annotate CADDSuite-1.6/galaxyconfigs/tools/ScoreAnalyzer.xml @ 8:dbb480e39d95 draft

Uploaded
author marcel
date Sat, 15 Dec 2012 13:15:46 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
1
dbb480e39d95 Uploaded
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.-->
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
3 <tool id="scoreanalyzer" name="ScoreAnalyzer" version="1.6">
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
4 <description>generate ROC or enrichment plots</description>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../ScoreAnalyzer
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
6 #if str( $mode ) != '' and str( $mode ) != 'None' :
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
7 -mode "$mode"
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
8 #end if
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
9 #if str( $title ) != '' and str( $title ) != 'None' :
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
10 -title "$title"
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
11 #end if
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
12 #if str( $o ) != '' and str( $o ) != 'None' :
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
13 -o "$o"
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
14 #end if
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
15 #if str( $i ) != '' and str( $i ) != 'None' :
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
16 -i "$i"
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
17 #end if
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
18 #if str( $s ) != '' and str( $s ) != 'None' :
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
19 -s "$s"
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
20 #end if
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
21 #if str( $e ) != '' and str( $e ) != 'None' :
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
22 -e "$e"
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
23 #end if
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
24 #if str( $t ) != '' and str( $t ) != 'None' :
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
25 -t "$t"
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
26 #end if
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
27 #if str( $b ) != '' and str( $b ) != 'None' :
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
28 -b
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
29 #end if
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
30 | tail -n 5
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
31 ]]></command>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
32 <inputs>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
33 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
34 <param name="mode" optional="false" label="'roc', 'top50', 'scatter' or 'enrichment'" type="select">
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
35 <option value="roc">roc</option>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
36 <option value="top50">top50</option>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
37 <option value="scatter">scatter</option>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
38 <option value="enrichment">enrichment</option>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
39 </param>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
40 <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
41 <param name="s" optional="false" label="score label" area="true" type="text" size="1x15" value="score"/>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
42 <param name="e" optional="false" label="binding-free-energy/class label name" area="true" type="text" size="1x15" value="binding_free_energy"/>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
43 <param name="t" optional="true" label="Optional: only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" area="true" type="text" size="1x15"/>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
44 <param name="b" optional="true" label="binary experimental activity data" type="boolean" truevalue="true" falsevalue=""/>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
45 </inputs>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
46 <outputs>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
47 <data name="o" format="png"/>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
48 </outputs>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
49 <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring.
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
50
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
51 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'.
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
52 The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
53
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
54 The output of this tool is a plot in form of an eps or png-file (as chosen).</help>
dbb480e39d95 Uploaded
marcel
parents:
diff changeset
55 </tool>