|
0
|
1 <tool id="tedenovo" name="REPET Lite - TEdenovo" version="2.2.0">
|
|
|
2
|
|
|
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
|
|
|
4 <description> Compute a library of transposable element</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 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
|
|
|
21 <version_command>
|
|
|
22 TEdenovo.py --version
|
|
|
23 </version_command>
|
|
|
24
|
|
|
25 <!-- [REQUIRED] The command to execute -->
|
|
|
26 <command interpreter="bash">
|
|
|
27 TEdenovo.sh $fasta $outputfasta $classif $outputlog $outputconfig $outputstats
|
|
|
28 #if str( $classif ) == "yes":
|
|
|
29 $outputclassif
|
|
|
30 #else
|
|
|
31 ''
|
|
|
32 #end if
|
|
|
33 </command>
|
|
|
34
|
|
|
35 <!-- [REQUIRED] Input files and tool parameters -->
|
|
|
36 <inputs>
|
|
|
37 <param name="fasta" type="data" format="fasta" optional="false" label="Fasta alignment input" />
|
|
|
38 <param name="classif" type="select" label="Get classification informations" help="To add the informations at annotation file on next step." >
|
|
|
39 <option value="no" selected="true">No</option>
|
|
|
40 <option value="yes">Yes</option>
|
|
|
41 </param>
|
|
|
42 <param name="label" type="text" label="Output name" />
|
|
|
43 </inputs>
|
|
|
44
|
|
|
45 <!-- [REQUIRED] Output files -->
|
|
|
46 <outputs>
|
|
|
47 <data name="outputlog" type="data" format="txt" label="TEdenovo-#if str($label)=='' then $fasta.name else $label #.log" />
|
|
|
48 <data name="outputfasta" type="data" format="fasta" label="TEdenovo-#if str($label)=='' then $fasta.name else $label #.TElib.fa" />
|
|
|
49 <data name="outputstats" type="data" format="txt" label="TEdenovo-#if str($label)=='' then $fasta.name else $label #.classif_stats.txt" />
|
|
|
50 <data name="outputclassif" type="data" format="tabular" label="TEdenovo-#if str($label)=='' then $fasta.name else $label #.classif" >
|
|
|
51 <filter>(classif == 'yes')</filter>
|
|
|
52 </data>
|
|
|
53 <data name="outputconfig" type="data" format="txt" label="TEdenovo-#if str($label)=='' then $fasta.name else $label #.cfg" />
|
|
|
54 </outputs>
|
|
|
55
|
|
|
56
|
|
|
57 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
|
|
|
58 <tests>
|
|
|
59 <!-- [HELP] Test files have to be in the ~/test-data directory -->
|
|
|
60 <test>
|
|
|
61 <param name="fasta" value="DmelChr4Chr3.fa" />
|
|
|
62 <output name="outputfasta">
|
|
|
63 <assert_contents>
|
|
|
64 <has_line_matching expression="^>\w+" />
|
|
|
65 <has_line_matching expression="[ACTG]{60}" />
|
|
|
66 </assert_contents>
|
|
|
67 </output>
|
|
|
68 <output name="outputlog">
|
|
|
69 <assert_contents>
|
|
|
70 <has_line_matching expression="^step 7 finished successfully" />
|
|
|
71 <has_line_matching expression="^END time: \d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}" />
|
|
|
72 <has_line_matching expression="^Writing fasta file" />
|
|
|
73 </assert_contents>
|
|
|
74 </output>
|
|
|
75 <output name="outputconfig">
|
|
|
76 <assert_contents>
|
|
|
