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author vmarcon
date Mon, 06 Feb 2017 13:37:49 -0500
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1 <tool id="teannot" name="REPET Lite - TEannot" version="1.5.0">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Genome annotation for masking transposable elements</description>
5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements>
8 <requirement type="binary">python</requirement>
9 <requirement type="package" version="2.5">repet</requirement>
10 </requirements>
11
12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
13 <stdio>
14 <!-- Anything other than zero is an error -->
15 <exit_code range="1:" level="fatal"/>
16 <exit_code range=":-1" level="fatal"/>
17
18 </stdio>
19
20
21 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
22 <version_command>
23 <!--
24 tool_binary -v
25 -->
26 </version_command>
27
28 <!-- [REQUIRED] The command to execute -->
29 <command interpreter="bash">
30 TEannot.sh $fasta $library $outputfile $outputmaskedfile $outputlog $outputconfig
31 #if str( $withStats ) == "yes":
32 $outputstatsfile
33 #else :
34 $withStats
35 #end if
36 $classif
37 $outputmasked_SSRmaskfile
38 </command>
39
40 <!-- [REQUIRED] Input files and tool parameters -->
41 <inputs>
42 <param name="fasta" type="data" format="fasta" optional="false" label="Fasta alignment input" />
43 <param name="library" type="data" format="fasta" optional="false" label="Fasta TE library [from TEdenovo]" />
44 <param name="classif" type="data" format="tabular" optional="true" label="Classification file" help="To add classification information in the output file." />
45 <param name="label" type="text" label="Output name" />
46 <param name="withStats" type="select" label="Get statistical file">
47 <option value="yes" selected="true">Yes</option>
48 <option value="no">No</option>
49 </param>
50 </inputs>
51
52 <!-- [REQUIRED] Output files -->
53 <outputs>
54 <data name="outputlog" type="data" format="txt" label="TEannot-#if str($label)=='' then $fasta.name else $label #.log" />
55 <data name="outputfile" type="data" format="gff3" label="TEannot-#if str($label)=='' then $fasta.name else $label #.gff3" />
56 <data name="outputmaskedfile" type="data" format="fasta" label="TEannot-#if str($label)=='' then $fasta.name else $label #_masked.fa" />
57 <data name="outputmasked_SSRmaskfile" type="data" format="fasta" label="TEannot-#if str($label)=='' then $fasta.name else $label #_SSRmask.fa" />
58 <data name="outputstatsfile" type="data" format="txt" label="TEannot-#if str($label)=='' then $fasta.name else $label #.stats" >
59 <filter>(withStats == 'yes')</filter>
60 </data>
61 <data name="outputconfig" type="data" format="txt" label="TEannot-#if str($label)=='' then $fasta.name else $label #.cfg" />
62 </outputs>
63
64
65 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
66 <tests>
67 <!-- [HELP] Test files have to be in the ~/test-data directory -->
68 <test>
69 <param name="fasta" value="alignment.fa" />
70 <param name="library" value="libTE.fa" />
71 <output name="outputfile" >
72 <assert_contents>
73 <has_line_matching expression="^##gff-version 3" />
74 <has_n_columns n="9" />
75 </assert_contents>
76 </output>
77 <output name="outputmaskedfile" >
78 <assert_contents>
79 <has_line_matching expression="^>\w+" />
80 <has_line_matching expression="[ACTGX]{60}" />
81 </assert_contents>
82 </output>
83 <output name="outputstatsfile">
84 <assert_contents>
85 <has_line_matching expression="^nb of sequences:" />
86 <has_line_matching expression="^mean of median length percentage of all families:" />
87 </assert_contents>
88 </output>
89 <output name="outputlog">
90 <assert_contents>
91 <has_line_matching expression="^step 7 finished successfully" />
92 <has_line_matching expression="^END time: \d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}" />
93 <has_line_matching expression="^Writing fasta file" />
94 </assert_contents>
95 </output>
96 <output name="outputconfig">
97 <assert_contents>
