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comparison galaxy_stubs/MolFilter.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="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="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="SMARTS pattern" help="(-smarts) ">
64 <sanitizer>
65 <valid initial="string.printable">
66 <remove value="'"/>
67 <remove value="&quot;"/>
68 </valid>
69 </sanitizer>
70 </param>
71 <param name="param_smarts_file" type="data" format="txt" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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>