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comparison GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml @ 10:c6640c49fd01 draft

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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 09:00:24 -0400
parents ebb0ac9b6fa9
children 88748d846a20
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9:98c37a5d67f4 10:c6640c49fd01
1 <tool id="getHaplotypesFromPhasedVCF" name="Get Haplotypes From Phased VCF" version="1.0.0"> 1 <tool id="getHaplotypesFromPhasedVCF" name="Get Haplotypes From Phased VCF" version="2.0.0">
2 <description>Get Haplotypes From Phased VCF</description>
3
2 <requirements> 4 <requirements>
3 <requirement type="binary">perl</requirement> 5 <requirement type="binary">perl</requirement>
4 </requirements> 6 </requirements>
5 <stdio> 7 <stdio>
6 <exit_code range="1:" /> 8 <exit_code range="1:" />
17 <data name="output_haplo" format="fasta" label="${output_label}.haplo.fas"/> 19 <data name="output_haplo" format="fasta" label="${output_label}.haplo.fas"/>
18 </outputs> 20 </outputs>
19 <tests> 21 <tests>
20 <test> 22 <test>
21 <param name="input" value="getHaplotypesFromPhasedVCF-input.vcf"/> 23 <param name="input" value="getHaplotypesFromPhasedVCF-input.vcf"/>
22 <output name="output_distinct" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt"/> 24 <output name="output_distinct" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt" compare="sim_size" delta="0"/>
23 <output name="output_haplo" file="getHaplotypesFromPhasedVCF-result.haplo.fas"/> 25 <output name="output_haplo" file="getHaplotypesFromPhasedVCF-result.haplo.fas" compare="sim_size" delta="0"/>
24 </test> 26 </test>
25 </tests> 27 </tests>
26 <help><![CDATA[ 28 <help><![CDATA[
27 29
28 .. class:: infomark 30 .. class:: infomark
31 33
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). 34 | **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 35
34 .. class:: infomark 36 .. class:: infomark
35 37
36 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. 38 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
37 39
38 .. class:: infomark 40 .. class:: infomark
39 41
40 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr 42 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
41 43
42 --------------------------------------------------- 44 ---------------------------------------------------
43 45
44 ============================== 46 ==============================
45 Get Haplotypes From Phased VCF 47 Get Haplotypes From Phased VCF
49 Description 51 Description
50 ----------- 52 -----------
51 53
52 | Get Haplotype from phased VCF 54 | Get Haplotype from phased VCF
53 55
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 ---------- 56 ----------
76 Input file 57 Input file
77 ---------- 58 ----------
78 59
79 VCF file 60 VCF file
80 Phased VCF file 61 Phased VCF file
81 62
82 ---------- 63 ---------
83 Parameters 64 Parameter
84 ---------- 65 ---------
85 66
86 Output file basename 67 Output file basename
87 Prefix for the output VCF file 68 Prefix for the output VCF file
88 69
89 ------------ 70 ------------
101 82
102 --------------- 83 ---------------
103 Working example 84 Working example
104 --------------- 85 ---------------
105 86
106 Input files 87 Input file
107 =========== 88 ==========
108 89
109 VCF file 90 VCF file
110 --------- 91 ---------
111 92
112 :: 93 ::
117 [...] 98 [...]
118 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA 99 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|0:0:1,0,0 100 Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0
120 101
121 102
122 Parameters 103 Parameter
123 ========== 104 =========
124 105
125 Output name -> haplotypes 106 Output name -> haplotypes
126 107
127 108
128 Output files 109 Output files