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comparison SMART/bacteriaRegulatoryRegion_Detection/interElementGff.xml @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 <tool id="interElementGff" name="interElementGff">
2 <description>Creates a new Gff output, which corresponds to the region of two successive Elements. </description>
3 <command interpreter="perl">
4 interElementGff.pl -i $inputFile
5
6 #if $Optionf5ff.option == "Yes":
7 -f5ff $Optionf5ff.f5ffValue
8 #end if
9
10 #if $Optionff3f.option == "Yes":
11 -ff3f $Optionff3f.ff3fValue
12 #end if
13
14 #if $Optionf5fr.option == "Yes":
15 -f5fr $Optionf5fr.f5frValue
16 #end if
17
18 #if $Optionff3r.option == "Yes":
19 -ff3r $Optionff3r.ff3rValue
20 #end if
21
22 #if $Optionf3rf.option == "Yes":
23 -f3rf $Optionf3rf.f3rfValue
24 #end if
25
26 #if $Optionfr5f.option == "Yes":
27 -fr5f $Optionfr5f.fr5fValue
28 #end if
29
30 #if $Optionf3rr.option == "Yes":
31 -f3rr $Optionf3rr.f3rrValue
32 #end if
33
34 #if $Optionfr5r.option == "Yes":
35 -fr5r $Optionfr5r.fr5rValue
36 #end if
37
38 #if $Optionr5ff.option == "Yes":
39 -r5ff $Optionr5ff.r5ffValue
40 #end if
41
42 #if $Optionrf3f.option == "Yes":
43 -rf3f $Optionrf3f.rf3fValue
44 #end if
45
46 #if $Optionr5fr.option == "Yes":
47 -r5fr $Optionr5fr.r5frValue
48 #end if
49
50 #if $Optionrf3r.option == "Yes":
51 -rf3r $Optionrf3r.rf3rValue
52 #end if
53
54 #if $Optionr3rf.option == "Yes":
55 -r3rf $Optionr3rf.r3rfValue
56 #end if
57
58 #if $Optionrr5f.option == "Yes":
59 -rr5f $Optionrr5f.rr5fValue
60 #end if
61
62 #if $Optionr3rr.option == "Yes":
63 -r3rr $Optionr3rr.r3rrValue
64 #end if
65
66 #if $Optionrr5r.option == "Yes":
67 -rr5r $Optionrr5r.rr5rValue
68 #end if
69
70 -o $outputFile
71 </command>
72
73 <inputs>
74 <param name="inputFile" type="data" label="Input File" format="gff"/>
75
76 <conditional name="Optionf5ff">
77 <param name="option" type="select" label="Option[f5ff]" help="number of nt to exclude from 5' seed when gene before is Forward, seed is Forward and next gene is Forward [default 0]">
78 <option value="Yes">Yes</option>
79 <option value="No" selected="true">No</option>
80 </param>
81 <when value="Yes">
82 <param name="f5ffValue" type="integer" value="10"/>
83 </when>
84 <when value="No">
85 </when>
86 </conditional>
87
88 <conditional name="Optionff3f">
89 <param name="option" type="select" label="Option[ff3f]">
90 <option value="Yes">Yes</option>
91 <option value="No" selected="true">No</option>
92 </param>
93 <when value="Yes">
94 <param name="ff3fValue" type="integer" value="30"/>
95 </when>
96 <when value="No">
97 </when>
98 </conditional>
99
100 <conditional name="Optionf5fr">
101 <param name="option" type="select" label="Option[f5fr]">
102 <option value="Yes">Yes</option>
103 <option value="No" selected="true">No</option>
104 </param>
105 <when value="Yes">
106 <param name="f5frValue" type="integer" value="10"/>
107 </when>
108 <when value="No">
109 </when>
110 </conditional>
111
112 <conditional name="Optionff3r">
113 <param name="option" type="select" label="Option[ff3r]">
114 <option value="Yes">Yes</option>
115 <option value="No" selected="true">No</option>
116 </param>
117 <when value="Yes">
118 <param name="ff3rValue" type="integer" value="-10"/>
119 </when>
120 <when value="No">
121 </when>
122 </conditional>
123
124 <conditional name="Optionf3rf">
125 <param name="option" type="select" label="Option[f3rf]">
126 <option value="Yes">Yes</option>
127 <option value="No" selected="true">No</option>
128 </param>
129 <when value="Yes">
130 <param name="f3rfValue" type="integer" value="-10"/>
131 </when>
132 <when value="No">
133 </when>
134 </conditional>
135
136 <conditional name="Optionfr5f">
137 <param name="option" type="select" label="Option[fr5f]">
138 <option value="Yes">Yes</option>
139 <option value="No" selected="true">No</option>
140 </param>
141 <when value="Yes">
142 <param name="fr5fValue" type="integer" value="10"/>
143 </when>
