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comparison galaxy_stubs/PartialChargesCopy.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: [Preparation]-->
4 <tool id="PartialChargesCopy" name="PartialChargesCopy" version="1.1.0">
5 <description>transfer part. charges between files</description>
6 <macros>
7 <token name="@EXECUTABLE@">PartialChargesCopy</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>PartialChargesCopy
13
14 #if $param_i:
15 -i $param_i
16 #end if
17 #if $param_chr:
18 -chr $param_chr
19 #end if
20 #if $param_o:
21 -o $param_o
22 #end if
23 </command>
24 <inputs>
25 <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 molecule file" help="(-i) "/>
26 <param name="param_chr" type="data" format="mol2,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="file containing the same molecules as the input file, but with (different) partial charges" help="(-chr) "/>
27 </inputs>
28 <expand macro="advanced_options"/>
29 <outputs>
30 <data name="param_o" metadata_source="param_chr" format="input"/>
31 </outputs>
32 <help>This tool copies partial charges from a given file to the conformations read from a different file.
33 This can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties.
34
35 </help>
36 </tool>