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comparison galaxy_stubs/LigandFileSplitter.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="LigandFileSplitter" name="LigandFileSplitter" version="1.1.0">
5 <description>split molecule files</description>
6 <macros>
7 <token name="@EXECUTABLE@">LigandFileSplitter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>LigandFileSplitter
13
14 #if $param_i:
15 -i $param_i
16 #end if
17 #if $param_no:
18 -no $param_no
19 #end if
20 #if $param_mpf:
21 -mpf $param_mpf
22 #end if
23 #if $param_outname_pattern:
24 -outname_pattern "$param_outname_pattern"
25 #end if
26
27 #if $rep_param_o:
28 -o
29 #for token in $rep_param_o:
30 #if " " in str(token):
31 "$token.param_o"
32 #else
33 $token.param_o
34 #end if
35 #end for
36 #end if
37 </command>
38 <inputs>
39 <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) "/>
40 <param name="param_no" type="integer" value="0" label="Number of output files to be created" help="(-no) "/>
41 <param name="param_mpf" type="integer" value="0" label="Number of molecules per output file" help="(-mpf) "/>
42 <param name="param_outname_pattern" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="Pattern that will be used to generate the names of the output files, see notes and examples below" help="(-outname_pattern) ">
43 <sanitizer>
44 <valid initial="string.printable">
45 <remove value="'"/>
46 <remove value="&quot;"/>
47 </valid>
48 </sanitizer>
49 </param>
50 </inputs>
51 <expand macro="advanced_options"/>
52 <outputs>
53 <data name="param_o" metadata_source="param_i" format="input"/>
54 </outputs>
55 <help>LigandFileSplitter splits a molecule file into a given number of subsets.
56
57 Examples:
58
59 $ LigandFileSplitter -i Trypsin_actives.sdf -o batch_1 batch_2
60 will split the input file Trypsin_actives.sdf in the two output files batch_1.sdf and batch_2.sdf.
61
62 $ LigandFileSplitter -i Trypsin_actives.sdf -no 3
63 will split the input file Trypsin_actives.sdf in three files named Trypsin_actives_0.sdf, Trypsin_actives_1.sdf and Trypsin_actives_2.sdf
64
65 $ LigandFileSplitter -i ligands.sdf -ligands_per_file 4
66 will split the input file ligands.sdf in as many files needed to fit at most 4 ligands per file.
67 The files will be named ligands_0.sdf, ligands_1.sdf ... ligands_N.sdf
68
69 $ LigandFileSplitter -i ligands.sdf -ligands_per_file 5 -outname_pattern split_ligands-%d.sdf
70 will split the input file ligands.sdf in as many files needed to fit at most 5 ligands per file.
71 The files will be named split_ligands-0.sdf, split_ligands-1.sdf, ... , split_ligands-N.sdf.
72
73 $ LigandFileSplitter -i ligands.sdf -outname_pattern split_ligands_%d.sdf -no 100
74 will split the input file ligands.sdf in 100 files using the following names:
75 split_ligands_0.sdf, split_ligands_1.sdf, ... , split_ligands_99.sdf.
76
77 NOTES:
78 - Molecules are not sorted in any way.
79 - The tool is no format converter and the format of the output files will be the same as of the input file.
80 - Output_name_pattern accepts a printf-like pattern, expecting exactly one decimal integer placeholder, %d.
81 - The following are valid patterns: output_ligand.sdf_%d, split_%d.mol, %d_lig.drf
82 - The following are invalid patterns: output_%f.sdf, ligands.drf_%u, %d_lig_%d.mol, molecules.sdf
83
84 WARNING:
85 - If the parameter outname_pattern is specified, the user is responsible for the occurrence of a valid file extension
86 in the outname_pattern, which has to be of the same file format as the input file.
87
88
89
90 </help>
91 </tool>