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comparison hapmap2mlmm/HapmapToMLMMFiles.xml @ 3:345f88a8f483 draft

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author dereeper
date Fri, 10 Jul 2015 10:38:43 -0400
parents 420b57c3c185
children 10627af23f10
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2:feb40a9a8eae 3:345f88a8f483
1 <tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="1.1">
2 <description>converts a hapmap file into MLMM input files</description>
3 <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot
4 </command>
5 <inputs>
6 <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
7 </inputs>
8 <outputs>
9 <data format="txt" name="snp_info" label="SNP Info file"/>
10 <data format="txt" name="genot" label="Genotyping file for MLMM"/>
11 </outputs>
12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
13 <stdio>
14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
15 <exit_code range="1:" level="fatal" />
16 </stdio>
17
18 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
19 <tests>
20 <!-- [HELP] Test files have to be in the ~/test-data directory -->
21 <!-- [HELP] Multiple tests can be defined with different parameters -->
22 <!--
23 <test>
24 </test>
25 -->
26 </tests>
27 <help>
28
29
30
31
32 .. class:: infomark
33
34 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
35
36 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
37
38 .. class:: infomark
39
40 **Galaxy integration** South Green.
41
42 ---------------------------------------------------
43
44
45 =================
46 HapmapToMLMMFiles
47 =================
48
49 -----------
50 Description
51 -----------
52
53 | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software.
54
55
56 -----------------
57 Workflow position
58 -----------------
59
60 **Upstream tool**
61
62 =============== ====================== ===========
63 Name output file(s) format
64 =============== ====================== ===========
65 VCF to Hapmap Fasta alignment fasta
66 =============== ====================== ===========
67
68
69 **Downstream tool**
70
71 =========== ========================== =======
72 Name input file(s) format
73 =========== ========================== =======
74 MLMM
75 =========== ========================== =======
76
77
78
79 ----------
80 Input file
81 ----------
82
83 Hapmap file
84 Allelic file in Hapmap format
85
86
87
88 ------------
89 Output files
90 ------------
91
92 SNP Info file
93
94 Genotyping file for MLMM
95
96
97
98 ---------------------------------------------------
99
100 ---------------
101 Working example
102 ---------------
103
104 Input files
105 ===========
106
107 Hapmap file
108 -----------
109
110 ::
111
112 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2
113 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA
114 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA
115
116
117 Output files
118 ============
119
120 SNP Info file
121 -------------
122
123 ::
124
125 SNP Chr Pos
126 SNP1 1 3102
127 SNP2 1 4648
128 SNP3 1 7601
129
130
131 Genotyping file for MLMM
132 ------------------------
133
134 ::
135
136 Ind_id SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 SNP13 SNP14
137 Ind1 0 0 0 0 0 0 2 0 2 0 0 0 2 0
138 Ind2 0 0 0 0 0 2 2 0 0 0 0 0 0 0
139
140
141 </help>
142 <citations>
143 <!-- [HELP] As DOI or BibTex entry -->
144 <citation type="bibtex">@article{Dereeper03062015,
145 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel},
146 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
147 year = {2015},
148 doi = {10.1093/nar/gkv351},
149 abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.},
150 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
151 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
152 journal = {Nucleic Acids Research}
153 }
154
155 </citation>
156
157 </citations>
158 </tool>