annotate CADDSuite/galaxyconfigs/tools/InputReader.xml @ 1:0dcf542923ab

Uploaded
author g2cmnty@test-web1.g2.bx.psu.edu
date Tue, 28 Jun 2011 10:39:47 -0400
parents 8ce0411aaeb3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
1
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
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.-->
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
3 <tool id="inputreader" name="InputReader" version="1.1">
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
4 <description>generate QSAR data set</description>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../InputReader
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
6 #if str( $i ) != '' and str( $i ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
7 -i "$i"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
8 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
9 #if str( $o ) != '' and str( $o ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
10 -o "$o"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
11 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
12 #if str( $act ) != '' and str( $act ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
13 -act "$act"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
14 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
15 #if str( $csv ) != '' and str( $csv ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
16 -csv "$csv"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
17 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
18 #if str( $csv_nr ) != '' and str( $csv_nr ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
19 -csv_nr "$csv_nr"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
20 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
21 #if str( $csv_sep ) != '' and str( $csv_sep ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
22 -csv_sep "$csv_sep"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
23 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
24 #if str( $sdp ) != '' and str( $sdp ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
25 -sdp
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
26 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
27 #if str( $no_cd ) != '' and str( $no_cd ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
28 -no_cd
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
29 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
30 #if str( $no_cr ) != '' and str( $no_cr ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
31 -no_cr
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
32 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
33 #if str( $csv_cl ) != '' and str( $csv_cl ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
34 -csv_cl
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
35 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
36 #if str( $csv_dl ) != '' and str( $csv_dl ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
37 -csv_dl
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
38 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
39 | tail -n 5
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
40 ]]></command>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
41 <inputs>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
42 <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
43 <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
44 <param name="act" label="sd-property containing response values" optional="true" area="true" type="text" size="1x15"/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
45 <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
46 <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
47 <param name="sdp" label="use sd-properties as additional descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
48 <param name="no_cd" label="do not center descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
49 <param name="no_cr" label="do not center response values" optional="true" type="boolean" truevalue="true" falsevalue=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
50 <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
51 <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
52 </inputs>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
53 <outputs>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
54 <data name="o" format="dat"/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
55 </outputs>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
56 <help>This tool reads input from sd-files and generate features for QSAR analysis.
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
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'.
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
58 The following number of features will be automatically created for each molecule in your sd-file:
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
59
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
60 * 40 atom and bond count descriptors
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
61 * 2 connectivity indices (Balaban and Zagreb index)
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
62 * 4 partial charge descriptors
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
63 * 14 surface descriptors
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
64 * 133 topological descriptors (functional group counts)
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
65
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
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.
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
67 Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).</help>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
68 </tool>