98 <has_line_matching expression="^project_name: \d{8}" />
99 <has_line_matching expression="^repet_version: 2.5" />
100 <has_line_matching expression="^tmpDir:" />
101 <has_line_matching expression="^clean: yes" />
102 </assert_contents>
103 </output>
104 </test>
105 <test>
106 <param name="fasta" value="alignment.fa" />
107 <param name="library" value="libTE.fa" />
108 <param name="classif" value="libTE.classif" />
109 <param name="withStats" value="no"/>
110 <output name="outputfile">
111 <assert_contents>
112 <has_line_matching expression="^##gff-version 3" />
113 <has_n_columns n="9" />
114 </assert_contents>
115 </output>
116 <output name="outputmaskedfile">
117 <assert_contents>
118 <has_line_matching expression="^>\w+" />
119 <has_line_matching expression="[ACTGX]{60}" />
120 </assert_contents>
121 </output>
122 <output name="outputlog">
123 <assert_contents>
124 <has_line_matching expression="^step 7 finished successfully" />
125 <has_line_matching expression="^END time: \d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}" />
126 <has_line_matching expression="^Writing fasta file" />
127 </assert_contents>
128 </output>
129 <output name="outputconfig">
130 <assert_contents>
131 <has_line_matching expression="^project_name: \d{8}" />
132 <has_line_matching expression="^repet_version: 2.5" />
133 <has_line_matching expression="^tmpDir:" />
134 <has_line_matching expression="^clean: yes" />
135 </assert_contents>
136 </output>
137 </test>
138 </tests>
139
140 <!-- [OPTIONAL] Help displayed in Galaxy -->
141 <help>
142 <![CDATA[
143 .. class:: infomark
144
145 **Authors**
146 Gwendoline Andres
147 Valentin Marcon
148 Veronique Jamilloux
149 Olivier Inizan
150
151 ---------------------------------------------------
152
153 .. class:: infomark
154
155 **Please cite** If you use this tool, please cite
156
157 ---------------------------------------------------
158
159 ==============
160 TEannot Lite
161 ==============
162
163 -----------
164 Description
165 -----------
166
167 REPET is for detection and annotation of transposable elements (TE). The ligth version available on Galaxy is specialised on transposable element masking.
168 TEannot is the second and last step to mask TE on the genome.
169 For a detailed description of each parameter used, please consult the Galaxy page in "Shared Data > Published Pages"
170
171 -----------------
172 Workflow position
173 -----------------
174
175 **Upstream tools**
176
177 =========== ========================== =======
178 Name output file(s) format
179 =========== ========================== =======
180 TEdenovo Fasta file with TE library fasta
181 =========== ========================== =======
182
183
184 ----------
185 Input file
186 ----------
187
188 Fasta file
189 Genome file at fasta format
190
191 Library file
192 Fasta file with a library of transposable elements from TEdenovo.
193
194 ----------
195 Parameters
196 ----------
197
198 Masked file
199 To get an additionnal output file : Masked fasta file
200
201
202 ------------
203 Output files
204 ------------
205
206 Output_gff3
207 GFF3 file with transposable elements
208 Output_masked_fasta
209 Input fasta file masked with TE infos
210 Output_config
211 File to show which params have been used
212 Output_stats
213 File with statistics on TE library
214
215 ------------
216 Dependencies
217 ------------
218
219
220 ---------------------------------------------------
221
222 ---------------
223 Working example
224 ---------------
225
226 Input files
227 ===========
228
229 Fasta file
230 ----------
231
232 ::
233
234 >dmel_chr4
235 GAGAACCGTCCTGTAAGTACTCTTGCTTTAAATACGAAAGTAATACTAATCCATGACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATGTTCATCATGAATCTATAGTTAACTTGATGTTGTGCTCCATGTACGATATAAAAAGTTAGATA
236
237
238 Fasta Library
239 -------------
240
241 ::
242
243 >DTX-incomp_20150325110123-B-G1-Map3
244 ATACAGCTGCGGTTAAAATAATAGCACTACTGCAGGTGGAAAGTTGATTTCCTAAAAAAA
245 ATTATTAAATGTTTATATTTTTTTAAGTCAGATTGCATGAATAATAAGTACCATATGTTG
246 GCTCTCTGAGCAAGAAATTTTTAGTCTCT
