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comparison smart_toolShed/SMART/galaxy/compareOverlapping.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
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>