Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/getDistance.xml @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 <tool id="GetDistance" name="get distance"> 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> 2 <description>Give the distances between every data from the first input set and the data from the second input set</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/getDistance.py -i $formatType.inputFileName1 4 ../Java/Python/getDistance.py -i $formatType.inputFileName1
8 #if $formatType.FormatInputFileName1 == 'bed': 5 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff': 7 #elif $formatType.FormatInputFileName1 == 'gff':
41 -c 38 -c
42 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens': 39 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
43 -a 40 -a
44 #end if 41 #end if
45 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
46 #if $OptionMinDistance.MinD == "Yes": 53 #if $OptionMinDistance.MinD == "Yes":
47 -m $OptionMinDistance.minDistance 54 -m $OptionMinDistance.minDistance
48 #end if 55 #end if
49 56
50 #if $OptionMaxDistance.MaxD == "Yes": 57 #if $OptionMaxDistance.MaxD == "Yes":
68 #if $OptionTitle.OTitle == "Yes": 75 #if $OptionTitle.OTitle == "Yes":
69 -t $OptionTitle.title 76 -t $OptionTitle.title
70 #end if 77 #end if
71 78
72 -o $outputFilePng 79 -o $outputFilePng
80 $outputDistance $outputFileDistance
81
73 </command> 82 </command>
74 83
75 <inputs> 84 <inputs>
76 <conditional name="formatType"> 85 <conditional name="formatType">
77 <param name="FormatInputFileName1" type="select" label="Input File Format 1"> 86 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
129 <when value="gtf"> 138 <when value="gtf">
130 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/> 139 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
131 </when> 140 </when>
132 </conditional> 141 </conditional>
133 142
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
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."/> 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."/>
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."/> 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."/>
136 147
137 <conditional name="OptionColinearOrAntiSens"> 148 <conditional name="OptionColinearOrAntiSens">
138 <param name="OptionCA" type="select" label="Provide distribution of distances between collinear/antisense pairs of features"> 149 <param name="OptionCA" type="select" label="Colinear or anti-sens">
139 <option value="Colinear">Collinear</option> 150 <option value="Colinear">Colinear</option>
140 <option value="AntiSens">AntiSens</option> 151 <option value="AntiSens">AntiSens</option>
141 <option value="NONE" selected="true">NONE</option> 152 <option value="NONE" selected="true">NONE</option>
142 </param> 153 </param>
143 <when value="Colinear"> 154 <when value="Colinear">
144 </when> 155 </when>
146 </when> 157 </when>
147 <when value="NONE"> 158 <when value="NONE">
148 </when> 159 </when>
149 </conditional> 160 </conditional>
150 161
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
151 <conditional name="OptionMinDistance"> 188 <conditional name="OptionMinDistance">
152 <param name="MinD" type="select" label="Minimum distance between two features"> 189 <param name="MinD" type="select" label="minimum distance considered between two transcripts">
153 <option value="Yes">Yes</option> 190 <option value="Yes">Yes</option>
154 <option value="No" selected="true">No</option> 191 <option value="No" selected="true">No</option>
155 </param> 192 </param>
156 <when value="Yes"> 193 <when value="Yes">
157 <param name="minDistance" type="integer" value="1"/> 194 <param name="minDistance" type="integer" value="1"/>
159 <when value="No"> 196 <when value="No">
160 </when> 197 </when>
161 </conditional> 198 </conditional>
162 199
163 <conditional name="OptionMaxDistance"> 200 <conditional name="OptionMaxDistance">
164 <param name="MaxD" type="select" label="Maximum distance between two features"> 201 <param name="MaxD" type="select" label="maximum distance considered between two transcripts">
165 <option value="Yes">Yes</option> 202 <option value="Yes">Yes</option>
166 <option value="No" selected="true">No</option> 203 <option value="No" selected="true">No</option>
167 </param> 204 </param>
168 <when value="Yes"> 205 <when value="Yes">
169 <param name="maxDistance" type="integer" value="1000"/> 206 <param name="maxDistance" type="integer" value="1000"/>
228 </inputs> 265 </inputs>
229 266
230 267
231 <outputs> 268 <outputs>
232 <data name="outputFilePng" format="png"/> 269 <data name="outputFilePng" format="png"/>
270 <data name="outputFileDistance" format="gff3">
271 <filter>outputDistance</filter>
272 </data>
233 </outputs> 273 </outputs>
234 274
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> 275 </tool>