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comparison galaxy_stubs/ScoreAnalyzer.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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1:31013b5cd066 2:605370bc1def
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: [Analysis]-->
4 <tool id="ScoreAnalyzer" name="ScoreAnalyzer" version="1.1.0">
5 <description>generate ROC or enrichment plots</description>
6 <macros>
7 <token name="@EXECUTABLE@">ScoreAnalyzer</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>ScoreAnalyzer
13
14 #if $param_mode:
15 -mode
16 #if " " in str($param_mode):
17 "$param_mode"
18 #else
19 $param_mode
20 #end if
21 #end if
22 #if $param_title:
23 -title "$param_title"
24 #end if
25 #if $param_o:
26 -o $param_o
27 #end if
28 #if $param_i:
29 -i $param_i
30 #end if
31 #if $param_s:
32 -s "$param_s"
33 #end if
34 #if $param_e:
35 -e "$param_e"
36 #end if
37 #if $param_t:
38 -t "$param_t"
39 #end if
40 #if $param_b:
41 -b $param_b
42 #end if
43 </command>
44 <inputs>
45 <param name="param_mode" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="'roc', 'top50', 'scatter' or 'enrichment'" help="(-mode) ">
46 <option value="roc">roc</option>
47 <option value=" top50"> top50</option>
48 <option value=" scatter"> scatter</option>
49 <option value=" enrichment"> enrichment</option>
50 </param>
51 <param name="param_title" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="plot title" help="(-title) ">
52 <sanitizer>
53 <valid initial="string.printable">
54 <remove value="'"/>
55 <remove value="&quot;"/>
56 </valid>
57 </sanitizer>
58 </param>
59 <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file" help="(-i) "/>
60 <param name="param_s" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="score label" help="(-s) ">
61 <sanitizer>
62 <valid initial="string.printable">
63 <remove value="'"/>
64 <remove value="&quot;"/>
65 </valid>
66 </sanitizer>
67 </param>
68 <param name="param_e" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="binding-free-energy/class label name" help="(-e) ">
69 <sanitizer>
70 <valid initial="string.printable">
71 <remove value="'"/>
72 <remove value="&quot;"/>
73 </valid>
74 </sanitizer>
75 </param>
76 <param name="param_t" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="only in case of non-binary act" help="(-t) data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder">
77 <sanitizer>
78 <valid initial="string.printable">
79 <remove value="'"/>
80 <remove value="&quot;"/>
81 </valid>
82 </sanitizer>
83 </param>
84 <param name="param_b" type="integer" min="0" max="1" optional="True" value="0" label="binary experimental activity data" help="(-b) "/>
85 </inputs>
86 <expand macro="advanced_options"/>
87 <outputs>
88 <data name="param_o" format="eps"/>
89 </outputs>
90 <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring.
91
92 The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'.
93 The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
94
95 The output of this tool is a plot in form of an eps or png-file (as chosen).
96
97 </help>
98 </tool>