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comparison galaxy_stubs/SeparateMolecules.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="SeperateMolecules" name="SeperateMolecules" version="1.1.0">
5 <description>Split each multi molecule entry to separate single molecule entries</description>
6 <macros>
7 <token name="@EXECUTABLE@">SeperateMolecules</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>SeperateMolecules
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_min_atoms:
21 -min_atoms $param_min_atoms
22 #end if
23 #if $param_all:
24 -all $param_all
25 #end if
26 </command>
27 <inputs>
28 <param name="param_i" type="data" format="sdf,sd,mol2,mol" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file (mol mol2 sd sdf)" help="(-i) "/>
29 <param name="param_min_atoms" type="integer" value="0" label="only keep molecules having at least a minimal number of atoms" help="(-min_atoms) "/>
30 <param name="param_all" type="integer" min="0" max="1" optional="True" value="0" label="keep all contained molecules, but each in separated entries" help="(-all) "/>
31 </inputs>
32 <expand macro="advanced_options"/>
33 <outputs>
34 <data name="param_o" metadata_source="param_i" format="input"/>
35 </outputs>
36 <help>This tool splits each molecule entry contained in a structure file (mol, sdf, mol2) into possibly multiple molecule entries, so that the new entries contain only a single connected molecule. The results will always be written to a single structure file in the same format as the input format, or a sdf-file in the case of a mol input file. The tool works with the given bond information, which needs to be correct.
37
38 Standard behaviour: only the largest molecule from each entry is retained ('largest' according to the number of atoms).
39
40 Optional parameters:
41 Retain all molecules contained in a molecule entry ('-all'). Alternatively the minimal number of atoms required for a molecule to be kept can be specified ('-min_atoms').
42
43 </help>
44 </tool>