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comparison galaxy_stubs/Converter.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: [Convert, combine and store]-->
4 <tool id="Converter" name="Converter" version="1.1.0">
5 <description>interconvert molecular file-formats</description>
6 <macros>
7 <token name="@EXECUTABLE@">Converter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>Converter
13
14 #if $param_i:
15 -i $param_i
16 #end if
17 #if $param_if:
18 -if
19 #if " " in str($param_if):
20 "$param_if"
21 #else
22 $param_if
23 #end if
24 #end if
25 #if $param_o:
26 -o $param_o
27 #end if
28 #if $param_of:
29 -of
30 #if " " in str($param_of):
31 "$param_of"
32 #else
33 $param_of
34 #end if
35 #end if
36 #if $param_rm:
37 -rm $param_rm
38 #end if
39 </command>
40 <inputs>
41 <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input filename" help="(-i) "/>
42 <param name="param_if" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input format" help="(-if) ">
43 <option value="mol2">mol2</option>
44 <option value=" sdf"> sdf</option>
45 <option value=" drf"> drf</option>
46 <option value=" pdb"> pdb</option>
47 <option value=" ac"> ac</option>
48 <option value=" ent"> ent</option>
49 <option value=" brk"> brk</option>
50 <option value=" hin"> hin</option>
51 <option value=" mol"> mol</option>
52 <option value=" xyz"> xyz</option>
53 <option value=" mol2.gz"> mol2.gz</option>
54 <option value=" sdf.gz"> sdf.gz</option>
55 <option value=" drf.gz"> drf.gz</option>
56 <option value=" pdb.gz"> pdb.gz</option>
57 <option value=" ac.gz"> ac.gz</option>
58 <option value=" ent.gz"> ent.gz</option>
59 <option value=" brk.gz"> brk.gz</option>
60 <option value=" hin.gz"> hin.gz</option>
61 <option value=" mol.gz"> mol.gz</option>
62 <option value=" xyz.gz"> xyz.gz</option>
63 </param>
64 <param name="param_of" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="output format" help="(-of) ">
65 <option value="mol2">mol2</option>
66 <option value=" sdf"> sdf</option>
67 <option value=" drf"> drf</option>
68 <option value=" pdb"> pdb</option>
69 <option value=" ac"> ac</option>
70 <option value=" ent"> ent</option>
71 <option value=" brk"> brk</option>
72 <option value=" hin"> hin</option>
73 <option value=" mol"> mol</option>
74 <option value=" xyz"> xyz</option>
75 <option value=" mol2.gz"> mol2.gz</option>
76 <option value=" sdf.gz"> sdf.gz</option>
77 <option value=" drf.gz"> drf.gz</option>
78 <option value=" pdb.gz"> pdb.gz</option>
79 <option value=" ac.gz"> ac.gz</option>
80 <option value=" ent.gz"> ent.gz</option>
81 <option value=" brk.gz"> brk.gz</option>
82 <option value=" hin.gz"> hin.gz</option>
83 <option value=" mol.gz"> mol.gz</option>
84 <option value=" xyz.gz"> xyz.gz</option>
85 </param>
86 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
87 </inputs>
88 <expand macro="advanced_options"/>
89 <outputs>
90 <data name="param_o" metadata_source="param_i" format="input"/>
91 </outputs>
92 <help>This tool can be used to convert between different molecular file-formats.
93 Supported formats are mol2,sdf,drf,pdb,ac,ent,brk,hin,mol,xyz,mol2.gz,sdf.gz,drf.gz,pdb.gz,ac.gz,ent.gz,brk.gz,hin.gz,mol.gz,xyz.gz. File extensions of input and output filenames are ignored.
94
95 </help>
96 </tool>