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comparison gbsx_barcodeGenerator.xml @ 1:29fc2bb7bc18 draft

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Uploaded gbsx_barcodeGenerator.xml
author koen
date Wed, 13 Jan 2016 10:45:07 -0500
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0:e9be4649dd28 1:29fc2bb7bc18
1 <tool id="gbsx_barcodeGenerator" name="GBSX: Barcode Generator" version="1.1.5">
2 <description>creates inline barcodes for a given enzyme</description>
3 <requirements>
4 <requirement type="set_environment">GBSX_PATH</requirement>
5 <requirement type="package" version="1.1.5">GBSX</requirement>
6 </requirements>
7 <command interpreter="sh">gbsx_barcodeGenerator.sh $barcode $enzyme $barcode_list $barcode_summary</command>
8 <inputs>
9 <param name="barcode" size="4" type="integer" value="5" min="1" max="20000" label="Number of barcodes to generate" />
10 <param name="enzyme" size="4" type="select" label="The enzyme to use" >
11 <option value="ApeKI">ApeKI</option>
12 <option value="PstI">PstI</option>
13 <option value="EcoT22I">EcoT22I</option>
14 <option value="PasI">PasI</option>
15 <option value="HpaII">HpaII</option>
16 <option value="MspI">MspI</option>
17 <option value="PstI-EcoT22I">PstI-EcoT22I</option>
18 <option value="PstI-MspI">PstI-MspI</option>
19 <option value="PstI-TaqI">PstI-TaqI</option>
20 <option value="SbfI-MspI">SbfI-MspI</option>
21 <option value="AsiSI-MspI">AsiSI-MspI</option>
22 <option value="BssHII-MspI">BssHII-MspI</option>
23 <option value="FseI-MspI">FseI-MspI</option>
24 <option value="SalI-MspI">SalI-MspI</option>
25 <option value="ApoI">ApoI</option>
26 <option value="BamHI">BamHI</option>
27 <option value="MseI">MseI</option>
28 <option value="Sau3AI">Sau3AI</option>
29 <option value="RBSTA">RBSTA</option>
30 <option value="RBSCG">RBSCG</option>
31 <option value="NspI">NspI</option>
32 <option value="AvaII">AvaII</option>
33 <option value="NA">NA</option>
34 </param>
35 </inputs>
36 <outputs>
37 <data format="tabular" name="barcode_list" label="GBSX: Barcode Generator: Barcode List" />
38 <data format="txt" name="barcode_summary" label="GBSX: Barcode Generator: Summary" />
39 </outputs>
40
41 <tests>
42 <test>
43 <param name="barcode" value="5"/>
44 <param name="enzyme" value="ApeKI"/>
45 <output name="barcode_list">
46 <assert_contents>
47 <has_n_columns n="3" />
48 <has_text_matching expression="^sample[1-9]+\t[AGCT]*\tApeKI" />
49 </assert_contents>
50 </output>
51 </test>
52 </tests>
53
54 <help>
55
56 .. class:: infomark
57
58 **Overview**
59
60 Genotyping by Sequencing is an emerging technology for cost effective variant discovery and genotyping. However, current analysis tools do not fulfill all experimental design and analysis needs.
61
62 GBSX is a package of tools to first aid in experimental design, including choice of enzymes and barcode design. Secondly, it provides a first analysis step to demultiplex samples using in-line barcodes, providing fastq files that can easily be plugged into existing variant analysis pipelines.
63
64 ----
65
66 This toolkit generates the given number of variating barcodes in combination with the given enzyme for GBS and RAD experiments.
67
68 The outcome of this tool will always be different. This is because the generated barcodes are completely random. The best practice is to manually check the position matrix to see if every bases occurs equally on every position.
69
70 Only the most used options are included. For more options, please use the command line version of GBSX.
71
72 ----
73
74 **Created by:**
75
76 Koen Herten,
77
78 Genomics Core Leuven,
79
80 Belgium
81
82
83 ----
84
85 **Example:**
86
87 The outcome of this tool will always be different.
88
89 ----
90
91 **Project links:**
92
93 https://github.com/GenomicsCoreLeuven/GBSX
94
95 ----
96
97 **Integrated by:**
98
99 Koen Herten
100
101 Genomics Core
102
103 Center for Human Genetics
104
105 UZ – KU Leuven
106
107 Herestraat 49 PO box 602
108
109 B-3000 Leuven, Belgium
110
111
112
113 If you use this tool in Galaxy, please cite:
114
115
116 </help>
117 <citations>
118 <citation type="doi">10.1186/s12859-015-0514-3</citation>
119
120 <citation type="bibtex">@INPROCEEDINGS{
121 author = {Herten, Koen and Hestand, Matthew S. and Vermeesch, Joris R. and Van Houdt, Jeroen KJ},
122 doi = {10.1186/s12859-015-0514-3},
123 issn = {1471-2105},
124 journal = {BMC Bioinformatics},
125 number = {1},
126 pages = {1–6},
127 title = {GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments},
128 url = {http://dx.doi.org/10.1186/s12859-015-0514-3},
129 volume = {16},
130 year = {2015}
131 }</citation>
132 </citations>
133
134
135 </tool>