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comparison SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.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="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
7 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
8 <requirements>
9 <requirement type="binary">perl</requirement>
10 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
11 <requirement type="package" version="0.1.14">vcftools</requirement>
12 <requirement type="package" version="0.1.14">perl-vcftools-vcf</requirement>
13 </requirements>
14
15 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
16 <stdio>
17 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
18 <exit_code range="1:" level="fatal" />
19 </stdio>
20
21 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
22 <version_command>
23 <!--
24 tool_binary -v
25 -->
26 </version_command>
27
28 <!-- [REQUIRED] The command to execute -->
29 <command interpreter="bash">
30 calculateSlidingWindowsSNPdensitiesFromVCF.sh $filein $fileout $fileout_bysample $step
31 </command>
32
33 <!-- [REQUIRED] Input files and tool parameters -->
34 <inputs>
35 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
36 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
37 <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />
38 </inputs>
39
40 <!-- [REQUIRED] Output files -->
41 <outputs>
42 <data name="fileout" format="txt" label="${fileout_label}" />
43 <data name="fileout_bysample" format="txt" label="${fileout_label}.by_sample" />
44 </outputs>
45
46 <tests>
47 <test>
48 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
49 <param name="step" value="20000" />
50 <output name="fileout" file="SNPden-result.txt" />
51 <output name="fileout_bysample" file="SNPden-result_bysample.txt" />
52 </test>
53 <!-- [HELP] Multiple tests can be defined with different parameters -->
54 <!--
55 <test>
56 </test>
57 -->
58 </tests>
59
60 <!-- [OPTIONAL] Help displayed in Galaxy -->
61 <help>
62
63 .. class:: infomark
64
65 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
66
67 | **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).
68
69
70 .. class:: infomark
71
72 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
73
74 .. class:: infomark
75
76 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
77
78 ---------------------------------------------------
79
80
81
82 =============
83 SNP densities
84 =============
85
86 -----------
87 Description
88 -----------
89
90 Calculate SNP densities along chromosome from a VCF file
91
92
93 -----------------
94 Workflow position
95 -----------------
96
97 **Upstream tool**
98
99 =============== ====================== ===========
100 Name output file(s) format
101 =============== ====================== ===========
102 =============== ====================== ===========
103
104
105 ----------
106 Input file
107 ----------
108
109 VCF file
110 File with SNPs
111
112
113 ----------
114 Parameters
115 ----------
116
117 Step
118 Step in bp for the window to calculate SNP density
119
120 Output name
121 Output base name for the two ouput files
122
123
124 ------------
125 Output files
126 ------------
127
128 Output_name
129 Tabular file with SNP density in each postion
130
131 Output_name.by_sample
132 Tabular file with SNP density for each sample
133
134
135 ---------------------------------------------------
136
137 ---------------
138 Working example
139 ---------------
140
141 Input files
142 ===========
143
144 vcf file
145 -----------
146
147 ::
148
149 #fileformat=VCFv4.1
150 #FILTER=&lt;ID=LowQual,Description="Low quality">
151 #FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
152 [...]
153 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
154 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
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>