|
20
|
1 <!--Matrix Scan - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
|
|
|
2 Copyright (C) 2015 Institut Curie
|
|
|
3
|
|
|
4 This program is free software: you can redistribute it and/or modify
|
|
|
5 it under the terms of the GNU General Public License as published by
|
|
|
6 the Free Software Foundation, either version 3 of the License, or
|
|
|
7 (at your option) any later version.
|
|
|
8
|
|
|
9 This program is distributed in the hope that it will be useful,
|
|
|
10 but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
|
11 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
|
12 GNU General Public License for more details.
|
|
|
13
|
|
|
14 You should have received a copy of the GNU General Public License
|
|
|
15 along with this program. If not, see <http://www.gnu.org/licenses/>.-->
|
|
|
16 <tool id="rsat_matrix_scan" name="RSAT Matrix Scan" version="1.0">
|
|
|
17 <description>Scan a DNA sequence with a profile matrix</description>
|
|
|
18 <requirements>
|
|
40
|
19 <requirement type="package" version="0.6">python_suds</requirement>
|
|
20
|
20 </requirements>
|
|
|
21 <command interpreter="python">
|
|
|
22 matrixScan_wrapper.py -sequence $sequenceFile -matrix $matrixFile -outGalaxy $txtFile -matrix_format $matrix_format -n_treatment $n_treatment -markov $markov
|
|
|
23 #if $background_method_condition.background_method == "bgfile":
|
|
|
24 -organism $background_method_condition.serverChoice.organism
|
|
|
25 -server $background_method_condition.serverChoice.server
|
|
|
26 -background $background_method_condition.background
|
|
|
27 #else:
|
|
|
28 -server $background_method_condition.organism
|
|
|
29 #end if
|
|
|
30 #if $scanning_options_condition.scanning_options == "yes":
|
|
|
31 -origin $scanning_options_condition.origin
|
|
|
32 -return $scanning_options_condition.return
|
|
|
33 -uth $scanning_options_condition.pval
|
|
|
34 #end if
|
|
|
35 </command>
|
|
|
36 <inputs>
|
|
|
37 <param name="sequenceFile" type="data" format="fasta" label="Sequences File (FASTA file)" />
|
|
|
38 <param name="matrix_format" type="select" label="Matrix format" help="" >
|
|
|
39 <option value="tab" selected="true">tab</option>
|
|
|
40 <option value="cb" >cb</option>
|
|
|
41 <option value="transfac" >transfac</option>
|
|
|
42 <option value="jaspar" >jaspar</option>
|
|
|
43 <option value="consensus" >consensus</option>
|
|
|
44 <option value="gibbs" >gibbs</option>
|
|
|
45 <option value="meme" >meme</option>
|
|
|
46 <option value="assembly" >assembly</option>
|
|
|
47 </param>
|
|
|
48 <param name="matrixFile" type="data" format="txt" label="Matrix (or matrices) (TXT file)" />
|
|
|
49 <param name="n_treatment" type="select" label="Treatment of N characters" help="" >
|
|
|
50 <option value="score" selected="true">N-containing regions are skipped</option>
|
|
|
51 <option value="skip" >N-containing regions are scored</option>
|
|
|
52 </param>
|
|
|
53 <param name="markov" type="select" label="Markov order" help="" >
|
|
|
54 <option value="0" >0</option>
|
|
|
55 <option value="1" selected="true">1</option>
|
|
|
56 <option value="2">2</option>
|
|
|
57 </param>
|
|
|
58 <conditional name="background_method_condition" >
|
|
|
59 <param name="background_method" type="select" label="Background model estimation method" help="" >
|
|
|
60 <option value="bginput" selected="true">Estimate residue probabilities from input sequences</option>
|
|
|
61 <option value="bgfile">Organism-specific</option>
|
|
|
62 </param>
|
|
|
63 <when value="bginput"/>
|
|
|
64 <param name="server" type="select" label="RSAT server (if Time out error, change server)" >
|
|
|
65 <option value="fr_ens" selected="true">RSAT Protists</option>
|
|
|
66 <option value="fr_mrs" >RSAT Fungis</option>
|
|
|
67 <option value="fr_ro" >RSAT Metazoa</option>
|
|
|
68 <option value="fr_mrs_2" >RSAT Teaching</option>
|
|
|
