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comparison SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml @ 6:ebb0ac9b6fa9 draft

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author gandres
date Mon, 23 May 2016 17:49:17 -0400
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1 <tool id="sniplay_density" name="SNP density" version="2.0.0">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Calculate SNP densities along chromosome from a VCF input</description>
5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements>
8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="0.1.12b">vcftools</requirement>
10 </requirements>
11
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] Command to be executed to get the tool's version string -->
19 <version_command>
20 <!--
21 tool_binary -v
22 -->
23 </version_command>
24
25 <!-- [REQUIRED] The command to execute -->
26 <command interpreter="bash">
27 calculateSlidingWindowsSNPdensitiesFromVCF.sh $filein $fileout $fileout_bysample $step
28 </command>
29
30 <!-- [REQUIRED] Input files and tool parameters -->
31 <inputs>
32 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
33 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
34 <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />
35 </inputs>
36
37 <!-- [REQUIRED] Output files -->
38 <outputs>
39 <data name="fileout" type="data" format="txt" label="${fileout_label}" />
40 <data name="fileout_bysample" type="data" format="txt" label="${fileout_label}.by_sample" />
41 </outputs>
42
43 <tests>
44 <test>
45 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
46 <param name="step" value="20000" />
47 <output name="fileout" file="SNPden-result.txt" />
48 <output name="fileout_bysample" file="SNPden-result_bysample.txt" />
49 </test>
50 <!-- [HELP] Multiple tests can be defined with different parameters -->
51 <!--
52 <test>
53 </test>
54 -->
55 </tests>
56
57 <!-- [OPTIONAL] Help displayed in Galaxy -->
58 <help>
59
60 .. class:: infomark
61
62 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
63
64 | **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).
65
66
67 .. class:: infomark
68
69 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
70
71 .. class:: infomark
72
73 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
74
75 ---------------------------------------------------
76
77
78
79 =============
80 SNP densities
81 =============
82
83 -----------
84 Description
85 -----------
86
87 Calculate SNP densities along chromosome from a VCF file
88
89
90 -----------------
91 Workflow position
92 -----------------
93
94 **Upstream tool**
95
96 =============== ====================== ===========
97 Name output file(s) format
98 =============== ====================== ===========
99 =============== ====================== ===========
100
101
102 ----------
103 Input file
104 ----------
105
106 VCF file
107 File with SNPs
108
109
110 ----------
111 Parameters
112 ----------
113
114 Step
115 Step in bp for the window to calculate SNP density
116
117 Output name
118 Output base name for the two ouput files
119
120
121 ------------
122 Output files
123 ------------
124
125 Output_name
126 Tabular file with SNP density in each postion
127
128 Output_name.by_sample
129 Tabular file with SNP density for each sample
130
131
132 ---------------------------------------------------
133
134 ---------------
135 Working example
136 ---------------
137
138 Input files
139 ===========
140
141 vcf file
142 -----------
143
144 ::
145
146 #fileformat=VCFv4.1
147 #FILTER=&lt;ID=LowQual,Description="Low quality">
148 #FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
149 [...]
150 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
151 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0
152
153 Parameters
154 ==========
155
156 Step -> 200000
157
158 Output name -> densities
159
160
161 Output files
162 ============
163
164 densities
165 ---------
166
167 ::
168
169 Chromosome Position SNPs
170 chr1 200000 355
171 chr1 400000 228
172 chr1 600000 63
173 chr1 800000 191
174
175
176 densities.by_sample
177 -------------------
178
179 ::
180
181 Chromosome BA58 BA59 BD54
182 chr1 220 197 225
183 chr1 130 119 133
184 chr1 43 43 40
185 chr1 139 167 141
186
187 </help>
188 <citations>
189 <!-- [HELP] As DOI or BibTex entry -->
190 <citation type="bibtex">@article{Dereeper03062015,
191 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},
192 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
193 year = {2015},
194 doi = {10.1093/nar/gkv351},
195 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.},
196 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
197 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
198 journal = {Nucleic Acids Research}
199 }
200
201 </citation>
202
203 </citations>
204 </tool>