|
6
|
1 <tool id="GetDistance" name="get distance">
|
|
|
2 <description>Give the distances between every data from the first input set and the data from the second input set</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 ../Java/Python/getDistance.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
|
|
|
35 $absolute $proportion
|
|
|
36
|
|
|
37 #if $OptionColinearOrAntiSens.OptionCA == "Colinear":
|
|
|
38 -c
|
|
|
39 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
|
|
|
40 -a
|
|
|
41 #end if
|
|
|
42
|
|
|
43 #if $OptionFirstNucl5.FirstNu5 == "Yes":
|
|
|
44 -s $OptionFirstNucl5.first5File1
|
|
|
45 -S $OptionFirstNucl5.first5File2
|
|
|
46 #end if
|
|
|
47
|
|
|
48 #if $OptionFirstNucl3.FirstNu3 == "Yes":
|
|
|
49 -e $OptionFirstNucl3.first3File1
|
|
|
50 -E $OptionFirstNucl3.first3File2
|
|
|
51 #end if
|
|
|
52
|
|
|
53 #if $OptionMinDistance.MinD == "Yes":
|
|
|
54 -m $OptionMinDistance.minDistance
|
|
|
55 #end if
|
|
|
56
|
|
|
57 #if $OptionMaxDistance.MaxD == "Yes":
|
|
|
58 -M $OptionMaxDistance.maxDistance
|
|
|
59 #end if
|
|
|
60
|
|
|
61 $fivePrime $threePrime $spearMan
|
|
|
62
|
|
|
63 #if $OptionBuckets.OBuckets == "Yes":
|
|
|
64 -u $OptionBuckets.buckets
|
|
|
65 #end if
|
|
|
66
|
|
|
67 #if $OptionMinXaxis.MinX == "Yes":
|
|
|
68 -x $OptionMinXaxis.minXaxis
|
|
|
69 #end if
|
|
|
70
|
|
|
71 #if $OptionMaxXaxis.MaxX == "Yes":
|
|
|
72 -X $OptionMaxXaxis.maxXaxis
|
|
|
73 #end if
|
|
|
74
|
|
|
75 #if $OptionTitle.OTitle == "Yes":
|
|
|
76 -t $OptionTitle.title
|
|
|
77 #end if
|
|
|
78
|
|
|
79 -o $outputFilePng
|
|
|
80 $outputDistance $outputFileDistance
|
|
|
81
|
|
|
82 </command>
|
|
|
83
|
|
|
84 <inputs>
|
|
|
85 <conditional name="formatType">
|
|
|
86 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
|
|
|
87 <option value="bed">bed</option>
|
|
|
88 <option value="gff">gff</option>
|
|
|
89 <option value="gff2">gff2</option>
|
|
|
90 <option value="gff3">gff3</option>
|
|
|
91 <option value="sam">sam</option>
|
|
|
92 <option value="gtf">gtf</option>
|
|
|
93 </param>
|
|
|
94 <when value="bed">
|
|
|
95 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
|
|
|
96 </when>
|
|
|
97 <when value="gff">
|
|
|
98 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
|
|
|
99 </when>
|
|
|
100 <when value="gff2">
|
|
|
101 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
|
|
|
102 </when>
|
|
|
103 <when value="gff3">
|
|
|
104 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
|
|
|
105 </when>
|
|
|
106 <when value="sam">
|
|
|
107 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
|
|
|
108 </when>
|
|
|
109 <when value="gtf">
|
|
|
110 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
|
|
|
111 </when>
|
|
|
112 </conditional>
|
|
|
113
|
|
|
114 <conditional name="formatType2">
|
|
|
115 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
|
|
|
116 <option value="bed">bed</option>
|
|
|
117 <option value="gff">gff</option>
|
|
|
118 <option value="gff2">gff2</option>
|
|
|
119 <option value="gff3">gff3</option>
|
|
|
120 <option value="sam">sam</option>
|
|
|
121 <option value="gtf">gtf</option>
|
|
|
122 </param>
|
|
|
123 <when value="bed">
|
|
|
124 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
|
|
|
125 </when>
|
|
|
126 <when value="gff">
|
|
|
