2
|
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="MolFilter" name="MolFilter" version="0.9">
|
|
5 <description>filter molecule files </description>
|
|
6 <macros>
|
|
7 <token name="@EXECUTABLE@">MolFilter</token>
|
|
8 <import>macros.xml</import>
|
|
9 </macros>
|
|
10 <expand macro="stdio"/>
|
|
11 <expand macro="requirements"/>
|
|
12 <command>MolFilter
|
|
13
|
|
14 #if $param_i:
|
|
15 -i $param_i
|
|
16 #end if
|
|
17 #if $param_min_logP:
|
|
18 -min_logP $param_min_logP
|
|
19 #end if
|
|
20 #if $param_max_logP:
|
|
21 -max_logP $param_max_logP
|
|
22 #end if
|
|
23 #if $param_min_MW:
|
|
24 -min_MW $param_min_MW
|
|
25 #end if
|
|
26 #if $param_max_MW:
|
|
27 -max_MW $param_max_MW
|
|
28 #end if
|
|
29 #if $param_q:
|
|
30 -q $param_q
|
|
31 #end if
|
|
32 #if $param_min_sim:
|
|
33 -min_sim $param_min_sim
|
|
34 #end if
|
|
35 #if $param_max_sim:
|
|
36 -max_sim $param_max_sim
|
|
37 #end if
|
|
38 #if $param_smarts:
|
|
39 -smarts "$param_smarts"
|
|
40 #end if
|
|
41 #if $param_smarts_file:
|
|
42 -smarts_file $param_smarts_file
|
|
43 #end if
|
|
44 #if $param_o:
|
|
45 -o $param_o
|
|
46 #end if
|
|
47 #if $param_quiet:
|
|
48 -quiet $param_quiet
|
|
49 #end if
|
|
50 #if $param_rm:
|
|
51 -rm $param_rm
|
|
52 #end if
|
|
53 </command>
|
|
54 <inputs>
|
|
55 <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule-file" help="(-i) "/>
|
|
56 <param name="param_min_logP" type="float" value="0.0" label="minimal logP value" help="(-min_logP) "/>
|
|
57 <param name="param_max_logP" type="float" value="20.0" label="maximal logP value" help="(-max_logP) "/>
|
|
58 <param name="param_min_MW" type="float" value="0.0" label="minimal molecular weight" help="(-min_MW) "/>
|
|
59 <param name="param_max_MW" type="float" value="10000000000.0" label="maximal molecular weight" help="(-max_MW) "/>
|
|
60 <param name="param_q" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="query molecules for similarity searching" help="(-q) "/>
|
|
61 <param name="param_min_sim" type="float" value="0.0" label="minimal average similarity" help="(-min_sim) "/>
|
|
62 <param name="param_max_sim" type="float" value="1.0" label="maximal similarity" help="(-max_sim) "/>
|
|
63 <param name="param_smarts" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="SMARTS pattern" help="(-smarts) ">
|
|
64 <sanitizer>
|
|
65 <valid initial="string.printable">
|
|
66 <remove value="'"/>
|
|
67 <remove value="""/>
|
|
68 </valid>
|
|
69 </sanitizer>
|
|
70 </param>
|
|
71 <param name="param_smarts_file" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="SMARTS pattern" help="(-smarts_file) "/>
|
|
72 <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not show progress information" help="(-quiet) "/>
|
|
73 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
|
|
74 </inputs>
|
|
75 <expand macro="advanced_options"/>
|
|
76 <outputs>
|
|
77 <data name="param_o" metadata_source="param_i" format="input"/>
|
|
78 </outputs>
|
|
79 <help>MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s).
|
|
80
|
|
81 Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.
|
|
82
|
|
83 </help>
|
|
84 </tool>
|