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comparison galaxy_stubs/InputReader.xml @ 2:605370bc1def draft default tip

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author luis
date Tue, 12 Jul 2016 12:33:33 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [QuEasy (QSAR)]-->
4 <tool id="InputReader" name="InputReader" version="1.1.0">
5 <description>generate QSAR data set </description>
6 <macros>
7 <token name="@EXECUTABLE@">InputReader</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>InputReader
13
14 #if $param_i:
15 -i $param_i
16 #end if
17 #if $param_o:
18 -o $param_o
19 #end if
20 #if $param_act:
21 -act "$param_act"
22 #end if
23 #if $param_csv:
24 -csv $param_csv
25 #end if
26 #if $param_csv_nr:
27 -csv_nr $param_csv_nr
28 #end if
29 #if $param_csv_sep:
30 -csv_sep $param_csv_sep
31 #end if
32 #if $param_sdp:
33 -sdp $param_sdp
34 #end if
35 #if $param_no_cd:
36 -no_cd $param_no_cd
37 #end if
38 #if $param_no_cr:
39 -no_cr $param_no_cr
40 #end if
41 #if $param_csv_cl:
42 -csv_cl $param_csv_cl
43 #end if
44 #if $param_csv_dl:
45 -csv_dl $param_csv_dl
46 #end if
47 </command>
48 <inputs>
49 <param name="param_i" type="data" format="sdf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input sd-file" help="(-i) "/>
50 <param name="param_act" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="sd-property containing response values" help="(-act) ">
51 <sanitizer>
52 <valid initial="string.printable">
53 <remove value="'"/>
54 <remove value="&quot;"/>
55 </valid>
56 </sanitizer>
57 </param>
58 <param name="param_csv" type="data" format="csv" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input csv-file w/ additional descriptors" help="(-csv) "/>
59 <param name="param_csv_nr" type="integer" value="0" label="no. of response variables in csv-file" help="(-csv_nr) "/>
60 <param name="param_csv_sep" type="integer" value="0" label="separator symbol in csv-file" help="(-csv_sep) "/>
61 <param name="param_sdp" type="integer" min="0" max="1" optional="True" value="0" label="use sd-properties as additional descriptors" help="(-sdp) "/>
62 <param name="param_no_cd" type="integer" min="0" max="1" optional="True" value="0" label="do not center descriptors" help="(-no_cd) "/>
63 <param name="param_no_cr" type="integer" min="0" max="1" optional="True" value="0" label="do not center response values" help="(-no_cr) "/>
64 <param name="param_csv_cl" type="integer" min="0" max="1" optional="True" value="0" label="csv-file has compound (row) labels" help="(-csv_cl) "/>
65 <param name="param_csv_dl" type="integer" min="0" max="1" optional="True" value="0" label="csv-file has descriptor (column) labels" help="(-csv_dl) "/>
66 </inputs>
67 <expand macro="advanced_options"/>
68 <outputs>
69 <data name="param_o" format="dat"/>
70 </outputs>
71 <help>This tool reads input from sd-files and generate features for QSAR analysis.
72 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'.
73 The following number of features will be automatically created for each molecule in your sd-file:
74
75 * 40 atom and bond count descriptors
76 * 2 connectivity indices (Balaban and Zagreb index)
77 * 4 partial charge descriptors
78 * 14 surface descriptors
79 * 133 topological descriptors (functional group counts)
80
81 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.
82 Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).
83
84 </help>
85 </tool>