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comparison galaxy_stubs/PropertyModifier.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: [Preparation]-->
4 <tool id="PropertyModifier" name="PropertyModifier" version="1.1.0">
5 <description>modify molecule property tags</description>
6 <macros>
7 <token name="@EXECUTABLE@">PropertyModifier</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>PropertyModifier
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 $param_mode:
21 -mode
22 #if " " in str($param_mode):
23 "$param_mode"
24 #else
25 $param_mode
26 #end if
27 #end if
28 #if $param_name:
29 -name "$param_name"
30 #end if
31 #if $param_value:
32 -value "$param_value"
33 #end if
34 #if $param_new_name:
35 -new_name "$param_new_name"
36 #end if
37 #if $param_rm:
38 -rm $param_rm
39 #end if
40 </command>
41 <inputs>
42 <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file" help="(-i) "/>
43 <param name="param_mode" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="'delete', 'add' or 'rename' properties" help="(-mode) ">
44 <option value="add">add</option>
45 <option value=" rename"> rename</option>
46 <option value=" delete"> delete</option>
47 </param>
48 <param name="param_name" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="property name ('all' will erase all properties if in delete-mode)" help="(-name) ">
49 <sanitizer>
50 <valid initial="string.printable">
51 <remove value="'"/>
52 <remove value="&quot;"/>
53 </valid>
54 </sanitizer>
55 </param>
56 <param name="param_value" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="property value (in case of prop. adding only)" help="(-value) ">
57 <sanitizer>
58 <valid initial="string.printable">
59 <remove value="'"/>
60 <remove value="&quot;"/>
61 </valid>
62 </sanitizer>
63 </param>
64 <param name="param_new_name" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="new property name (in case of renaming only)" help="(-new_name) ">
65 <sanitizer>
66 <valid initial="string.printable">
67 <remove value="'"/>
68 <remove value="&quot;"/>
69 </valid>
70 </sanitizer>
71 </param>
72 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
73 </inputs>
74 <expand macro="advanced_options"/>
75 <outputs>
76 <data name="param_o" metadata_source="param_i" format="input"/>
77 </outputs>
78 <help>With this tools you can add, rename or delete molecule property tags.
79 These tags can for example contain information about scores, binding-free-energy, IDs or names for the resp. molecule.
80 The output of this tool is a molecule file in which the desired property tags have been added/renamed/deleted (as chosen).
81
82 </help>
83 </tool>