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comparison galaxy_stubs/DockResultMerger.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: [Convert, combine and store]-->
4 <tool id="DockResultMerger" name="DockResultMerger" version="1.1.0">
5 <description>merge docking output files</description>
6 <macros>
7 <token name="@EXECUTABLE@">DockResultMerger</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>DockResultMerger
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 $param_score:
21 -score "$param_score"
22 #end if
23 #if $param_min:
24 -min $param_min
25 #end if
26 #if $param_max:
27 -max $param_max
28 #end if
29 #if $param_k:
30 -k $param_k
31 #end if
32 #if $param_rm:
33 -rm $param_rm
34 #end if
35 </command>
36 <inputs>
37 <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input files" help="(-i) "/>
38 <param name="param_score" type="text" size="30" value="score" label="score property name" help="(-score) ">
39 <sanitizer>
40 <valid initial="string.printable">
41 <remove value="'"/>
42 <remove value="&quot;"/>
43 </valid>
44 </sanitizer>
45 </param>
46 <param name="param_min" type="float" value="-30.0" label="minimal score value" help="(-min) "/>
47 <param name="param_max" type="float" value="0.0" label="maximal score value" help="(-max) "/>
48 <param name="param_k" type="integer" value="20" label="number of output molecules" help="(-k) "/>
49 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input files after merging" help="(-rm) "/>
50 </inputs>
51 <expand macro="advanced_options"/>
52 <outputs>
53 <data name="param_o" metadata_source="param_i" format="input"/>
54 </outputs>
55 <help>This tool merges and sorts molecule files as generated by docking or rescoring.
56
57 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.
58
59 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.
60
61 </help>
62 </tool>