Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/getDistance.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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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> |