77 <has_line_matching expression="^project_name: \d{8}" />
|
|
|
78 <has_line_matching expression="^repet_version: 2.5" />
|
|
|
79 <has_line_matching expression="^tmpDir:" />
|
|
|
80 <has_line_matching expression="^clean: yes" />
|
|
|
81 </assert_contents>
|
|
|
82 </output>
|
|
|
83 <output name="outputstats">
|
|
|
84 <assert_contents>
|
|
|
85 <has_line_matching expression="-------Summary---------" />
|
|
|
86 <has_line_matching expression="TOTAL: \d+ (\d+.\d+%)" />
|
|
|
87 <has_line_matching expression="------NOTES---------" />
|
|
|
88 </assert_contents>
|
|
|
89 </output>
|
|
|
90 </test>
|
|
|
91 <test>
|
|
|
92 <param name="fasta" value="DmelChr4Chr3.fa" />
|
|
|
93 <param name="classif" value="yes" />
|
|
|
94 <output name="outputfasta">
|
|
|
95 <assert_contents>
|
|
|
96 <has_line_matching expression="^>\w+" />
|
|
|
97 <has_line_matching expression="[ACTG]{60}" />
|
|
|
98 </assert_contents>
|
|
|
99 </output>
|
|
|
100 <output name="outputlog">
|
|
|
101 <assert_contents>
|
|
|
102 <has_line_matching expression="^step 7 finished successfully" />
|
|
|
103 <has_line_matching expression="^END time: \d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}" />
|
|
|
104 <has_line_matching expression="^Writing fasta file" />
|
|
|
105 </assert_contents>
|
|
|
106 </output>
|
|
|
107 <output name="outputconfig">
|
|
|
108 <assert_contents>
|
|
|
109 <has_line_matching expression="^project_name: \d{8}" />
|
|
|
110 <has_line_matching expression="^repet_version: 2.5" />
|
|
|
111 <has_line_matching expression="^tmpDir:" />
|
|
|
112 <has_line_matching expression="^clean: yes" />
|
|
|
113 </assert_contents>
|
|
|
114 </output>
|
|
|
115 <output name="outputstats">
|
|
|
116 <assert_contents>
|
|
|
117 <has_line_matching expression="-------Summary---------" />
|
|
|
118 <has_line_matching expression="TOTAL: \d+ (\d+.\d+%)" />
|
|
|
119 <has_line_matching expression="------NOTES---------" />
|
|
|
120 </assert_contents>
|
|
|
121 </output>
|
|
|
122 <output name="outputclassif">
|
|
|
123 <assert_contents>
|
|
|
124 <has_n_columns n="8" />
|
|
|
125 </assert_contents>
|
|
|
126 </output>
|
|
|
127 </test>
|
|
|
128 </tests>
|
|
|
129
|
|
|
130 <!-- [OPTIONAL] Help displayed in Galaxy -->
|
|
|
131 <help>
|
|
|
132 <![CDATA[
|
|
|
133 .. class:: infomark
|
|
|
134
|
|
|
135
|
|
|
136 **Authors**
|
|
|
137 Gwendoline Andres
|
|
|
138 Valentin Marcon
|
|
|
139 Veronique Jamilloux
|
|
|
140 Olivier Inizan
|
|
|
141
|
|
|
142 ---------------------------------------------------
|
|
|
143
|
|
|
144 .. class:: infomark
|
|
|
145
|
|
|
146 **Please cite** If you use this tool, please cite
|
|
|
147
|
|
|
148 ---------------------------------------------------
|
|
|
149
|
|
|
150 ==============
|
|
|
151 TEdenovo Lite
|
|
|
152 ==============
|
|
|
153
|
|
|
154 -----------
|
|
|
155 Description
|
|
|
156 -----------
|
|
|
157 REPET is for detection and annotation of transposable elements (TE). The ligth version available on Galaxy is specialised on transposable element masking.
