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comparison AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml @ 6:ebb0ac9b6fa9 draft

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1 <tool id="annotationStatsFromVCF" name="Get annotation statistics" version="1.0.0">
2 <description> from VCF file </description>
3 <requirements>
4 <requirement type="binary">perl</requirement>
5 <requirement type="package" version="0.1.12b">vcftools</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" />
9 </stdio>
10 <command interpreter="perl">
11 AnnotationStatsFromVCF.pl -v $input -o $output_label -s $step &amp;&amp; mv ${output_label} $output_count &amp;&amp; mv ${output_label}.effect $output_stats_effect &amp;&amp; mv ${output_label}.location $output_stats_location
12 </command>
13 <inputs>
14 <param type="data" name="input" format="vcf" label="VCF file" />
15 <param type="text" name="output_label" label="Output_label" value='VCF_stats' />
16 </inputs>
17 <outputs>
18 <data name="output_count" format="txt" label="${output_label}."/>
19 <data name="output_stats_effect" format="txt" label="${output_label}."/>
20 <data name="output_stats_location" format="txt" label="${output_label}."/>
21 </outputs>
22 <tests>
23 <test>
24 <param name="input" value="vcf2fastaAndHapmap-sample.vcf"/>
25 <output name="output_count" file=".txt"/>
26 <output name="output_stats_effect" file=""/>
27 <output name="output_stats_location" file=""/>
28 </test>
29 </tests>
30 <help><![CDATA[
31
32 .. class:: infomark
33
34 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
35
36 | **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).
37
38 .. class:: infomark
39
40 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
41
42 .. class:: infomark
43
44 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr
45
46 ---------------------------------------------------
47
48 ==============================
49 Get Haplotypes From Phased VCF
50 ==============================
51
52 -----------
53 Description
54 -----------
55
56 | Get Haplotype from phased VCF
57
58 -----------------
59 Workflow position
60 -----------------
61
62 **Upstream tool**
63
64 =============== ========================== =======
65 Name output file(s) format
66 =============== ========================== =======
67 Beagle Phased VCF file VCF
68 =============== ========================== =======
69
70
71 **Downstream tool**
72
73 =============== ========================== ===========
74 Name input file(s) format
75 =============== ========================== ===========
76 =============== ========================== ===========
77
78
79 ----------
80 Input file
81 ----------
82
83 VCF file
84 Phased VCF file
85
86 ----------
87 Parameters
88 ----------
89
90 Output file basename
91 Prefix for the output VCF file
92
93 ------------
94 Output files
95 ------------
96
97
98 Text file
99 File describing haplotypes
100
101 Fasta file
102 Fasta file with haplotypes
103
104 ---------------------------------------------------
105
106 ---------------
107 Working example
108 ---------------
109
110 Input files
111 ===========
112
113 VCF file
114 ---------
115
116 ::
117
118 #fileformat=VCFv4.1
119 #FILTER=&lt;ID=LowQual,Description="Low quality">
120 #FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
121 [...]
122 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA
123 Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0
124
125
126 Parameters
127 ==========
128
129 Output name -> haplotypes
130
131
132 Output files
133 ============
134
135 haplotypes.distinct_haplotypes.txt
136 ----------------------------------
137
138 ::
139
140 ===Chr10===
141 haplo1:2:CIRAD403_1,CIRAD403_2,
142 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT
143 haplo2:2:MAHAE_1,MAHAE_2,
144 TAAATCTTGGTGCTGATCTGATATTTAATGCGT
145
146
147 haplotypes.haplo.fas
148 --------------------
149
150 ::
151
152 >Chr10_AZUCENA_1
153 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT
154 >Chr10_AZUCENA_2
155 TAAATCTTGGTGCTGATCTGATATTTAATGCGT
156
157 ]]></help>
158 <citations>
159 <!-- [HELP] As DOI or BibTex entry -->
160 <citation type="bibtex">@article{Dereeper03062015,
161 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},
162 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
163 year = {2015},
164 doi = {10.1093/nar/gkv351},
165 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.},
166 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
167 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
168 journal = {Nucleic Acids Research}
169 }
170
171 }</citation>
172
173 </citations>
174
175 </tool>