144 <when value="No">
145 </when>
146 </conditional>
147
148 <conditional name="Optionf3rr">
149 <param name="option" type="select" label="Option[f3rr]">
150 <option value="Yes">Yes</option>
151 <option value="No" selected="true">No</option>
152 </param>
153 <when value="Yes">
154 <param name="f3rrValue" type="integer" value="-10"/>
155 </when>
156 <when value="No">
157 </when>
158 </conditional>
159
160 <conditional name="Optionfr5r">
161 <param name="option" type="select" label="Option[fr5r]">
162 <option value="Yes">Yes</option>
163 <option value="No" selected="true">No</option>
164 </param>
165 <when value="Yes">
166 <param name="fr5rValue" type="integer" value="10"/>
167 </when>
168 <when value="No">
169 </when>
170 </conditional>
171
172 <conditional name="Optionr5ff">
173 <param name="option" type="select" label="Option[r5ff]">
174 <option value="Yes">Yes</option>
175 <option value="No" selected="true">No</option>
176 </param>
177 <when value="Yes">
178 <param name="r5ffValue" type="integer" value="10"/>
179 </when>
180 <when value="No">
181 </when>
182 </conditional>
183
184 <conditional name="Optionrf3f">
185 <param name="option" type="select" label="Option[rf3f]">
186 <option value="Yes">Yes</option>
187 <option value="No" selected="true">No</option>
188 </param>
189 <when value="Yes">
190 <param name="rf3fValue" type="integer" value="30"/>
191 </when>
192 <when value="No">
193 </when>
194 </conditional>
195
196 <conditional name="Optionr5fr">
197 <param name="option" type="select" label="Option[r5fr]">
198 <option value="Yes">Yes</option>
199 <option value="No" selected="true">No</option>
200 </param>
201 <when value="Yes">
202 <param name="r5frValue" type="integer" value="10"/>
203 </when>
204 <when value="No">
205 </when>
206 </conditional>
207
208 <conditional name="Optionrf3r">
209 <param name="option" type="select" label="Option[rf3r]">
210 <option value="Yes">Yes</option>
211 <option value="No" selected="true">No</option>
212 </param>
213 <when value="Yes">
214 <param name="rf3rValue" type="integer" value="-10"/>
215 </when>
216 <when value="No">
217 </when>
218 </conditional>
219
220 <conditional name="Optionr3rf">
221 <param name="option" type="select" label="Option[r3rf]">
222 <option value="Yes">Yes</option>
223 <option value="No" selected="true">No</option>
224 </param>
225 <when value="Yes">
226 <param name="r3rfValue" type="integer" value="30"/>
227 </when>
228 <when value="No">
229 </when>
230 </conditional>
231
232 <conditional name="Optionrr5f">
233 <param name="option" type="select" label="Option[rr5f]">
234 <option value="Yes">Yes</option>
235 <option value="No" selected="true">No</option>
236 </param>
237 <when value="Yes">
238 <param name="rr5fValue" type="integer" value="10"/>
239 </when>
240 <when value="No">
241 </when>
242 </conditional>
243
244 <conditional name="Optionr3rr">
245 <param name="option" type="select" label="Option[r3rr]">
246 <option value="Yes">Yes</option>
247 <option value="No" selected="true">No</option>
248 </param>
249 <when value="Yes">
250 <param name="r3rrValue" type="integer" value="30"/>
251 </when>
252 <when value="No">
253 </when>
254 </conditional>
255
256 <conditional name="Optionrr5r">
257 <param name="option" type="select" label="Option[rr5r]">
258 <option value="Yes">Yes</option>
259 <option value="No" selected="true">No</option>
260 </param>
261 <when value="Yes">
262 <param name="rr5rValue" type="integer" value="10"/>
263 </when>
264 <when value="No">
265 </when>
266 </conditional>
267
268 </inputs>
269
270 <outputs>
271 <data name="outputFile" format="gff" label="[interElementGff] Output File"/>
272 </outputs>
273
274 <help>
275 command example: interElementGff.pl -i ${i}_annot.gff -o ${i}_trans_IG.gff -f5ff 10 -ff3f 30 -f5fr 10 -ff3r -10 -f3rf -10 -fr5f 10 -f3rr -10 -fr5r 10 -r5ff 10 -rf3f 30 -r5fr 10 -rf3r -10 -r3rf 30 -rr5f 10 -r3rr 30 -rr5r 10
276 </help>
277
278 </tool>
279
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