author bgruening
date Wed, 15 Jul 2015 12:13:08 -0400
parents 527ecd2fc500
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1:b52872a1755a 2:125da3a296ca
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 <requirement type="package" version="1.7.1">numpy</requirement> 5 <requirement type="package" version="1.7.1">numpy</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python"> 7 <command interpreter="python">
8 <![CDATA[
8 ob_spectrophore_search.py 9 ob_spectrophore_search.py
9 --target $target 10 --target $target
10 --library $library 11 --library $library
11 --output $outfile 12 --output $outfile
12 --column $column 13 --column $column
14 ]]>
13 </command> 15 </command>
14 <inputs> 16 <inputs>
15 <param name="target" type="data" format="sdf" label="Target molecule in SDF format (it must contain its Spectrophores(TM) stored as meta-data)"/> 17 <param name="target" type="data" format="sdf" label="Target molecule in SDF format (it must contain its Spectrophores(TM) stored as meta-data)"/>
16 <param name="library" type="data" format="tabular" label="Tabular file with pre-computed Spectrophores(TM) in one column"/> 18 <param name="library" type="data" format="tabular" label="Tabular file with pre-computed Spectrophores(TM) in one column"/>
17 <param name="column" label="Specify the column number containing the Spectrophores(TM) descriptors" type="data_column" data_ref="library" accept_default="true" /> 19 <param name="column" label="Specify the column number containing the Spectrophores(TM) descriptors" type="data_column" data_ref="library" accept_default="true" />
26 <param name="column" value="8" /> 28 <param name="column" value="8" />
27 <output name="outfile" ftype="tabular" file="ob_spectrophore_search.tabular" /> 29 <output name="outfile" ftype="tabular" file="ob_spectrophore_search.tabular" />
28 </test> 30 </test>
29 </tests> 31 </tests>
30 <help> 32 <help>
33 <![CDATA[
31 34
32 .. class:: infomark 35 .. class:: infomark
33 36
34 **What does this tool do?** 37 **What does this tool do?**
35 38
57 60
58 ----- 61 -----
59 62
60 .. class:: infomark 63 .. class:: infomark
61 64
62 **Input** 65 **Input**
63 66
64 The target molecule must be a SD formatted file with the |Spectrophores (TM)| descriptors stored as metadata. Such files can be generated using the *Compute physico-chemical properties* tool. 67 The target molecule must be a SD formatted file with the |Spectrophores (TM)| descriptors stored as metadata. Such files can be generated using the *Compute physico-chemical properties* tool.
65 68
66 ----- 69 -----
67 70
82 Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel. 85 Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel.
83 86
84 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf 87 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
85 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html 88 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html
86 89
90 ]]>
87 </help> 91 </help>
88 </tool> 92 </tool>