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comparison check_gwas_inputs/CheckGWASInputs.xml @ 1:420b57c3c185 draft

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author dereeper
date Fri, 10 Jul 2015 04:39:30 -0400
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0:3e19d0dfcf3e 1:420b57c3c185
1 <tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0">
2 <description>checks concordance between input files for GWAS analysis</description>
3 <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats
4 </command>
5 <inputs>
6 <param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
7 <param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
8 </inputs>
9 <outputs>
10 <data format="txt" name="out_hapmap" label="Hapmap output"/>
11 <data format="txt" name="out_trait" label="Trait output"/>
12 <data format="txt" name="stats" label="Logfile and statistics"/>
13 </outputs>
14 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
15 <stdio>
16 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
17 <exit_code range="1:" level="fatal" />
18 </stdio>
19
20 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
21 <tests>
22 <!-- [HELP] Test files have to be in the ~/test-data directory -->
23 <!-- [HELP] Multiple tests can be defined with different parameters -->
24 <!--
25 <test>
26 </test>
27 -->
28 </tests>
29 <help>
30
31 <![CDATA[
32
33
34 .. class:: infomark
35
36 **Authors** South Green
37
38 | **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).
39
40 .. class:: infomark
41
42 **Galaxy integration** South Green.
43
44 ---------------------------------------------------
45
46
47 ===============
48 CheckGWASInputs
49 ===============
50
51 -----------
52 Description
53 -----------
54
55 | CheckGWASInputs checks concordance between input files for GWAS analysis.
56
57
58 -----------------
59 Workflow position
60 -----------------
61
62 **Upstream tool**
63
64 =============== ====================== ===========
65 Name output file(s) format
66 =============== ====================== ===========
67 VCF to Hapmap Hapmap file hapmap
68 =============== ====================== ===========
69
70
71
72
73 ----------
74 Input file
75 ----------
76
77 Hapmap file
78 Allelic file in Hapmap format
79
80 Trait file
81 Phenotypic file
82
83 ------------
84 Output files
85 ------------
86
87 Hapmap output
88
89 Trait output
90
91 Logfile and statistics
92
93 ---------------------------------------------------
94
95 ---------------
96 Working example
97 ---------------
98
99 Input files
100 ===========
101
102 Hapmap file
103 -----------
104
105 ::
106
107 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2
108 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA
109 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA
110
111 Trait file
112 ----------
113
114 ::
115
116 <Trait> Test
117 Ind1 -2.9985936006411
118 Ind2 -2.68669426456267
119
120 Output files
121 ============
122
123 Hapmap output
124 -------------
125
126 ::
127
128 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 Ind3 Ind4
129 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA AA AA
130 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA AA TT
131
132
133 Trait output
134 ------------
135
136 ::
137
138 <Trait> Test
139 Ind429 -26.2142525264157
140 Ind373 12.0306115988504
141 Ind81 1.98118654229534
142
143 Logfile and statistics
144 ----------------------
145
146 ::
147
148
149 ==============================================
150 Individuals
151 ==============================================
152 Individuals in hapmap file: 500
153 Individuals in trait file: 500
154 Individuals found in both files: 500
155 ==============================================
156 Markers
157 ==============================================
158 Discarded markers:
159 Monomorphic: 0
160 Not biallelic: 0
161 Modified markers:
162 Difference in variation: 0
163
164 ]]>
165
166
167 </help>
168 <citations>
169 <!-- [HELP] As DOI or BibTex entry -->
170 <citation type="bibtex">@article{Dereeper03062015,
171 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},
172 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
173 year = {2015},
174 doi = {10.1093/nar/gkv351},
175 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.},
176 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
177 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
178 journal = {Nucleic Acids Research}
179 }
180
181 </citation>
182
183 </citations>
184 </tool>