Mercurial > repos > dereeper > sniplay

comparison SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.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="sniplay_density" name="SNP density" version="1.2.0">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Calculate SNP densities along chromosome from HapMap</description>
5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements>
8 <requirement type="binary">perl</requirement>
9 </requirements>
10
11 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
12 <version_command>
13 <!--
14 tool_binary -v
15 -->
16 </version_command>
17
18 <!-- [REQUIRED] The command to execute -->
19 <command interpreter="bash">
20 calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step
21 </command>
22
23 <!-- [REQUIRED] Input files and tool parameters -->
24 <inputs>
25 <param name="filein" type="data" format="txt" optional="false" label="Hapmap input" />
26 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
27 <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />
28 </inputs>
29
30 <!-- [REQUIRED] Output files -->
31 <outputs>
32 <data name="fileout" type="data" format="tabular" label="${fileout_label}" />
33 <data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" />
34 </outputs>
35
36 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
37 <stdio>
38 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
39 <exit_code range="1:" level="fatal" />
40 </stdio>
41
42 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
43 <tests>
44 <!-- [HELP] Test files have to be in the ~/test-data directory -->
45 <!--
46 <test>
47 <param name="input" value="input_test.txt" />
48 <output name="output" file="output_test.txt" />
49 </test>
50 -->
51 <!-- [HELP] Multiple tests can be defined with different parameters -->
52 <!--
53 <test>
54 </test>
55 -->
56 </tests>
57
58 <!-- [OPTIONAL] Help displayed in Galaxy -->
59 <help>
60
61 .. class:: infomark
62
63 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
64
65 | **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).
66
67
68 .. class:: infomark
69
70 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
71
72 .. class:: infomark
73
74 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
75
76 ---------------------------------------------------
77
78
79
80 =============
81 SNP densities
82 =============
83
84 -----------
85 Description
86 -----------
87
88 Calculate SNP densities along chromosome from HapMap
89
90
91 -----------------
92 Workflow position
93 -----------------
94
95 **Upstream tool**
96
97 =============== ====================== ===========
98 Name output file(s) format
99 =============== ====================== ===========
100 VCF to Hapmap Hapmap file hapmap
101 =============== ====================== ===========
102
103
104 ----------
105 Input file
106 ----------
107
108 Hapmap file
109 File with SNPs
110
111
112 ----------
113 Parameters
114 ----------
115
116 Step
117 Step in bp for the window to calculate SNP density
118
119 Output name
120 Output base name for the two ouput files
121
122
123 ------------
124 Output files
125 ------------
126
127 Output_name
128 Tabular file with SNP density in each postion
129
130 Output_name.by_sample
131 Tabular file with SNP density for each sample
132
133
134 ---------------------------------------------------
135
136 ---------------
137 Working example
138 ---------------
139
140 Input files
141 ===========
142
143 hapmap file
144 -----------
145
146 ::
147
148 rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54
149 chr1:1774 [G/T] chr1 1774 Cc01_g00010:47 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 25.0% 4 GG TT TT TT
150 chr1:1640 [G/A] chr1 1640 Cc01_g00010:127 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 37.5% 4 GG GG AA GA
151 chr1:1629 [A/C] chr1 1629 Cc01_g00010:138 exon SYNONYMOUS_CODING ctT/ctG L/L 37.5% 4 AA CC CC AC
152 chr1:1628 [C/G] chr1 1628 Cc01_g00010:139 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 CC CC CC CG
153 chr1:1619 [T/G] chr1 1619 Cc01_g00010:148 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT TT GG TG
154 chr1:1405 [C/T] chr1 1405 Cc01_g00010:362 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 16.7% 3 CC CC NN CT
155
156 Parameters
157 ==========
158
159 Step -> 200000
160
161 Output name -> densities
162
163
164 Output files
165 ============
166
167 densities
168 ---------
169
170 ::
171
172 Chromosome Position SNPs
173 chr1 200000 355
174 chr1 400000 228
175 chr1 600000 63
176 chr1 800000 191
177
178
179 densities.by_sample
180 -------------------
181
182 ::
183
184 Chromosome BA58 BA59 BD54
185 chr1 220 197 225
186 chr1 130 119 133
187 chr1 43 43 40
188 chr1 139 167 141
189
190 </help>
191 <citations>
192 <!-- [HELP] As DOI or BibTex entry -->
193 <citation type="bibtex">@article{Dereeper03062015,
194 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},
195 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
196 year = {2015},
197 doi = {10.1093/nar/gkv351},
198 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.},
199 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
200 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
201 journal = {Nucleic Acids Research}
202 }
203
204 </citation>
205
206 </citations>
207 </tool>