247 >DTX-incomp_20150325110123-B-P1.0-Map3
248 CTTGTGTCCGCACTTCGTGCCTCAAGATATGAACAAAGCAAAGACACTAGAATAATTCTA
249 GTGTATTACTTTGATATTACTTTTGCAATAAACAGTTATCATATTTTTA
250
251
252 Output files
253 ============
254
255 GFF3 output :
256 -------------
257
258 ::
259
260 ##gff-version 3
261 dmel_chr4 test_REPET_TEs match 971161 971469 0.0 - . ID=ms1_dmel_chr4_DTX-incomp_DmelChr4-B-G1-Map3;Target=DTX-incomp_DmelChr4-B-G1-Map3 45 542
262 dmel_chr4 test_REPET_TEs match_part 971161 971271 0.0 - . ID=mp1-1_dmel_chr4_DTX-incomp_DmelChr4-B-G1-Map3;Parent=ms1_dmel_chr4_DTX-incomp_DmelChr4-B-G1-Map3;Target=DTX-incomp_DmelChr4-B-G1-Map3 435 542;Identity=94.4
263
264 Masked fasta output :
265 ---------------------
266
267 ::
268
269 >dmel_chr4
270 GAGAACCGTCCTGTAAGTACTCTTGCTTTAAATACGXXXXXXXXXXXXXXXXXXXXACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATGTTCATCATGAATCTATAGTTAACTTGATGTTGTGCTCCATGTACGATATAAAAAGTTAGATA
271
272 Config file :
273 -------------
274
275 ::
276
277 [repet_env]
278 repet_version: 2.4
279 repet_host: ******
280 repet_user: ******
281
282 Statistics file :
283 -----------------
284
285 ::
286
287 nb of sequences: 8
288 nb of matched sequences: 8
289 cumulative coverage: 133656 bp
290
291 ]]>
292 </help>
293
294 <citations>
295 <citation type="bibtex"><![CDATA[@article{10.1371/journal.pone.0016526,
296 author = {Flutre, Timothée AND Duprat, Elodie AND Feuillet, Catherine AND Quesneville, Hadi},
297 journal = {PLoS ONE},
298 publisher = {Public Library of Science},
299 title = {Considering Transposable Element Diversification in <italic>De Novo</italic> Annotation Approaches},
300 year = {2011},
301 month = {01},
302 volume = {6},
303 url = {http://dx.doi.org/10.1371%2Fjournal.pone.0016526},
304 pages = {e16526},
305 abstract = {
306 <p>Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the <italic>de novo</italic> identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the <italic>Drosophila melanogaster</italic> and <italic>Arabidopsis thaliana</italic> genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species.</p>
307 },
308 number = {1},
309 doi = {10.1371/journal.pone.0016526}
310 }]]></citation>
311 <citation type="bibtex"><![CDATA[@article{10.1371/journal.pone.0094101,
312 author = {Maumus, Florian AND Quesneville, Hadi},
313 journal = {PLoS ONE},
314 publisher = {Public Library of Science},
315 title = {Deep Investigation of <italic>Arabidopsis thaliana</italic> Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter},
316 year = {2014},
317 month = {04},
318 volume = {9},
319 url = {http://dx.doi.org/10.1371%2Fjournal.pone.0094101},
320 pages = {e94101},
321 abstract = {<p>Eukaryotic genomes contain highly variable amounts of DNA with no apparent function. This so-called junk DNA is composed of two components: repeated and repeat-derived sequences (together referred to as the repeatome), and non-annotated sequences also known as genomic dark matter. Because of their high duplication rates as compared to other genomic features, transposable elements are predominant contributors to the repeatome and the products of their decay is thought to be a major source of genomic dark matter. Determining the origin and composition of junk DNA is thus important to help understanding genome evolution as well as host biology. In this study, we have used a combination of tools enabling to show that the repeatome from the small and reducing <italic>A. thaliana</italic> genome is significantly larger than previously thought. Furthermore, we present the concepts and results from a series of innovative approaches suggesting that a significant amount of the <italic>A. thaliana</italic> dark matter is of repetitive origin. As a tentative standard for the community, we propose a deep compendium annotation of the <italic>A. thaliana</italic> repeatome that may help addressing farther genome evolution as well as transcriptional and epigenetic regulation in this model plant.</p>},
322 number = {4},
323 doi = {10.1371/journal.pone.0094101}
324 }]]></citation>
325 </citations>
326
327 </tool>