|
6
|
1 <tool id="CompareOverlapping" name="Compare Overlapping">
|
|
|
2 <description>Print all the transcripts from a first file which overlap with the transcripts from a second file.</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 ../Java/Python/CompareOverlapping.py -i $formatType.inputFileName1
|
|
|
5 #if $formatType.FormatInputFileName1 == 'bed':
|
|
|
6 -f bed
|
|
|
7 #elif $formatType.FormatInputFileName1 == 'gff':
|
|
|
8 -f gff
|
|
|
9 #elif $formatType.FormatInputFileName1 == 'gff2':
|
|
|
10 -f gff2
|
|
|
11 #elif $formatType.FormatInputFileName1 == 'gff3':
|
|
|
12 -f gff3
|
|
|
13 #elif $formatType.FormatInputFileName1 == 'sam':
|
|
|
14 -f sam
|
|
|
15 #elif $formatType.FormatInputFileName1 == 'gtf':
|
|
|
16 -f gtf
|
|
|
17 #end if
|
|
|
18
|
|
|
19 -j $formatType2.inputFileName2
|
|
|
20 #if $formatType2.FormatInputFileName2 == 'bed':
|
|
|
21 -g bed
|
|
|
22 #elif $formatType2.FormatInputFileName2 == 'gff':
|
|
|
23 -g gff
|
|
|
24 #elif $formatType2.FormatInputFileName2 == 'gff2':
|
|
|
25 -g gff2
|
|
|
26 #elif $formatType2.FormatInputFileName2 == 'gff3':
|
|
|
27 -g gff3
|
|
|
28 #elif $formatType2.FormatInputFileName2 == 'sam':
|
|
|
29 -g sam
|
|
|
30 #elif $formatType2.FormatInputFileName2 == 'gtf':
|
|
|
31 -g gtf
|
|
|
32 #end if
|
|
|
33
|
|
|
34 -o $outputFileGff
|
|
|
35
|
|
|
36 #if $optionNFirstFile1.NFirstForFile1 == 'Yes':
|
|
|
37 -S $optionNFirstFile1.firstNtFile1
|
|
|
38 #end if
|
|
|
39 #if $optionNFirstFile2.NFirstForFile2 == 'Yes':
|
|
|
40 -s $optionNFirstFile2.firstNtFile2
|
|
|
41 #end if
|
|
|
42 #if $optionNLastFile1.NLastForFile1 == 'Yes':
|
|
|
43 -U $optionNLastFile1.lastNtFile1
|
|
|
44 #end if
|
|
|
45 #if $optionNLastFile2.NLastForFile2 == 'Yes':
|
|
|
46 -u $optionNLastFile2.lastNtFile2
|
|
|
47 #end if
|
|
|
48
|
|
|
49 #if $optionExtentionCinqFile1.extentionFile1 == 'Yes':
|
|
|
50 -E $optionExtentionCinqFile1.extention51
|
|
|
51 #end if
|
|
|
52 #if $optionExtentionCinqFile2.extentionFile2 == 'Yes':
|
|
|
53 -e $optionExtentionCinqFile2.extention52
|
|
|
54 #end if
|
|
|
55
|
|
|
56 #if $optionExtentionTroisFile1.extentionFile1 == 'Yes':
|
|
|
57 -N $optionExtentionTroisFile1.extention31
|
|
|
58 #end if
|
|
|
59 #if $optionExtentionTroisFile2.extentionFile2 == 'Yes':
|
|
|
60 -n $optionExtentionTroisFile2.extention32
|
|
|
61 #end if
|
|
|
62
|
|
|
63 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
|
|
|
64 -c
|
|
|
65 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
|
|
|
66 -a
|
|
|
67 #end if
|
|
|
68
|
|
|
69 #if $OptionDistance.Dist == 'Yes':
|
|
|
70 -d $OptionDistance.distance
|
|
|
71 #end if
|
|
|
72
|
|
|
73 #if $OptionMinOverlap.MO == 'Yes':
|
|
|
74 -m $OptionMinOverlap.minOverlap
|
|
|
75 #end if
|
|
|
76
|
|
|
77 $InvertMatch
|
|
|
78 $ReportIntron
|
|
|
79 $NotOverlapping
|
|
|
80
|
|
|
81 </command>
|
|
|
82
|
|
|
83 <inputs>
|
|
|
84 <conditional name="formatType">
|
|
|
85 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
|
|
|
86 <option value="bed">bed</option>
|
|
|
87 <option value="gff">gff</option>
|
|
|
88 <option value="gff2">gff2</option>
|
|
|
89 <option value="gff3">gff3</option>
|
|
|
90 <option value="sam">sam</option>
|
|
|
91 <option value="gtf">gtf</option>
|
|
|
92 </param>
|
|
|
93 <when value="bed">
|
|
|
94 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
|
|
|
95 </when>
|
|
|
96 <when value="gff">
|
|
|
97 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
|
|
|
98 </when>
|
|
|
99 <when value="gff2">
|
|
|
100 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
|
|
|
101 </when>
|
