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comparison CADDSuite-1.0.1/galaxyconfigs/tools/InputReader.xml @ 9:2cff9609f2c7

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author marcel
date Tue, 15 Nov 2011 10:40:26 -0500
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2 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
3 <tool id="inputreader" name="InputReader" version="1.0.1">
4 <description>generate QSAR data set</description>
5 <command interpreter="bash"><![CDATA[../../InputReader
6 #if str( $i ) != '' and str( $i ) != 'None' :
7 -i "$i"
8 #end if
9 #if str( $o ) != '' and str( $o ) != 'None' :
10 -o "$o"
11 #end if
12 #if str( $act ) != '' and str( $act ) != 'None' :
13 -act "$act"
14 #end if
15 #if str( $csv ) != '' and str( $csv ) != 'None' :
16 -csv "$csv"
17 #end if
18 #if str( $csv_nr ) != '' and str( $csv_nr ) != 'None' :
19 -csv_nr "$csv_nr"
20 #end if
21 #if str( $csv_sep ) != '' and str( $csv_sep ) != 'None' :
22 -csv_sep "$csv_sep"
23 #end if
24 #if str( $sdp ) != '' and str( $sdp ) != 'None' :
25 -sdp
26 #end if
27 #if str( $no_cd ) != '' and str( $no_cd ) != 'None' :
28 -no_cd
29 #end if
30 #if str( $no_cr ) != '' and str( $no_cr ) != 'None' :
31 -no_cr
32 #end if
33 #if str( $csv_cl ) != '' and str( $csv_cl ) != 'None' :
34 -csv_cl
35 #end if
36 #if str( $csv_dl ) != '' and str( $csv_dl ) != 'None' :
37 -csv_dl
38 #end if
39 | tail -n 5
40 ]]></command>
41 <inputs>
42 <param name="i" optional="false" label="input sd-file" type="data" format="sdf"/>
43 <param name="csv" optional="true" label="input csv-file w/ additional descriptors" type="data" format="csv"/>
44 <param name="act" optional="true" label="Optional: sd-property containing response values" area="true" type="text" size="1x15"/>
45 <param name="csv_nr" optional="true" label="Optional: no. of response variables in csv-file" type="text" area="true" size="1x5" value=""/>
46 <param name="csv_sep" optional="true" label="Optional: separator symbol in csv-file" type="text" area="true" size="1x5" value=""/>
47 <param name="sdp" optional="true" label="use sd-properties as additional descriptors" type="boolean" truevalue="true" falsevalue=""/>
48 <param name="no_cd" optional="true" label="do not center descriptors" type="boolean" truevalue="true" falsevalue=""/>
49 <param name="no_cr" optional="true" label="do not center response values" type="boolean" truevalue="true" falsevalue=""/>
50 <param name="csv_cl" optional="true" label="csv-file has compound (row) labels" type="boolean" truevalue="true" falsevalue=""/>
51 <param name="csv_dl" optional="true" label="csv-file has descriptor (column) labels" type="boolean" truevalue="true" falsevalue=""/>
52 </inputs>
53 <outputs>
54 <data name="o" format="dat"/>
55 </outputs>
56 <help>This tool reads input from sd-files and generate features for QSAR analysis.
57 Activity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'.
58 The following number of features will be automatically created for each molecule in your sd-file:
59
60 * 40 atom and bond count descriptors
61 * 2 connectivity indices (Balaban and Zagreb index)
62 * 4 partial charge descriptors
63 * 14 surface descriptors
64 * 133 topological descriptors (functional group counts)
65
66 If desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options.
67 Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).</help>
68 </tool>