|
|
|
158 TEdenovo is the first step to constitute a consensus library of TE.
|
|
|
159 For a detailed description of each parameter used, please consult the Galaxy page in "Shared Data > Published Pages"
|
|
|
160
|
|
|
161 -----------------
|
|
|
162 Workflow position
|
|
|
163 -----------------
|
|
|
164
|
|
|
165 **Downstream tools**
|
|
|
166
|
|
|
167 =========== ========================== =======
|
|
|
168 Name output file(s) format
|
|
|
169 =========== ========================== =======
|
|
|
170 TEannot GFF with TE masked gff
|
|
|
171 =========== ========================== =======
|
|
|
172
|
|
|
173
|
|
|
174 ----------
|
|
|
175 Input file
|
|
|
176 ----------
|
|
|
177
|
|
|
178 Fasta file
|
|
|
179 Genome file at fasta format
|
|
|
180
|
|
|
181
|
|
|
182 ------------
|
|
|
183 Output files
|
|
|
184 ------------
|
|
|
185
|
|
|
186 Output_name.fa
|
|
|
187 TE library
|
|
|
188
|
|
|
189 Output_name.log
|
|
|
190 log file to see each steps progress
|
|
|
191
|
|
|
192 Output_name.cfg
|
|
|
193 File to show which params have been used
|
|
|
194
|
|
|
195 Output_name.classif_stats.txt
|
|
|
196 File with statistics you can visualize
|
|
|
197
|
|
|
198 Output_name.classif
|
|
|
199 If asked, the classification file to give to next step (TEannot)
|
|
|
200
|
|
|
201
|
|
|
202 ---------------
|
|
|
203 Working example
|
|
|
204 ---------------
|
|
|
205
|
|
|
206 Input files
|
|
|
207 ===========
|
|
|
208
|
|
|
209 Fasta file
|
|
|
210 -----------
|
|
|
211
|
|
|
212 ::
|
|
|
213
|
|
|
214 >dmel_chr4
|
|
|
215 GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC
|
|
|
216 GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT
|
|
|
217 GGAGGGTTCTACAAGAAAGCGGTGGAGGATTGCTCGCATACTGCGAGACCGTTTCTGAAG
|
|
|
218 GAGATGGCTCATGGAGTACCTGCCTACGCTTGTGCGCCGCGAGAAGTGGTGAAGAAGAAC
|
|
|
219 GGAGCCCATACACCAGGGTGATATGGTCTTCGTCTGCGATCCCGCCTTGCCCCGGCGAGA
|
|
|
220 GTGGTGCAAGGGCATCATGGAGGAAGTCTCCAGCAGAGCAGATGGAGCAACGGCCTATAG
|
|
|
221 AGGACACTGATGCTACCCGTCTCTAAGCTTGCAGTTTTGGATTTAAGTGAATCGGTTATT
|
|
|
222 CACGGGGTCGGGGATGTCGCGGATCGAACGGTGCAATCGATAGGCGTAATCAGTATTTCC
|
|
|
223 AGATAGTGATAAGATTTGGTGGATAAATGTGTGCGGGCACACTAATGGCCGCCATCGTAA
|
|
|
224 GCCGCGAAAAGCTTAGCGTGCATTGTCGATCGAGAGTTTGGAGGGCAAACTGCGGTAAGA
|
|
|
225 TAAGATTAAATAATTTGTACTGAATAATCTTAAAGAATCCTGATGGAAAGCGCCATGCAG
|
|
|
226 TCACATATAATATGTGCAGAGCTCTCCTC
|
|
|
227
|
|
|
228
|
|
|
229 Output files
|
|
|
230 ============
|
|
|
231
|
|
|
232 output fasta : TE library
|
|
|
233 -------------------------
|
|
|
234
|
|
|
235 ::
|
|
|
236
|
|
|
237 >DTX-incomp_20150313101806-B-G1-Map3
|
|
|
238 ATACAGCTGCGGTTAAAATAATAGCACTACTGCAGGTGGAAAGTTGATTTCCTAAAAAAA
|
|
|
239 ATTATTAAATGTTTATATTTTTTTAAGTCAGATTGCATGAATAATAAGTACCATATGTTG
|
|
|
240 GCTCTCTGAGCAAGAAATTTTTAG
|
|
|
241 >RLX-incomp_20150313101806-B-R12-Map3_reversed
|
|
|
242 ATGATAAGTAGGCAAACTATAAAAATGTTCTATTTATGGGCTGCAATAAACATGTCACCG
|
|
|
243 GACAGCATAAGTGGCAACTACAG
|
|
|
244
|
|
|
245
|
|
|
246 output config : .cfg
|
|
|
247 --------------------
