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comparison SMART/galaxy/getDistance.xml @ 15:440ceca58672

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author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
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14:c79b9ae3f65f 15:440ceca58672
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 and the data from the second input set</description> 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"> 3 <command interpreter="python">
4 ../Java/Python/getDistance.py -i $formatType.inputFileName1 4 ../Java/Python/getDistance.py -i $formatType.inputFileName1
5 #if $formatType.FormatInputFileName1 == 'bed': 5 #if $formatType.FormatInputFileName1 == 'bed':
6 -f bed 6 -f bed
7 #elif $formatType.FormatInputFileName1 == 'gff': 7 #elif $formatType.FormatInputFileName1 == 'gff':
38 -c 38 -c
39 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens': 39 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
40 -a 40 -a
41 #end if 41 #end if
42 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": 43 #if $OptionMinDistance.MinD == "Yes":
54 -m $OptionMinDistance.minDistance 44 -m $OptionMinDistance.minDistance
55 #end if 45 #end if
56 46
57 #if $OptionMaxDistance.MaxD == "Yes": 47 #if $OptionMaxDistance.MaxD == "Yes":
75 #if $OptionTitle.OTitle == "Yes": 65 #if $OptionTitle.OTitle == "Yes":
76 -t $OptionTitle.title 66 -t $OptionTitle.title
77 #end if 67 #end if
78 68
79 -o $outputFilePng 69 -o $outputFilePng
80 $outputDistance $outputFileDistance
81
82 </command> 70 </command>
83 71
84 <inputs> 72 <inputs>
85 <conditional name="formatType"> 73 <conditional name="formatType">
86 <param name="FormatInputFileName1" type="select" label="Input File Format 1"> 74 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
138 <when value="gtf"> 126 <when value="gtf">
139 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/> 127 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
140 </when> 128 </when>
141 </conditional> 129 </conditional>
142 130
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."/> 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."/>
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."/> 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."/>
147 133
148 <conditional name="OptionColinearOrAntiSens"> 134 <conditional name="OptionColinearOrAntiSens">
149 <param name="OptionCA" type="select" label="Colinear or anti-sens"> 135 <param name="OptionCA" type="select" label="Provide distribution of distances between collinear/antisense pairs of features">
150 <option value="Colinear">Colinear</option> 136 <option value="Colinear">Collinear</option>
151 <option value="AntiSens">AntiSens</option> 137 <option value="AntiSens">AntiSens</option>
152 <option value="NONE" selected="true">NONE</option> 138 <option value="NONE" selected="true">NONE</option>
153 </param> 139 </param>
154 <when value="Colinear"> 140 <when value="Colinear">
155 </when> 141 </when>
157 </when> 143 </when>
158 <when value="NONE"> 144 <when value="NONE">
159 </when> 145 </when>
160 </conditional> 146 </conditional>
161 147
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"> 148 <conditional name="OptionMinDistance">
189 <param name="MinD" type="select" label="minimum distance considered between two transcripts"> 149 <param name="MinD" type="select" label="Minimum distance between two features">
190 <option value="Yes">Yes</option> 150 <option value="Yes">Yes</option>
191 <option value="No" selected="true">No</option> 151 <option value="No" selected="true">No</option>
192 </param> 152 </param>
193 <when value="Yes"> 153 <when value="Yes">
194 <param name="minDistance" type="integer" value="1"/> 154 <param name="minDistance" type="integer" value="1"/>
196 <when value="No"> 156 <when value="No">
197 </when> 157 </when>
198 </conditional> 158 </conditional>
199 159
200 <conditional name="OptionMaxDistance"> 160 <conditional name="OptionMaxDistance">
201 <param name="MaxD" type="select" label="maximum distance considered between two transcripts"> 161 <param name="MaxD" type="select" label="Maximum distance between two features">
202 <option value="Yes">Yes</option> 162 <option value="Yes">Yes</option>
203 <option value="No" selected="true">No</option> 163 <option value="No" selected="true">No</option>
204 </param> 164 </param>
205 <when value="Yes"> 165 <when value="Yes">
206 <param name="maxDistance" type="integer" value="1000"/> 166 <param name="maxDistance" type="integer" value="1000"/>
265 </inputs> 225 </inputs>
266 226
267 227
268 <outputs> 228 <outputs>
269 <data name="outputFilePng" format="png"/> 229 <data name="outputFilePng" format="png"/>
270 <data name="outputFileDistance" format="gff3">
271 <filter>outputDistance</filter>
272 </data>
273 </outputs> 230 </outputs>
274 231
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
275 </tool> 244 </tool>