|
|
102 <when value="gff3">
|
|
|
103 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
|
|
|
104 </when>
|
|
|
105 <when value="sam">
|
|
|
106 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
|
|
|
107 </when>
|
|
|
108 <when value="gtf">
|
|
|
109 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
|
|
|
110 </when>
|
|
|
111 </conditional>
|
|
|
112
|
|
|
113 <conditional name="formatType2">
|
|
|
114 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
|
|
|
115 <option value="bed">bed</option>
|
|
|
116 <option value="gff">gff</option>
|
|
|
117 <option value="gff2">gff2</option>
|
|
|
118 <option value="gff3">gff3</option>
|
|
|
119 <option value="sam">sam</option>
|
|
|
120 <option value="gtf">gtf</option>
|
|
|
121 </param>
|
|
|
122 <when value="bed">
|
|
|
123 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
|
|
|
124 </when>
|
|
|
125 <when value="gff">
|
|
|
126 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
|
|
|
127 </when>
|
|
|
128 <when value="gff2">
|
|
|
129 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
|
|
|
130 </when>
|
|
|
131 <when value="gff3">
|
|
|
132 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
|
|
|
133 </when>
|
|
|
134 <when value="sam">
|
|
|
135 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
|
|
|
136 </when>
|
|
|
137 <when value="gtf">
|
|
|
138 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
|
|
|
139 </when>
|
|
|
140 </conditional>
|
|
|
141
|
|
|
142
|
|
|
143
|
|
|
144 <conditional name="optionNFirstFile1">
|
|
|
145 <param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1">
|
|
|
146 <option value="Yes">Yes</option>
|
|
|
147 <option value="No" selected="true">No</option>
|
|
|
148 </param>
|
|
|
149 <when value="Yes">
|
|
|
150 <param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" />
|
|
|
151 </when>
|
|
|
152 <when value="No">
|
|
|
153 </when>
|
|
|
154 </conditional>
|
|
|
155 <conditional name="optionNFirstFile2">
|
|
|
156 <param name="NFirstForFile2" type="select" label="NFirst for file 2" help="only consider the n first nucleotides of the transcripts in file 2">
|
|
|
157 <option value="Yes">Yes</option>
|
|
|
158 <option value="No" selected="true">No</option>
|
|
|
159 </param>
|
|
|
160 <when value="Yes">
|
|
|
161 <param name="firstNtFile2" type="integer" value="1" label="n first nucleotides for input file 1" />
|
|
|
162 </when>
|
|
|
163 <when value="No">
|
|
|
164 </when>
|
|
|
165 </conditional>
|
|
|
166
|
|
|
167 <conditional name="optionNLastFile1">
|
|
|
168 <param name="NLastForFile1" type="select" label="NLast for file 1">
|
|
|
169 <option value="Yes">Yes</option>
|
|
|
170 <option value="No" selected="true">No</option>
|
|
|
171 </param>
|
|
|
172 <when value="Yes">
|
|
|
173 <param name="lastNtFile1" type="integer" value="1" label="n last nucleotides for input file 1" help="only consider the n last nucleotides of the transcripts in file 1"/>
|
|
|
174 </when>
|
|
|
175 <when value="No">
|
|
|
176 </when>
|
|
|
177 </conditional>
|
|
|
178 <conditional name="optionNLastFile2">
|
|
|
179 <param name="NLastForFile2" type="select" label="NLast for file 2">
|
|
|
180 <option value="Yes">Yes</option>
|
|
|
181 <option value="No" selected="true">No</option>
|
|
|
182 </param>
|
|
|
183 <when value="Yes">
|
|
|
184 <param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/>
|
|
|
185 </when>
|
|
|
186 <when value="No">
|
|
|
187 </when>
|
|
|
188 </conditional>
|
|
|
189
|
|
|
190
|
|
|
191
|
|
|
192 <conditional name="optionExtentionCinqFile1">
|
|
|