127 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
|
|
|
128 </when>
|
|
|
129 <when value="gff2">
|
|
|
130 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
|
|
|
131 </when>
|
|
|
132 <when value="gff3">
|
|
|
133 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
|
|
|
134 </when>
|
|
|
135 <when value="sam">
|
|
|
136 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
|
|
|
137 </when>
|
|
|
138 <when value="gtf">
|
|
|
139 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
|
|
|
140 </when>
|
|
|
141 </conditional>
|
|
|
142
|
|
|
143 <param name="outputDistance" type="boolean" truevalue="-O" falsevalue="" checked="false" label="distance option" help="This option create a GFF3 output file containing the distance for each element of the query."/>
|
|
|
144
|
|
|
145 <param name="absolute" type="boolean" truevalue="-b" falsevalue="" checked="false" label="absolute value option" help="This option gives the absolute value of the distance."/>
|
|
|
146 <param name="proportion" type="boolean" truevalue="-p" falsevalue="" checked="false" label="proportion option" help="This option gives the proportion on the y-axis instead of the number of distances."/>
|
|
|
147
|
|
|
148 <conditional name="OptionColinearOrAntiSens">
|
|
|
149 <param name="OptionCA" type="select" label="Colinear or anti-sens">
|
|
|
150 <option value="Colinear">Colinear</option>
|
|
|
151 <option value="AntiSens">AntiSens</option>
|
|
|
152 <option value="NONE" selected="true">NONE</option>
|
|
|
153 </param>
|
|
|
154 <when value="Colinear">
|
|
|
155 </when>
|
|
|
156 <when value="AntiSens">
|
|
|
157 </when>
|
|
|
158 <when value="NONE">
|
|
|
159 </when>
|
|
|
160 </conditional>
|
|
|
161
|
|
|
162 <conditional name="OptionFirstNucl5">
|
|
|
163 <param name="FirstNu5" type="select" label="only consider the n first 5' nucleotides for input files">
|
|
|
164 <option value="Yes">Yes</option>
|
|
|
165 <option value="No" selected="true">No</option>
|
|
|
166 </param>
|
|
|
167 <when value="Yes">
|
|
|
168 <param name="first5File1" type="integer" value="1" label="in file 1" help="Be Careful! The value must be upper than 0"/>
|
|
|
169 <param name="first5File2" type="integer" value="1" label="in file 2" help="Be Careful! The value must be upper than 0"/>
|
|
|
170 </when>
|
|
|
171 <when value="No">
|
|
|
172 </when>
|
|
|
173 </conditional>
|
|
|
174
|
|
|
175 <conditional name="OptionFirstNucl3">
|
|
|
176 <param name="FirstNu3" type="select" label="only consider the n first 3' nucleotides for input files">
|
|
|
177 <option value="Yes">Yes</option>
|
|
|
178 <option value="No" selected="true">No</option>
|
|
|
179 </param>
|
|
|
180 <when value="Yes">
|
|
|
181 <param name="first3File1" type="integer" value="1" label="in file 1" help="Be Careful! The value must be upper than 0"/>
|
|
|
182 <param name="first3File2" type="integer" value="1" label="in file 2" help="Be Careful! The value must be upper than 0"/>
|
|
|
183 </when>
|
|
|
184 <when value="No">
|
|
|
185 </when>
|
|
|
186 </conditional>
|
|
|
187
|
|
|
188 <conditional name="OptionMinDistance">
|
|
|
189 <param name="MinD" type="select" label="minimum distance considered between two transcripts">
|
|
|
190 <option value="Yes">Yes</option>
|
|
|
191 <option value="No" selected="true">No</option>
|
|
|
192 </param>
|
|
|
193 <when value="Yes">
