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comparison PedToFasta/pedToFasta.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_pedToFasta" name="Ped2Fasta" version="1.0.0">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Convert PED file to Fasta File </description>
5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements>
8 <requirement type="binary">perl</requirement>
9 </requirements>
10
11 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
12 <stdio>
13 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
14 <exit_code range="1:" level="fatal" />
15 </stdio>
16
17 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
18 <version_command>
19 <!--
20 tool_binary -v
21 -->
22 </version_command>
23
24 <!-- [REQUIRED] The command to execute -->
25 <command interpreter="perl">
26 Ped2Fasta.pl --in $filein --out $fileout
27 </command>
28
29 <!-- [REQUIRED] Input files and tool parameters -->
30 <inputs>
31 <param name="filein" type="data" format="txt" optional="false" label="PED input" />
32 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/>
33 </inputs>
34
35 <!-- [REQUIRED] Output files -->
36 <outputs>
37 <data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" />
38 </outputs>
39
40 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
41 <tests>
42 <!-- [HELP] Test files have to be in the ~/test-data directory -->
43 <test>
44 <param name="filein" value="ped2fasta-sample.ped" />
45 <output name="fileout" file="ped2fasta-result.fa" />
46 </test>
47 </tests>
48
49 <!-- [OPTIONAL] Help displayed in Galaxy -->
50 <help>
51
52 .. class:: infomark
53
54 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
55
56 | **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).
57
58 .. class:: infomark
59
60 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
61
62 .. class:: infomark
63
64 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr
65
66 ---------------------------------------------------
67
68 =========
69 Ped2Fasta
70 =========
71
72 -----------
73 Description
74 -----------
75
76 Convert PED file to Fasta File
77
78 -----------------
79 Workflow position
80 -----------------
81
82 **Upstream tool**
83
84 =============== ========================== =======
85 Name output file(s) format
86 =============== ========================== =======
87 VCFtools Filter VCF file VCF
88 =============== ========================== =======
89
90
91 **Downstream tool**
92
93 =========== ========================== =======
94 Name input file(s) format
95 =========== ========================== =======
96 Readseq Fasta alignment fasta
97 =========== ========================== =======
98
99
100 ----------
101 Input file
102 ----------
103
104 PED file
105 PED file usually from VCF tools
106
107 ----------
108 Parameters
109 ----------
110
111 Output file name
112 Prefix for the output fasta file
113
114 ------------
115 Output files
116 ------------
117
118 Fasta file
119 PED file conversion
120
121 ---------------------------------------------------
122
123 ---------------
124 Working example
125 ---------------
126
127 Input files
128 ===========
129
130 PED file
131 ---------
132
133 ::
134
135 CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A
136
137 Parameters
138 ==========
139
140 Output name -> pedFile
141
142 Output files
143 ============
144
145 pedFile.fa
146 ----------
147
148 ::
149
150 YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY
151
152
153 </help>
154
155 <citations>
156 <!-- [HELP] As DOI or BibTex entry -->
157 <citation type="bibtex">@article{Dereeper03062015,
158 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},
159 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
160 year = {2015},
161 doi = {10.1093/nar/gkv351},
162 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.},
163 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
164 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
165 journal = {Nucleic Acids Research}
166 }
167
168 </citation>
169
170 </citations>
171 </tool>