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comparison SMART/galaxy/plotCoverage.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="plotCoverage" name="plot coverage">
2 <description>Plot the coverage of the first data with respect to the second one.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/WrappPlotCoverage.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 #if $optionRef.Ref == 'Yes':
39 -q $optionRef.inputSequenceFile
40 #end if
41
42 #if $optionwidth.width == 'Yes':
43 -w $optionwidth.widthVal
44 #end if
45 #if $optionheight.height == 'Yes':
46 -e $optionheight.heightVal
47 #end if
48 #if $optionXlab.Xlab == 'Yes':
49 -x $optionXlab.XlabVal
50 #end if
51 #if $optionYlab.Ylab == 'Yes':
52 -y $optionYlab.YlabVal
53 #end if
54 #if $optiontitle.title == 'Yes':
55 -t $optiontitle.titleVal
56 #end if
57
58 #if $optionplusColor.plusColor == 'Yes':
59 -p $optionplusColor.plusColorVal
60 #end if
61 #if $optionminusColor.minusColor == 'Yes':
62 -m $optionminusColor.minusColorVal
63 #end if
64
65 #if $optionsumColor.sumColor == 'Yes':
66 -s $optionsumColor.sumColorVal
67 #end if
68 #if $optionlineColor.lineColor == 'Yes':
69 -l $optionlineColor.lineColorVal
70 #end if
71
72 $merge
73 -o $outputFile
74 </command>
75
76 <inputs>
77 <conditional name="formatType">
78 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
79 <option value="bed">bed</option>
80 <option value="gff">gff</option>
81 <option value="gff2">gff2</option>
82 <option value="gff3">gff3</option>
83 <option value="sam">sam</option>
84 <option value="gtf">gtf</option>
85 </param>
86 <when value="bed">
87 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
88 </when>
89 <when value="gff">
90 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
91 </when>
92 <when value="gff2">
93 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
94 </when>
95 <when value="gff3">
96 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
97 </when>
98 <when value="sam">
99 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
100 </when>
101 <when value="gtf">
102 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
103 </when>
104 </conditional>
105
106 <conditional name="formatType2">
107 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
108 <option value="bed">bed</option>
109 <option value="gff">gff</option>
110 <option value="gff2">gff2</option>
111 <option value="gff3">gff3</option>
112 <option value="sam">sam</option>
113 <option value="gtf">gtf</option>
114 </param>
115 <when value="bed">
116 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
117 </when>
118 <when value="gff">
119 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
120 </when>
121 <when value="gff2">
122 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
123 </when>
124 <when value="gff3">
125 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
126 </when>
127 <when value="sam">
128 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
129 </when>
130 <when value="gtf">
131 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
132 </when>
133 </conditional>
134
135 <conditional name="optionRef">
136 <param name="Ref" type="select" label="reference sequence file">
137 <option value="Yes">Yes</option>
138 <option value="No" selected="true">No</option>
139 </param>
140 <when value="Yes">
141 <param name="inputSequenceFile" format="fasta" type="data" value="None"/>
142 </when>
143 <when value="No">
144 </when>
145 </conditional>
146
147
148
149
150 <conditional name="optionwidth">
151 <param name="width" type="select" label="width of the plots (in px)">
152 <option value="Yes">Yes</option>
153 <option value="No" selected="true">No</option>
154 </param>
155 <when value="Yes">
156 <param name="widthVal" type="integer" value="1500" />
157 </when>
158 <when value="No">
159 </when>
160 </conditional>
161
162 <conditional name="optionheight">
163 <param name="height" type="select" label="height of the plots (in px)">
164 <option value="Yes">Yes</option>
165 <option value="No" selected="true">No</option>
166 </param>
167 <when value="Yes">
168 <param name="heightVal" type="integer" value="1000" />
169 </when>
170 <when value="No">
171 </when>
172 </conditional>
173
174 <conditional name="optiontitle">
175 <param name="title" type="select" label="title for the figure">
176 <option value="Yes">Yes</option>
177 <option value="No" selected="true">No</option>
178 </param>
179 <when value="Yes">
180 <param name="titleVal" type="text" value=" " />
181 </when>
182 <when value="No">
183 </when>
184 </conditional>
185
186 <conditional name="optionXlab">
187 <param name="Xlab" type="select" label="label on the x-axis">
188 <option value="Yes">Yes</option>
189 <option value="No" selected="true">No</option>
190 </param>
191 <when value="Yes">
192 <param name="XlabVal" type="text" value=" "/>
193 </when>
194 <when value="No">
195 </when>
196 </conditional>
197
198 <conditional name="optionYlab">
199 <param name="Ylab" type="select" label="label on the y-axis">
200 <option value="Yes">Yes</option>
201 <option value="No" selected="true">No</option>
202 </param>
203 <when value="Yes">
204 <param name="YlabVal" type="text" value=" " />
205 </when>
206 <when value="No">
207 </when>
208 </conditional>
209
210 <conditional name="optionplusColor">
211 <param name="plusColor" type="select" label="color for the elements on the plus strand">
212 <option value="Yes">Yes</option>
213 <option value="No" selected="true">No</option>
214 </param>
215 <when value="Yes">
216 <param name="plusColorVal" type="text" value="red"/>
217 </when>
218 <when value="No">
219 </when>
220 </conditional>
221
222 <conditional name="optionminusColor">
223 <param name="minusColor" type="select" label="color for the elements on the minus strand">
224 <option value="Yes">Yes</option>
225 <option value="No" selected="true">No</option>
226 </param>
227 <when value="Yes">
228 <param name="minusColorVal" type="text" value="blue"/>
229 </when>
230 <when value="No">
231 </when>
232 </conditional>
233
234 <conditional name="optionsumColor">
235 <param name="sumColor" type="select" label="color for 2 strands coverage line">
236 <option value="Yes">Yes</option>
237 <option value="No" selected="true">No</option>
238 </param>
239 <when value="Yes">
240 <param name="sumColorVal" type="text" value="black"/>
241 </when>
242 <when value="No">
243 </when>
244 </conditional>
245
246 <conditional name="optionlineColor">
247 <param name="lineColor" type="select" label="color for the lines">
248 <option value="Yes">Yes</option>
249 <option value="No" selected="true">No</option>
250 </param>
251 <when value="Yes">
252 <param name="lineColorVal" type="text" value="black"/>
253 </when>
254 <when value="No">
255 </when>
256 </conditional>
257
258 <param name="merge" type="boolean" truevalue="-1" falsevalue="" checked="false" label="merge the 2 plots in 1"/>
259 </inputs>
260
261 <outputs>
262 <data name="outputFile" format="tar" label="[plot coverage] tar output file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
263 </outputs>
264
265 <help>
266 Plot the coverage of the first set of genomic coordinates with respect to the second set of genomic coordinates. For each element of the second set (we will suppose that they are annotated genes), it computes the number of elements of the first set (reads, for instance) which overlap it.
267
268 Alternatively, if the first file is in GFF format, and contains the **Target** file, you can omit the second file. However, a fasta file corresponding to the second file should be given (to compute the size of the reference elements).
269
270 The tool produces two plots per gene. The first plot gives the coverage: a point (*x*, *y*) means that *y* reads cover the *x* th nucleotide of the gene. The second figure displays the (possibly spliced) gene in black, and the overlapping reads (blue is colinear, red is anti-sense).
271
272 This script gives a .tar out file, if you want to take look at the results, you have to download it.
273 </help>
274 </tool>