Mercurial > repos > dereeper > sniplay

comparison Rooting/rooting.xml @ 9:98c37a5d67f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Wed, 07 Feb 2018 22:08:47 -0500
parents
children c6640c49fd01
comparison
equal deleted inserted replaced
8:6bf69b40365c 9:98c37a5d67f4
1 <tool id="sniplay_rooting" name="Rooting" version="1.0.3">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Midpoint rooting of newick tree </description>
5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements>
8 <requirement type="binary">perl</requirement>
9 <requirement type="package">Rootings_54.jar</requirement>
10 </requirements>
11
12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
13 <stdio>
14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
15 <exit_code range="1:" level="fatal" />
16 </stdio>
17
18
19 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
20 <version_command>
21 <!--
22 tool_binary -v
23 -->
24 </version_command>
25
26 <!-- [REQUIRED] The command to execute -->
27 <command interpreter="perl">
28 Rooting.pl -i $filein -o $fileout &amp;&amp; mv ${filein}.rooting.log $fileout_log
29 </command>
30
31 <!-- [REQUIRED] Input files and tool parameters -->
32 <inputs>
33 <param name="filein" type="data" format="nwk" optional="false" label="Fasta alignment input" />
34 <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" />
35 </inputs>
36
37 <!-- [REQUIRED] Output files -->
38 <outputs>
39 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
40 <data name="fileout" type="data" format="nwk" label="${fileout_label}" />
41 </outputs>
42
43 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
44 <tests>
45 <!-- [HELP] Test files have to be in the ~/test-data directory -->
46
47 <test>
48 <param name="filein" value="rooting-newick" />
49 <output name="fileout" file="rooting-out_tree" />
50 </test>
51
52 <!-- [HELP] Multiple tests can be defined with different parameters -->
53 <!--
54 <test>
55 </test>
56 -->
57 </tests>
58
59 <!-- [OPTIONAL] Help displayed in Galaxy -->
60 <help>
61
62
63 .. class:: infomark
64
65 **Authors** Jean-François Dufayard, CIRAD, South Green platform
66
67
68 .. class:: infomark
69
70 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
71
72 .. class:: infomark
73
74 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
75
76 .. class:: infomark
77
78 **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).
79
80 ---------------------------------------------------
81
82
83
84
85 =======
86 Rooting
87 =======
88
89 -----------
90 Description
91 -----------
92
93 Compute a midpoint newick rooted tree.
94
95
96 -----------------
97 Workflow position
98 -----------------
99
100 **Upstream tool**
101
102 =========== ========================== =======
103 Name output file(s) format
104 =========== ========================== =======
105 fastme Newick tree Newick
106 =========== ========================== =======
107
108
109
110 ----------
111 Input file
112 ----------
113
114 Newick file
115
116
117 ----------
118 Parameters
119 ----------
120
121 Output name
122 Output base name for the ouput files
123
124
125 ------------
126 Output files
127 ------------
128
129 Output_name
130 Resulting tree rooted in newick format
131
132 Output_name.log
133 Log file
134
135 ------------
136 Dependencies
137 ------------
138 Rooting
139 CIRAD tool. Contact jean-francois.dufayard@cirad.fr
140
141 ---------------------------------------------------
142
143 ---------------
144 Working example
145 ---------------
146
147 Input files
148 ===========
149
150 Newick file
151 -----------
152
153 ::
154
155 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
156
157
158 Parameters
159 ==========
160
161 Output name -> out tree
162
163
164 Output files
165 ============
166
167 out tree
168 --------
169
170 ::
171
172 (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662...
173
174
175 </help>
176 <citations>
177 <!-- [HELP] As DOI or BibTex entry -->
178 <citation type="bibtex">@article{Dereeper03062015,
179 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},
180 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
181 year = {2015},
182 doi = {10.1093/nar/gkv351},
183 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.},
184 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
185 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
186 journal = {Nucleic Acids Research}
187 }
188
189 </citation>
190
191 </citations>
192
193 </tool>