Mercurial > repos > luis > ball

comparison galaxy_stubs/MolCombine.xml @ 2:605370bc1def draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author luis
date Tue, 12 Jul 2016 12:33:33 -0400
parents
children
comparison
equal deleted inserted replaced
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="MolCombine" name="MolCombine" version="1.1.0">
5 <description>combine molecular files</description>
6 <macros>
7 <token name="@EXECUTABLE@">MolCombine</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>MolCombine
13
14 #if $param_i1:
15 -i1 $param_i1
16 #end if
17 #if $param_i2:
18 -i2 $param_i2
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_o:
29 -o $param_o
30 #end if
31 #if $param_ignH:
32 -ignH $param_ignH
33 #end if
34 #if $param_replace_prop:
35 -replace_prop $param_replace_prop
36 #end if
37 #if $param_rm:
38 -rm $param_rm
39 #end if
40 </command>
41 <inputs>
42 <param name="param_i1" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file A" help="(-i1) "/>
43 <param name="param_i2" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file B" help="(-i2) "/>
44 <param name="param_mode" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="'intersection', 'union' or 'b_not_a'" help="(-mode) ">
45 <option value="intersection">intersection</option>
46 <option value=" union"> union</option>
47 <option value=" b_not_a"> b_not_a</option>
48 </param>
49 <param name="param_ignH" type="integer" min="0" max="1" optional="True" value="1" label="ignore hydrogens, i.e" help="(-ignH) match molecules to any protonation state"/>
50 <param name="param_replace_prop" type="integer" min="0" max="1" optional="True" value="0" label="replace properties from file 1 w/ those from file 2" help="(-replace_prop) "/>
51 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input files when finished" help="(-rm) "/>
52 </inputs>
53 <expand macro="advanced_options"/>
54 <outputs>
55 <data name="param_o" metadata_source="param_i1" format="input"/>
56 </outputs>
57 <help>This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged.
58
59 If you want to match molecules regardless of their protonation state, use option '-ignH'.
60
61 Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.
62
63 </help>
64 </tool>