193 <param name="extentionFile1" type="select" label="Extension towards 5 for file 1">
|
|
|
194 <option value="Yes">Yes</option>
|
|
|
195 <option value="No" selected="true">No</option>
|
|
|
196 </param>
|
|
|
197 <when value="Yes">
|
|
|
198 <param name="extention51" type="integer" value="1" label="in file 1" />
|
|
|
199 </when>
|
|
|
200 <when value="No">
|
|
|
201 </when>
|
|
|
202 </conditional>
|
|
|
203
|
|
|
204
|
|
|
205 <conditional name="optionExtentionCinqFile2">
|
|
|
206 <param name="extentionFile2" type="select" label="Extension towards 5 for file 2">
|
|
|
207 <option value="Yes">Yes</option>
|
|
|
208 <option value="No" selected="true">No</option>
|
|
|
209 </param>
|
|
|
210 <when value="Yes">
|
|
|
211 <param name="extention52" type="integer" value="1" label="in file 2"/>
|
|
|
212 </when>
|
|
|
213 <when value="No">
|
|
|
214 </when>
|
|
|
215 </conditional>
|
|
|
216
|
|
|
217 <conditional name="optionExtentionTroisFile1">
|
|
|
218 <param name="extentionFile1" type="select" label="Extension towards 3 for file 1">
|
|
|
219 <option value="Yes">Yes</option>
|
|
|
220 <option value="No" selected="true">No</option>
|
|
|
221 </param>
|
|
|
222 <when value="Yes">
|
|
|
223 <param name="extention31" type="integer" value="1" label="in file 1" />
|
|
|
224 </when>
|
|
|
225 <when value="No">
|
|
|
226 </when>
|
|
|
227 </conditional>
|
|
|
228
|
|
|
229 <conditional name="optionExtentionTroisFile2">
|
|
|
230 <param name="extentionFile2" type="select" label="Extension towards 3 for file 2">
|
|
|
231 <option value="Yes">Yes</option>
|
|
|
232 <option value="No" selected="true">No</option>
|
|
|
233 </param>
|
|
|
234 <when value="Yes">
|
|
|
235 <param name="extention32" type="integer" value="1" label="in file 2" />
|
|
|
236 </when>
|
|
|
237 <when value="No">
|
|
|
238 </when>
|
|
|
239 </conditional>
|
|
|
240
|
|
|
241 <conditional name="OptionColinearOrAntiSens">
|
|
|
242 <param name="OptionCA" type="select" label="Colinear or anti-sens">
|
|
|
243 <option value="Colinear">Colinear</option>
|
|
|
244 <option value="AntiSens">AntiSens</option>
|
|
|
245 <option value="NONE" selected="true">NONE</option>
|
|
|
246 </param>
|
|
|
247 <when value="Colinear">
|
|
|
248 </when>
|
|
|
249 <when value="AntiSens">
|
|
|
250 </when>
|
|
|
251 <when value="NONE">
|
|
|
252 </when>
|
|
|
253 </conditional>
|
|
|
254
|
|
|
255 <conditional name="OptionDistance">
|
|
|
256 <param name="Dist" type="select" label="Maximum Distance between two reads">
|
|
|
257 <option value="Yes">Yes</option>
|
|
|
258 <option value="No" selected="true">No</option>
|
|
|
259 </param>
|
|
|
260 <when value="Yes">
|
|
|
261 <param name="distance" type="integer" value="0"/>
|
|
|
262 </when>
|
|
|
263 <when value="No">
|
|
|
264 </when>
|
|
|
265 </conditional>
|
|
|
266
|
|
|
267 <conditional name="OptionMinOverlap">
|
|
|
268 <param name="MO" type="select" label="Minimum number of overlapping between two reads">
|
|
|
269 <option value="Yes">Yes</option>
|
|
|
270 <option value="No" selected="true">No</option>
|
|
|
271 </param>
|
|
|
272 <when value="Yes">
|
|
|
273 <param name="minOverlap" type="integer" value="1"/>
|
|
|
274 </when>
|
|
|
275 <when value="No">
|
|
|
276 </when>
|
|
|
277 </conditional>
|
|
|
278 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
|
|
|
279 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/>
|
|
|
280 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
|
|
|
281
|
|
|
282 </inputs>
|
|
|
283
|
|
|
284 <outputs>
|
|
|
285 <data name="outputFileGff" format="gff3"/>
|
|
|
286 </outputs>
|
|
|
287
|
|
|
288 </tool>
|