69 <option value="es" >RSAT Plants</option>
|
|
|
70 <option value="mx" >RSAT Prokaryotes</option>
|
|
|
71 </param>
|
|
|
72 <when value="bgfile">
|
|
|
73 <conditional name="serverChoice">
|
|
|
74 <param name="server" type="select" label="RSAT server (if Time out error, change server)" >
|
|
|
75 <option value="fr_ens" selected="true">RSAT Protists</option>
|
|
|
76 <option value="fr_mrs" >RSAT Fungis</option>
|
|
|
77 <option value="fr_ro" >RSAT Metazoa</option>
|
|
|
78 <option value="fr_mrs_2" >RSAT Teaching</option>
|
|
|
79 <option value="es" >RSAT Plants</option>
|
|
|
80 <option value="mx" >RSAT Prokaryotes</option>
|
|
|
81 </param>
|
|
|
82 <when value="fr_ens">
|
|
|
83 <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
|
|
|
84 <options from_file="RSAT_organisms_fr_ens.loc">
|
|
|
85 <column name="name" index="0" />
|
|
|
86 <column name="value" index="0" />
|
|
|
87 </options>
|
|
|
88 </param>
|
|
|
89 </when>
|
|
|
90 <when value="fr_mrs">
|
|
|
91 <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
|
|
|
92 <options from_file="RSAT_organisms_fr_mrs.loc">
|
|
|
93 <column name="name" index="0" />
|
|
|
94 <column name="value" index="0" />
|
|
|
95 </options>
|
|
|
96 </param>
|
|
|
97 </when>
|
|
|
98 <when value="fr_mrs_2">
|
|
|
99 <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
|
|
|
100 <options from_file="RSAT_organisms_fr_mrs_2.loc">
|
|
|
101 <column name="name" index="0" />
|
|
|
102 <column name="value" index="0" />
|
|
|
103 </options>
|
|
|
104 </param>
|
|
|
105 </when>
|
|
|
106 <when value="fr_ro">
|
|
|
107 <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
|
|
|
108 <options from_file="RSAT_organisms_fr_ro.loc">
|
|
|
109 <column name="name" index="0" />
|
|
|
110 <column name="value" index="0" />
|
|
|
111 </options>
|
|
|
112 </param>
|
|
|
113 </when>
|
|
|
114 <when value="mx">
|
|
|
115 <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
|
|
|
116 <options from_file="RSAT_organisms_mx.loc">
|
|
|
117 <column name="name" index="0" />
|
|
|
118 <column name="value" index="0" />
|
|
|
119 </options>
|
|
|
120 </param>
|
|
|
121 </when>
|
|
|
122 <when value="es">
|
|
|
123 <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
|
|
|
124 <options from_file="RSAT_organisms_es.loc">
|
|
|
125 <column name="name" index="0" />
|
|
|
126 <column name="value" index="0" />
|
|
|
127 </options>
|
|
|
128 </param>
|
|
|
129 </when>
|
|
|
130 </conditional>
|
|
|
131 <param name="background" type="select" label="Sequence type" help="" >
|
|
|
132 <option value="upstream" selected="true">Upstream</option>
|
|
|
133 <option value="upstream-noorf" >Upstream-noorf</option>
|
|
|
134 </param>
|
|
|
135 </when>
|
|
|
136 </conditional>
|
|
|
137 <conditional name="scanning_options_condition" >
|
|
|
138 <param name="scanning_options" type="select" label="Scanning options" help="" >
|
|
|
139 <option value="no" selected="true">No</option>
|
|
|
140 <option value="yes">Yes</option>
|
|
|
141 </param>
|
|
|
142 <when value="no"/>
|
|
|
143 <when value="yes">
|
|
|
144 <param name="origin" type="select" label="Sequence Origin">
|
|
|
145 <option value="start" selected="true">start</option>
|
|
|
146 <option value="center" >center</option>
|
|
|
147 <option value="end" >end</option>
|
|
|
148 </param>
|
|
|
149 <param name="return" type="select" label="Return" help="" >
|
|
|
150 <option value="limits" selected="true">sites only</option>
|
|
|
151 <option value="limits,pval" >sites + pval</option>
|
|
|
152 </param>
|
|
|
153 <param name="pval" type="float" value="0.0001" min="0" max="1" label="Threshold (if return is 'sites only', the threshold is set on the weight score and if return is 'sites + pval', the threshold is set on the pval)"/>
|
|
|
154 </when>
|
|
|
155 </conditional>
|
|
|
156 </inputs>
|
|
|
157 <outputs>
|
|
|
158 <data format="txt" name="txtFile" label="RSAT output - matrixScan results" />
