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comparison smart_toolShed/SMART/galaxy/getDistance.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="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>