|
|
|
194 <param name="minDistance" type="integer" value="1"/>
|
|
|
195 </when>
|
|
|
196 <when value="No">
|
|
|
197 </when>
|
|
|
198 </conditional>
|
|
|
199
|
|
|
200 <conditional name="OptionMaxDistance">
|
|
|
201 <param name="MaxD" type="select" label="maximum distance considered between two transcripts">
|
|
|
202 <option value="Yes">Yes</option>
|
|
|
203 <option value="No" selected="true">No</option>
|
|
|
204 </param>
|
|
|
205 <when value="Yes">
|
|
|
206 <param name="maxDistance" type="integer" value="1000"/>
|
|
|
207 </when>
|
|
|
208 <when value="No">
|
|
|
209 </when>
|
|
|
210 </conditional>
|
|
|
211
|
|
|
212 <param name="fivePrime" type="boolean" truevalue="-5" falsevalue="" checked="false" label="five prime option" help="Consider the elements from input file 1 which are upstream of elements of input file 2"/>
|
|
|
213 <param name="threePrime" type="boolean" truevalue="-3" falsevalue="" checked="false" label="three prime option" help="Consider the elements from input file1 which are downstream of elements of input file 2"/>
|
|
|
214 <param name="spearMan" type="boolean" truevalue="-r" falsevalue="" checked="false" label="spearman option" help="Compute Spearman rho."/>
|
|
|
215
|
|
|
216
|
|
|
217 <conditional name="OptionBuckets">
|
|
|
218 <param name="OBuckets" type="select" label="Plots histogram instead of line plot with given interval size.">
|
|
|
219 <option value="Yes">Yes</option>
|
|
|
220 <option value="No" selected="true">No</option>
|
|
|
221 </param>
|
|
|
222 <when value="Yes">
|
|
|
223 <param name="buckets" type="integer" value="1" label="Interval size"/>
|
|
|
224 </when>
|
|
|
225 <when value="No">
|
|
|
226 </when>
|
|
|
227 </conditional>
|
|
|
228
|
|
|
229 <conditional name="OptionMinXaxis">
|
|
|
230 <param name="MinX" type="select" label="Minimum value on the x-axis to plot.">
|
|
|
231 <option value="Yes">Yes</option>
|
|
|
232 <option value="No" selected="true">No</option>
|
|
|
233 </param>
|
|
|
234 <when value="Yes">
|
|
|
235 <param name="minXaxis" type="integer" value="1"/>
|
|
|
236 </when>
|
|
|
237 <when value="No">
|
|
|
238 </when>
|
|
|
239 </conditional>
|
|
|
240
|
|
|
241 <conditional name="OptionMaxXaxis">
|
|
|
242 <param name="MaxX" type="select" label="Maximum value on the x-axis to plot.">
|
|
|
243 <option value="Yes">Yes</option>
|
|
|
244 <option value="No" selected="true">No</option>
|
|
|
245 </param>
|
|
|
246 <when value="Yes">
|
|
|
247 <param name="maxXaxis" type="integer" value="1"/>
|
|
|
248 </when>
|
|
|
249 <when value="No">
|
|
|
250 </when>
|
|
|
251 </conditional>
|
|
|
252
|
|
|
253 <conditional name="OptionTitle">
|
|
|
254 <param name="OTitle" type="select" label="Title for the graph.">
|
|
|
255 <option value="Yes">Yes</option>
|
|
|
256 <option value="No" selected="true">No</option>
|
|
|
257 </param>
|
|
|
258 <when value="Yes">
|
|
|
259 <param name="title" type="text" value=""/>
|
|
|
260 </when>
|
|
|
261 <when value="No">
|
|
|
262 </when>
|
|
|
263 </conditional>
|
|
|
264
|
|
|
265 </inputs>
|
|
|
266
|
|
|
267
|
|
|
268 <outputs>
|
|
|
269 <data name="outputFilePng" format="png"/>
|
|
|
270 <data name="outputFileDistance" format="gff3">
|
|
|
271 <filter>outputDistance</filter>
|
|
|
272 </data>
|
|
|
273 </outputs>
|
|
|
274
|
|
|
275 </tool>
|
