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comparison SMART/galaxy/getDistance.xml @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
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 <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 $OptionMinDistance.MinD == "Yes":
44 -m $OptionMinDistance.minDistance
45 #end if
46
47 #if $OptionMaxDistance.MaxD == "Yes":
48 -M $OptionMaxDistance.maxDistance
49 #end if
50
51 $fivePrime $threePrime $spearMan
52
53 #if $OptionBuckets.OBuckets == "Yes":
54 -u $OptionBuckets.buckets
55 #end if
56
57 #if $OptionMinXaxis.MinX == "Yes":
58 -x $OptionMinXaxis.minXaxis
59 #end if
60
61 #if $OptionMaxXaxis.MaxX == "Yes":
62 -X $OptionMaxXaxis.maxXaxis
63 #end if
64
65 #if $OptionTitle.OTitle == "Yes":
66 -t $OptionTitle.title
67 #end if
68
69 -o $outputFilePng
70 </command>
71
72 <inputs>
73 <conditional name="formatType">
74 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
75 <option value="bed">bed</option>
76 <option value="gff">gff</option>
77 <option value="gff2">gff2</option>
78 <option value="gff3">gff3</option>
79 <option value="sam">sam</option>
80 <option value="gtf">gtf</option>
81 </param>
82 <when value="bed">
83 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
84 </when>
85 <when value="gff">
86 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
87 </when>
88 <when value="gff2">
89 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
90 </when>
91 <when value="gff3">
92 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
93 </when>
94 <when value="sam">
95 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
96 </when>
97 <when value="gtf">
98 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
99 </when>
100 </conditional>
101
102 <conditional name="formatType2">
103 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
104 <option value="bed">bed</option>
105 <option value="gff">gff</option>
106 <option value="gff2">gff2</option>
107 <option value="gff3">gff3</option>
108 <option value="sam">sam</option>
109 <option value="gtf">gtf</option>
110 </param>
111 <when value="bed">
112 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
113 </when>
114 <when value="gff">
115 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
116 </when>
117 <when value="gff2">
118 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
119 </when>
120 <when value="gff3">
121 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
122 </when>
123 <when value="sam">
124 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
125 </when>
126 <when value="gtf">
127 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
128 </when>
129 </conditional>
130
131 <param name="absolute" type="boolean" truevalue="-b" falsevalue="" checked="false" label="absolute value option" help="This option gives the absolute value of the distance."/>
132 <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."/>
133
134 <conditional name="OptionColinearOrAntiSens">
135 <param name="OptionCA" type="select" label="Provide distribution of distances between collinear/antisense pairs of features">
136 <option value="Colinear">Collinear</option>
137 <option value="AntiSens">AntiSens</option>
138 <option value="NONE" selected="true">NONE</option>
139 </param>
140 <when value="Colinear">
141 </when>
142 <when value="AntiSens">
143 </when>
144 <when value="NONE">
145 </when>
146 </conditional>
147
148 <conditional name="OptionMinDistance">
149 <param name="MinD" type="select" label="Minimum distance between two features">
150 <option value="Yes">Yes</option>
151 <option value="No" selected="true">No</option>
152 </param>
153 <when value="Yes">
154 <param name="minDistance" type="integer" value="1"/>
155 </when>
156 <when value="No">
157 </when>
158 </conditional>
159
160 <conditional name="OptionMaxDistance">
161 <param name="MaxD" type="select" label="Maximum distance between two features">
162 <option value="Yes">Yes</option>
163 <option value="No" selected="true">No</option>
164 </param>
165 <when value="Yes">
166 <param name="maxDistance" type="integer" value="1000"/>
167 </when>
168 <when value="No">
169 </when>
170 </conditional>
171
172 <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"/>
173 <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"/>
174 <param name="spearMan" type="boolean" truevalue="-r" falsevalue="" checked="false" label="spearman option" help="Compute Spearman rho."/>
175
176
177 <conditional name="OptionBuckets">
178 <param name="OBuckets" type="select" label="Plots histogram instead of line plot with given interval size.">
179 <option value="Yes">Yes</option>
180 <option value="No" selected="true">No</option>
181 </param>
182 <when value="Yes">
183 <param name="buckets" type="integer" value="1" label="Interval size"/>
184 </when>
185 <when value="No">
186 </when>
187 </conditional>
188
189 <conditional name="OptionMinXaxis">
190 <param name="MinX" type="select" label="Minimum value on the x-axis to plot.">
191 <option value="Yes">Yes</option>
192 <option value="No" selected="true">No</option>
193 </param>
194 <when value="Yes">
195 <param name="minXaxis" type="integer" value="1"/>
196 </when>
197 <when value="No">
198 </when>
199 </conditional>
200
201 <conditional name="OptionMaxXaxis">
202 <param name="MaxX" type="select" label="Maximum value on the x-axis to plot.">
203 <option value="Yes">Yes</option>
204 <option value="No" selected="true">No</option>
205 </param>
206 <when value="Yes">
207 <param name="maxXaxis" type="integer" value="1"/>
208 </when>
209 <when value="No">
210 </when>
211 </conditional>
212
213 <conditional name="OptionTitle">
214 <param name="OTitle" type="select" label="Title for the graph.">
215 <option value="Yes">Yes</option>
216 <option value="No" selected="true">No</option>
217 </param>
218 <when value="Yes">
219 <param name="title" type="text" value=""/>
220 </when>
221 <when value="No">
222 </when>
223 </conditional>
224
225 </inputs>
226
227
228 <outputs>
229 <data name="outputFilePng" format="png"/>
230 </outputs>
231
232 <help>
233 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.
234
235 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).
236
237 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.
238
239 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.
240
241 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.
242 </help>
243
244 </tool>