|
|
|
159 </outputs>
|
|
|
160
|
|
|
161 <help>
|
|
|
162
|
|
|
163 **What it does**
|
|
|
164
|
|
|
165 .. class:: infomark
|
|
|
166
|
|
|
167 Scan a DNA sequence with a profile matrix.
|
|
|
168
|
|
|
169 ------
|
|
|
170
|
|
|
171 *Example with transfac matrix and fasta file*::
|
|
|
172
|
|
|
173 AC m1
|
|
|
174 XX
|
|
|
175 ID m1
|
|
|
176 XX
|
|
|
177 DE m1 m1; from JASPAR
|
|
|
178 P0 A C G T
|
|
|
179 1 4 16 0 0
|
|
|
180 2 19 0 1 0
|
|
|
181 3 0 20 0 0
|
|
|
182 4 0 0 20 0
|
|
|
183 5 0 0 0 20
|
|
|
184 6 0 0 20 0
|
|
|
185 XX
|
|
|
186 CC program: jaspar
|
|
|
187 CC matrix.nb: 1
|
|
|
188 CC min.prior: 0.25
|
|
|
189 CC alphabet.size: 4
|
|
|
190 CC max.bits: 2
|
|
|
191 CC total.information: 6.56407409450406
|
|
|
192 CC information.per.column: 1.09401234908401
|
|
|
193 CC max.possible.info.per.col: 1.38629436111989
|
|
|
194 CC consensus.strict: CACGTG
|
|
|
195 CC consensus.strict.rc: CACGTG
|
|
|
196 CC consensus.IUPAC: CACGTG
|
|
|
197 CC consensus.IUPAC.rc: CACGTG
|
|
|
198 CC consensus.regexp: CACGTG
|
|
|
199 CC consensus.regexp.rc: CACGTG
|
|
|
200 CC residues.content.crude.freq: a:0.1917|c:0.3000|g:0.3417|t:0.1667
|
|
|
201 CC G+C.content.crude.freq: 0.641666666666667
|
|
|
202 CC residues.content.corrected.freq: a:0.1944|c:0.2976|g:0.3373|t:0.1706
|
|
|
203 CC G+C.content.corrected.freq: 0.634920634920635
|
|
|
204 XX
|
|
|
205 //
|
|
|
206
|
|
|
207 >mm9_chr3_121848111_121848740_+
|
|
|
208 tggggtgggttccaggacagccaggactgtcacacaaagaaaccttgtctcaaaaaaaca
|
|
|
209 aaaCAAAAAACAAAACAAAACCAAGCAAGCAAGCAAACATGGGCTTAAATctggatacag
|
|
|
210 tggcctttatttctagttccagtgactgggagactgaaacaagagagtcacttgagtaca
|
|
|
211 ggagtgcaaggctagcttgagcaatatagtaagactatctcaaaaTGTGAATTtagatca
|
|
|
212 acagaattgacatcaagaaaaatactgatatcactcaaagcaatctacagattcaacaca
|
|
|
213 atctccatcaacatgacaatgacttccatcaGCATGACAATGACTCCATCAACATGCCAA
|
|
|
214 TGGGCCCCATCAACATAACAATGACCCCTATCATCATGACAATGATCCCCATCAACATGA
|
|
|
215 CAATGACCTCCATCAACATGACAATTACTCCTGTCAACATGCCAATtgttggggttcaga
|
|
|
216 agtcaccctgcaaaccacaagaacactaatctcagtcaagcagggatggtttactgaacg
|
|
|
217 tatatccaaagactgagtgaccaagggaacagctcagactctagagctgaaagctagctg
|
|
|
218 tgcgctggacatttctcggggccaactta
|
|
|
219 >mm9_chr14_86795691_86796311_+
|
|
|
220 CTCAAGGAGGATCCAGAAGTTGGCAGTTTCTGAGGCGAGTCCCATATTCCTCCCCTAAGG
|
|
|
221 GGTCAGGATTTTTCAGGTCTGGGCTCTTCTTGTTCTTTTGACAGCGACATTAATAATTGT
|
|
|
222 ACCAGCTCTCCCCTGGCAGGGCCGCACCACAGAGTAAAGCCTGGAGTAGGAGCTGTGCCC
|
|
|
223 AGCGCAATAATACCAGTTAAATAAGTACGTTCATTACCTCCCAACAGTCAAGGAGTTTAA
|
|
|
224 AATCCGTCAATTCACCCCACATGAGGGAGATTATGTGATTTACATGTTAAAGTGCCCCTG
|
|
|
225 TGGTTTGATTTGCATAGCAAAGACTTTGGGGGCACAGAAACAAAGCATCCGCATGCATGA
|
|
|
226 CAAGAGGACTATTAGCATAGAGAGAGCAGGTTTTCCGACAGCCCAGCCTGGCAAACAATG
