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comparison GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml @ 6:ebb0ac9b6fa9 draft

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date Mon, 23 May 2016 17:49:17 -0400
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1 <tool id="getHaplotypesFromPhasedVCF" name="Get Haplotypes From Phased VCF" version="1.0.0">
2 <requirements>
3 <requirement type="binary">perl</requirement>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8 <command interpreter="perl">
9 GetHaplotypesFromPhasedVCF.pl $input $output_label &amp;&amp; mv ${output_label}.distinct_haplotypes.txt $output_distinct &amp;&amp; mv ${output_label}.haplo.fas $output_haplo
10 </command>
11 <inputs>
12 <param type="data" name="input" format="vcf" label="Phased VCF" />
13 <param type="text" name="output_label" label="Output_label" value='Haplotypes' />
14 </inputs>
15 <outputs>
16 <data name="output_distinct" format="txt" label="${output_label}.distinct_haplotypes.txt"/>
17 <data name="output_haplo" format="fasta" label="${output_label}.haplo.fas"/>
18 </outputs>
19 <tests>
20 <test>
21 <param name="input" value="getHaplotypesFromPhasedVCF-input.vcf"/>
22 <output name="output_distinct" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt"/>
23 <output name="output_haplo" file="getHaplotypesFromPhasedVCF-result.haplo.fas"/>
24 </test>
25 </tests>
26 <help><![CDATA[
27
28 .. class:: infomark
29
30 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
31
32 | **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).
33
34 .. class:: infomark
35
36 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
37
38 .. class:: infomark
39
40 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr
41
42 ---------------------------------------------------
43
44 ==============================
45 Get Haplotypes From Phased VCF
46 ==============================
47
48 -----------
49 Description
50 -----------
51
52 | Get Haplotype from phased VCF
53
54 -----------------
55 Workflow position
56 -----------------
57
58 **Upstream tool**
59
60 =============== ========================== =======
61 Name output file(s) format
62 =============== ========================== =======
63 Beagle Phased VCF file VCF
64 =============== ========================== =======
65
66
67 **Downstream tool**
68
69 =============== ========================== ===========
70 Name input file(s) format
71 =============== ========================== ===========
72 =============== ========================== ===========
73
74
75 ----------
76 Input file
77 ----------
78
79 VCF file
80 Phased VCF file
81
82 ----------
83 Parameters
84 ----------
85
86 Output file basename
87 Prefix for the output VCF file
88
89 ------------
90 Output files
91 ------------
92
93
94 Text file
95 File describing haplotypes
96
97 Fasta file
98 Fasta file with haplotypes
99
100 ---------------------------------------------------
101
102 ---------------
103 Working example
104 ---------------
105
106 Input files
107 ===========
108
109 VCF file
110 ---------
111
112 ::
113
114 #fileformat=VCFv4.1
115 #FILTER=&lt;ID=LowQual,Description="Low quality">
116 #FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
117 [...]
118 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA
119 Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0
120
121
122 Parameters
123 ==========
124
125 Output name -> haplotypes
126
127
128 Output files
129 ============
130
131 haplotypes.distinct_haplotypes.txt
132 ----------------------------------
133
134 ::
135
136 ===Chr10===
137 haplo1:2:CIRAD403_1,CIRAD403_2,
138 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT
139 haplo2:2:MAHAE_1,MAHAE_2,
140 TAAATCTTGGTGCTGATCTGATATTTAATGCGT
141
142
143 haplotypes.haplo.fas
144 --------------------
145
146 ::
147
148 >Chr10_AZUCENA_1
149 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT
150 >Chr10_AZUCENA_2
151 TAAATCTTGGTGCTGATCTGATATTTAATGCGT
152
153 ]]></help>
154 <citations>
155 <!-- [HELP] As DOI or BibTex entry -->
156 <citation type="bibtex">@article{Dereeper03062015,
157 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},
158 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
159 year = {2015},
160 doi = {10.1093/nar/gkv351},
161 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.},
162 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
163 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
164 journal = {Nucleic Acids Research}
165 }
166
167 }</citation>
168
169 </citations>
170
171 </tool>