Mercurial > repos > marcel > caddsuite_mac10_6

annotate CADDSuite/galaxyconfigs/tools/DockResultMerger.xml @ 0:8ce0411aaeb3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded CADDSuite version 0.94
author marcel
date Sun, 26 Jun 2011 14:01:09 -0400 (2011-06-26)
parents
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="dockresultmerger" name="DockResultMerger" version="0.94">
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
4 <description>merge docking output files</description>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../DockResultMerger
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
6 #for $s in $series_i
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
7 #if str( "${s.i.file_name}" ) != '' and str( "${s.i.file_name}" ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
8 -i "${s.i.file_name}"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
9 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
10 #end for
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
11 #if str( $o ) != '' and str( $o ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
12 -o "$o"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
13 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
14 #if str( $score ) != '' and str( $score ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
15 -score "$score"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
16 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
17 #if str( $min ) != '' and str( $min ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
18 -min "$min"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
19 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
20 #if str( $max ) != '' and str( $max ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
21 -max "$max"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
22 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
23 #if str( $k ) != '' and str( $k ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
24 -k "$k"
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
25 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
26 #if str( $rm ) != '' and str( $rm ) != 'None' :
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
27 -rm
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
28 #end if
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
29 | tail -n 5
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
30 ]]></command>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
31 <inputs>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
32 <repeat name="series_i" title="input files" min="1">
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
33 <param name="i" label="input files" optional="false" type="data" format="mol2/sdf/drf"/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
34 </repeat>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
35 <param name="score" label="score property name" optional="true" area="true" type="text" size="1x15" value="score"/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
36 <param name="min" label="minimal score value" optional="true" type="text" area="true" size="1x5" value=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
37 <param name="max" label="maximal score value" optional="true" type="text" area="true" size="1x5" value=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
38 <param name="k" label="number of output molecules" optional="true" type="text" area="true" size="1x5" value=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
39 <param name="rm" label="remove input files after merging" optional="true" type="boolean" truevalue="true" falsevalue=""/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
40 </inputs>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
41 <outputs>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
42 <data name="o" format="mol2/sdf/drf" format_source="i"/>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
43 </outputs>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
44 <help>This tool merges and sorts molecule files as generated by docking or rescoring.
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
45
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
46 You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file.
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
47
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
48 Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.</help>
8ce0411aaeb3 Uploaded CADDSuite version 0.94
marcel
parents:
diff changeset
49 </tool>