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comparison SMART/galaxy/getDistance.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="GetDistance" name="get distance">
2 <description>Give the distances between every data from the first input set with respect to the data from the second input set.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/getDistance.py -i $formatType.inputFileName1
8 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff':
11 -f gff
12 #elif $formatType.FormatInputFileName1 == 'gff2':
13 -f gff2
14 #elif $formatType.FormatInputFileName1 == 'gff3':
15 -f gff3
16 #elif $formatType.FormatInputFileName1 == 'sam':
17 -f sam
18 #elif $formatType.FormatInputFileName1 == 'gtf':
19 -f gtf
20 #end if
21
22 -j $formatType2.inputFileName2
23 #if $formatType2.FormatInputFileName2 == 'bed':
24 -g bed
25 #elif $formatType2.FormatInputFileName2 == 'gff':
26 -g gff
27 #elif $formatType2.FormatInputFileName2 == 'gff2':
28 -g gff2
29 #elif $formatType2.FormatInputFileName2 == 'gff3':
30 -g gff3
31 #elif $formatType2.FormatInputFileName2 == 'sam':
32 -g sam
33 #elif $formatType2.FormatInputFileName2 == 'gtf':
34 -g gtf
35 #end if
36
37
38 $absolute $proportion
39
40 #if $OptionColinearOrAntiSens.OptionCA == "Colinear":
41 -c
42 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
43 -a
44 #end if
45
46 #if $OptionMinDistance.MinD == "Yes":
47 -m $OptionMinDistance.minDistance
48 #end if
49
50 #if $OptionMaxDistance.MaxD == "Yes":
51 -M $OptionMaxDistance.maxDistance
52 #end if
53
54 $fivePrime $threePrime $spearMan
55
56 #if $OptionBuckets.OBuckets == "Yes":
57 -u $OptionBuckets.buckets
58 #end if
59
60 #if $OptionMinXaxis.MinX == "Yes":
61 -x $OptionMinXaxis.minXaxis
62 #end if
63
64 #if $OptionMaxXaxis.MaxX == "Yes":
65 -X $OptionMaxXaxis.maxXaxis
66 #end if
67
68 #if $OptionTitle.OTitle == "Yes":
69 -t $OptionTitle.title
70 #end if
71
72 -o $outputFilePng
73 </command>
74
75 <inputs>
76 <conditional name="formatType">
77 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
78 <option value="bed">bed</option>
79 <option value="gff">gff</option>
80 <option value="gff2">gff2</option>
81 <option value="gff3">gff3</option>
82 <option value="sam">sam</option>
83 <option value="gtf">gtf</option>
84 </param>
85 <when value="bed">
86 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
87 </when>
88 <when value="gff">
89 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
90 </when>
91 <when value="gff2">
92 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
93 </when>
94 <when value="gff3">
95 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
96 </when>
97 <when value="sam">
98 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
99 </when>
100 <when value="gtf">
101 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
102 </when>
103 </conditional>
104
105 <conditional name="formatType2">
106 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
107 <option value="bed">bed</option>
108 <option value="gff">gff</option>
109 <option value="gff2">gff2</option>
110 <option value="gff3">gff3</option>
111 <option value="sam">sam</option>
112 <option value="gtf">gtf</option>
113 </param>
114 <when value="bed">
115 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
116 </when>
117 <when value="gff">
118 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
119 </when>
120 <when value="gff2">
121 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
122 </when>
123 <when value="gff3">
124 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
125 </when>
126 <when value="sam">
127 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
128 </when>
129 <when value="gtf">
130 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
131 </when>
132 </conditional>
133
134 <param name="absolute" type="boolean" truevalue="-b" falsevalue="" checked="false" label="absolute value option" help="This option gives the absolute value of the distance."/>
135 <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."/>
136
137 <conditional name="OptionColinearOrAntiSens">
138 <param name="OptionCA" type="select" label="Provide distribution of distances between collinear/antisense pairs of features">
139 <option value="Colinear">Collinear</option>
140 <option value="AntiSens">AntiSens</option>
141 <option value="NONE" selected="true">NONE</option>
142 </param>
143 <when value="Colinear">