|
|
|
248
|
|
|
249 ::
|
|
|
250
|
|
|
251 [repet_env]
|
|
|
252 repet_version: 2.4
|
|
|
253 repet_host: ******
|
|
|
254 repet_user: ******
|
|
|
255
|
|
|
256
|
|
|
257 output stats : .classif_stats.txt
|
|
|
258 ---------------------------------
|
|
|
259
|
|
|
260 ::
|
|
|
261
|
|
|
262 LTR incomp: 1 (10.00%)
|
|
|
263 LTR total (RLX): 1 (10.00%)
|
|
|
264
|
|
|
265 ClassI + one order: 1 (10.00%)
|
|
|
266 ClassI total (RXX): 1 (10.00%)
|
|
|
267
|
|
|
268 -------------------------Summary--------------------------------
|
|
|
269
|
|
|
270 RXX: 1 (10.00%)
|
|
|
271 DXX: 9 (90.00%)
|
|
|
272 TOTAL: 10 (100.00%)
|
|
|
273
|
|
|
274 -----------------------------NOTES------------------------------
|
|
|
275
|
|
|
276
|
|
|
277 output classif : Classification file
|
|
|
278 ------------------------------------
|
|
|
279
|
|
|
280 ::
|
|
|
281
|
|
|
282 DTX-incomp_dataset_370.dat-B-G1-Map3 542 + ok II TIR incomplete CI=37; coding=(TE_BLRtx: TC1_DM:ClassII:TIR:Tc1-Mariner: 32.59%; TE_BLRx: Mariner-1_DAn_1p:ClassII:TIR:Tc1-Mariner: 18.43%); struct=(TElength: <700bps); other=(Other_profiles: PF13936.1_HTH_38_NA_OTHER_27.0: 77.27%(77.27%); SSRCoverage=0.03)
|
|
|
283 DTX-comp_dataset_370.dat-B-G8-Map20 1244 + ok II TIR complete CI=50; coding=(TE_BLRtx: PROTOP:ClassII:TIR:P: 12.03%, PROTOP_A:ClassII:TIR:P: 49.14%); struct=(TElength: >1000bps; TermRepeats: termTIR: 50); other=(SSRCoverage=0.25)
|
|
|
284
|
|
|
285 ]]>
|
|
|
286 </help>
|
|
|
287
|
|
|
288 <citations>
|
|
|
289 <citation type="bibtex"><![CDATA[@article{10.1371/journal.pone.0016526,
|
|
|
290 author = {Flutre, Timothée AND Duprat, Elodie AND Feuillet, Catherine AND Quesneville, Hadi},
|
|
|
291 journal = {PLoS ONE},
|
|
|
292 publisher = {Public Library of Science},
|
|
|
293 title = {Considering Transposable Element Diversification in <italic>De Novo</italic> Annotation Approaches},
|
|
|
294 year = {2011},
|
|
|
295 month = {01},
|
|
|
296 volume = {6},
|
|
|
297 url = {http://dx.doi.org/10.1371%2Fjournal.pone.0016526},
|
|
|
298 pages = {e16526},
|
|
|
299 abstract = {
|
|
|
300 <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>
|
|
|
301 },
|
|
|
302 number = {1},
|
|
|
303 doi = {10.1371/journal.pone.0016526}
|
|
|
304 }]]></citation>
|
|
|
305 <citation type="bibtex"><![CDATA[@article{10.1371/journal.pone.0094101,
|
|
|
306 author = {Maumus, Florian AND Quesneville, Hadi},
|
|
|
307 journal = {PLoS ONE},
|
|
|
308 publisher = {Public Library of Science},
|
|
|
309 title = {Deep Investigation of <italic>Arabidopsis thaliana</italic> Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter},
|
|
|
310 year = {2014},
|
|
|
311 month = {04},
|
|
|
312 volume = {9},
|
|
|
313 url = {http://dx.doi.org/10.1371%2Fjournal.pone.0094101},
|
|
|
314 pages = {e94101},
|
|
|
315 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>},
|
|
|
316 number = {4},
|
|
|
317 doi = {10.1371/journal.pone.0094101}
|
|
|
318 }]]></citation>
|
|
|
319 </citations>
|
|
|
320
|
|
|
321
|
|
|
322 </tool>
|