|
|
|
227 CTGCACCTTCGCTGCTCGCTGGAGTTTATAGGATTTGACAGTTTCTCATCTGAGGGAGGA
|
|
|
228 GAAGGTTAGGGAGTTGGGGTGGAATGAGGTTCGCTAGATTGGCTGTCTGCCTTAAGCACA
|
|
|
229 ATAATTTGTCTTTCTCTGAAGACCTCCCCTCCTCTTATCACCTTTATCGTTTCTTTCTGA
|
|
|
230 TGTTCATTCAAAGACGTCTT
|
|
|
231
|
|
|
232 ------
|
|
|
233
|
|
|
234 *Results with threshold (sites + pval) 0.0001*::
|
|
|
235
|
|
|
236 #seq_id ft_type ft_name strand start end sequence weight Pval ln_Pval sig
|
|
|
237 mm9_chr3_121848111_121848740_+ limit START_END D 1 629 . 0 0 0 0
|
|
|
238 mm9_chr14_86795691_86796311_+ limit START_END D 1 620 . 0 0 0 0
|
|
|
239 mm9_chr15_84452311_84453000_+ limit START_END D 1 689 . 0 0 0 0
|
|
|
240 mm9_chr1_134118761_134119120_+ limit START_END D 1 359 . 0 0 0 0
|
|
|
241 mm9_chr17_35640731_35641360_+ limit START_END D 1 629 . 0 0 0 0
|
|
|
242 mm9_chr18_66052791_66053190_+ limit START_END D 1 399 . 0 0 0 0
|
|
|
243 mm9_chr6_125165051_125165561_+ limit START_END D 1 510 . 0 0 0 0
|
|
|
244 mm9_chr16_35588051_35588520_+ limit START_END D 1 469 . 0 0 0 0
|
|
|
245 mm9_chr2_51927461_51927981_+ limit START_END D 1 520 . 0 0 0 0
|
|
|
246 mm9_chr2_51927461_51927981_+ site m1 D 106 111 CACGTG 9.1 7.2e-05 -9.545 4.145
|
|
|
247 mm9_chr2_51927461_51927981_+ site m1 R 106 111 CACGTG 9.1 7.2e-05 -9.545 4.145
|
|
|
248 mm9_chr3_18523921_18524271_+ limit START_END D 1 350 . 0 0 0 0
|
|
|
249 mm9_chr17_29324151_29324630_+ limit START_END D 1 479 . 0 0 0 0
|
|
|
250 mm9_chr5_111009921_111010390_+ limit START_END D 1 469 . 0 0 0 0
|
|
|
251 mm9_chr14_37727831_37728360_+ limit START_END D 1 529 . 0 0 0 0
|
|
|
252 mm9_chr11_77707171_77707751_+ limit START_END D 1 580 . 0 0 0 0
|
|
|
253 mm9_chr14_50067391_50067801_+ limit START_END D 1 410 . 0 0 0 0
|
|
|
254
|
|
|
255 </help>
|
|
|
256 <citations>
|
|
|
257 <citation type="bibtex">@article{Medina-Rivera22042015,
|
|
|
258 author = {Medina-Rivera, Alejandra and Defrance, Matthieu and Sand, Olivier and Herrmann, Carl and Castro-Mondragon, Jaime A. and Delerce, Jeremy and Jaeger, Sébastien and Blanchet, Christophe and Vincens, Pierre and Caron, Christophe and Staines, Daniel M. and Contreras-Moreira, Bruno and Artufel, Marie and Charbonnier-Khamvongsa, Lucie and Hernandez, Céline and Thieffry, Denis and Thomas-Chollier, Morgane and van Helden, Jacques},
|
|
|
259 title = {RSAT 2015: Regulatory Sequence Analysis Tools},
|
|
|
260 year = {2015},
|
|
|
261 doi = {10.1093/nar/gkv362},
|
|
|
262 URL = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.abstract},
|
|
|
263 eprint = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.full.pdf+html},
|
|
|
264 journal = {Nucleic Acids Research}
|
|
|
265 }</citation>
|
|
|
266 </citations>
|
|
|
267 </tool>
|
|
|
268
|
