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comparison check_gwas_inputs/CheckGWASInputs.xml @ 9:98c37a5d67f4 draft

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author dereeper
date Wed, 07 Feb 2018 22:08:47 -0500
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1 <tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.1">
2 <description>checks concordance between input files for GWAS analysis</description>
3
4 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
5 <requirements>
6 <requirement type="binary">perl</requirement>
7 </requirements>
8
9 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
10 <stdio>
11 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
12 <exit_code range="1:" level="fatal" />
13 </stdio>
14
15 <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats
16 </command>
17 <inputs>
18 <param format="txt" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
19 <param format="txt" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
20 </inputs>
21 <outputs>
22 <data format="txt" name="out_hapmap" label="Hapmap output"/>
23 <data format="txt" name="out_trait" label="Trait output"/>
24 <data format="txt" name="stats" label="Logfile and statistics"/>
25 </outputs>
26
27 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
28 <tests>
29 <!-- [HELP] Test files have to be in the ~/test-data directory -->
30 <!-- [HELP] Multiple tests can be defined with different parameters -->
31 <test>
32 <param name="hapmap" value="gwas-hapmap" />
33 <param name="trait" value="gwas-trait" />
34 <output name="out_hapmap" file="gwas-result.hapmap" />
35 <output name="out_trait" file="gwas-result.trait" />
36 <output name="stats" file="gwas-result.stats" />
37 </test>
38 </tests>
39 <help>
40
41 <![CDATA[
42
43
44 .. class:: infomark
45
46 **Authors** South Green
47
48 | **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).
49
50 .. class:: infomark
51
52 **Galaxy integration** South Green.
53
54 ---------------------------------------------------
55
56
57 ===============
58 CheckGWASInputs
59 ===============
60
61 -----------
62 Description
63 -----------
64
65 | CheckGWASInputs checks concordance between input files for GWAS analysis.
66
67
68 -----------------
69 Workflow position
70 -----------------
71
72 **Upstream tool**
73
74 =============== ====================== ===========
75 Name output file(s) format
76 =============== ====================== ===========
77 VCF to Hapmap Hapmap file hapmap
78 =============== ====================== ===========
79
80
81
82
83 ----------
84 Input file
85 ----------
86
87 Hapmap file
88 Allelic file in Hapmap format
89
90 Trait file
91 Phenotypic file
92
93 ------------
94 Output files
95 ------------
96
97 Hapmap output
98
99 Trait output
100
101 Logfile and statistics
102
103 ---------------------------------------------------
104
105 ---------------
106 Working example
107 ---------------
108
109 Input files
110 ===========
111
112 Hapmap file
113 -----------
114
115 ::
116
117 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2
118 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA
119 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA
120
121 Trait file
122 ----------
123
124 ::
125
126 <Trait> Test
127 Ind1 -2.9985936006411
128 Ind2 -2.68669426456267
129
130 Output files
131 ============
132
133 Hapmap output
134 -------------
135
136 ::
137
138 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 Ind3 Ind4
139 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA AA AA
140 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA AA TT
141
142
143 Trait output
144 ------------
145
146 ::
147
148 <Trait> Test
149 Ind429 -26.2142525264157
150 Ind373 12.0306115988504
151 Ind81 1.98118654229534
152
153 Logfile and statistics
154 ----------------------
155
156 ::
157
158
159 ==============================================
160 Individuals
161 ==============================================
162 Individuals in hapmap file: 500
163 Individuals in trait file: 500
164 Individuals found in both files: 500
165 ==============================================
166 Markers
167 ==============================================
168 Discarded markers:
169 Monomorphic: 0
170 Not biallelic: 0
171 Modified markers:
172 Difference in variation: 0
173
174 ]]>
175
176
177 </help>
178 <citations>
179 <!-- [HELP] As DOI or BibTex entry -->
180 <citation type="bibtex">@article{Dereeper03062015,
181 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},
182 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
183 year = {2015},
184 doi = {10.1093/nar/gkv351},
185 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.},
186 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
187 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
188 journal = {Nucleic Acids Research}
189 }
190
191 </citation>
192
193 </citations>
194 </tool>