144 </when>
145 <when value="AntiSens">
146 </when>
147 <when value="NONE">
148 </when>
149 </conditional>
150
151 <conditional name="OptionMinDistance">
152 <param name="MinD" type="select" label="Minimum distance between two features">
153 <option value="Yes">Yes</option>
154 <option value="No" selected="true">No</option>
155 </param>
156 <when value="Yes">
157 <param name="minDistance" type="integer" value="1"/>
158 </when>
159 <when value="No">
160 </when>
161 </conditional>
162
163 <conditional name="OptionMaxDistance">
164 <param name="MaxD" type="select" label="Maximum distance between two features">
165 <option value="Yes">Yes</option>
166 <option value="No" selected="true">No</option>
167 </param>
168 <when value="Yes">
169 <param name="maxDistance" type="integer" value="1000"/>
170 </when>
171 <when value="No">
172 </when>
173 </conditional>
174
175 <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"/>
176 <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"/>
177 <param name="spearMan" type="boolean" truevalue="-r" falsevalue="" checked="false" label="spearman option" help="Compute Spearman rho."/>
178
179
180 <conditional name="OptionBuckets">
181 <param name="OBuckets" type="select" label="Plots histogram instead of line plot with given interval size.">
182 <option value="Yes">Yes</option>
183 <option value="No" selected="true">No</option>
184 </param>
185 <when value="Yes">
186 <param name="buckets" type="integer" value="1" label="Interval size"/>
187 </when>
188 <when value="No">
189 </when>
190 </conditional>
191
192 <conditional name="OptionMinXaxis">
193 <param name="MinX" type="select" label="Minimum value on the x-axis to plot.">
194 <option value="Yes">Yes</option>
195 <option value="No" selected="true">No</option>
196 </param>
197 <when value="Yes">
198 <param name="minXaxis" type="integer" value="1"/>
199 </when>
200 <when value="No">
201 </when>
202 </conditional>
203
204 <conditional name="OptionMaxXaxis">
205 <param name="MaxX" type="select" label="Maximum value on the x-axis to plot.">
206 <option value="Yes">Yes</option>
207 <option value="No" selected="true">No</option>
208 </param>
209 <when value="Yes">
210 <param name="maxXaxis" type="integer" value="1"/>
211 </when>
212 <when value="No">
213 </when>
214 </conditional>
215
216 <conditional name="OptionTitle">
217 <param name="OTitle" type="select" label="Title for the graph.">
218 <option value="Yes">Yes</option>
219 <option value="No" selected="true">No</option>
220 </param>
221 <when value="Yes">
222 <param name="title" type="text" value=""/>
223 </when>
224 <when value="No">
225 </when>
226 </conditional>
227
228 </inputs>
229
230
231 <outputs>
232 <data name="outputFilePng" format="png"/>
233 </outputs>
234
235 <help>
236 Give the distances between every data from the first input set and the data from the second input set. It outputs the size distribution. Each point (*x*, *y*) tells you that there exists *y* pairs of elements which are separated by *x* nucleotides.
237
238 The general algorithm is the following. For each element of the first input set, it finds the closest element of the second set and computes the distance between the two elements. The distance is zero if the two elements overlap. This distance may not exist if the element of the first input set is alone on its chromosome (or contig).
239
240 Actually, considering an element from the first input set, the algorithm will look at the vicinity of this element (1kb by default). You can increase the size of the vicinity using the appropriate option.
241
242 As in *compare overlapping*, you can shrink or extend your sets of genomic coordinates, so that you can get the distance between starts of reads and starts or genes, for instance. You can also compute the distance from elements which are on the same strand only (which is not the case by default) or on the opposite strand only.
243
244 You have several options for the output plot. You can first choose the region on the *x*-axis you want to plot. You can also display histograms instead of line plot. In this case, the data are summed into buckets, whose sizes are given as an option. For instance, a bucket of size *s* at the point (*x*, *y*) means that there are *y* pairs of elements which are separated by *x* to *x + s* nucleotides.
245 </help>
246
247 </tool>