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comparison smart_toolShed/SMART/galaxy/plotCoverage.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 <tool id="plotCoverage" name="plot coverage">
2 <description>Plot the coverage of the first data with respect to the second one.</description>
3 <command interpreter="python">
4 ../Java/Python/WrappPlotCoverage.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 #if $optionRef.Ref == 'Yes':
36 -q $optionRef.inputSequenceFile
37 #end if
38
39 #if $optionwidth.width == 'Yes':
40 -w $optionwidth.widthVal
41 #end if
42 #if $optionheight.height == 'Yes':
43 -e $optionheight.heightVal
44 #end if
45 #if $optionXlab.Xlab == 'Yes':
46 -x $optionXlab.XlabVal
47 #end if
48 #if $optionYlab.Ylab == 'Yes':
49 -y $optionYlab.YlabVal
50 #end if
51 #if $optiontitle.title == 'Yes':
52 -t $optiontitle.titleVal
53 #end if
54
55 #if $optionplusColor.plusColor == 'Yes':
56 -p $optionplusColor.plusColorVal
57 #end if
58 #if $optionminusColor.minusColor == 'Yes':
59 -m $optionminusColor.minusColorVal
60 #end if
61
62 #if $optionsumColor.sumColor == 'Yes':
63 -s $optionsumColor.sumColorVal
64 #end if
65 #if $optionlineColor.lineColor == 'Yes':
66 -l $optionlineColor.lineColorVal
67 #end if
68
69 $merge
70 -o $outputFile
71 </command>
72
73 <inputs>
74 <conditional name="formatType">
75 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
76 <option value="bed">bed</option>
77 <option value="gff">gff</option>
78 <option value="gff2">gff2</option>
79 <option value="gff3">gff3</option>
80 <option value="sam">sam</option>
81 <option value="gtf">gtf</option>
82 </param>
83 <when value="bed">
84 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
85 </when>
86 <when value="gff">
87 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
88 </when>
89 <when value="gff2">
90 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
91 </when>
92 <when value="gff3">
93 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
94 </when>
95 <when value="sam">
96 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
97 </when>
98 <when value="gtf">
99 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
100 </when>
101 </conditional>
102
103 <conditional name="formatType2">
104 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
105 <option value="bed">bed</option>
106 <option value="gff">gff</option>
107 <option value="gff2">gff2</option>
108 <option value="gff3">gff3</option>
109 <option value="gff2">sam</option>
110 <option value="gff3">gtf</option>
111 </param>
112 <when value="bed">
113 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
114 </when>
115 <when value="gff">
116 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
117 </when>
118 <when value="gff2">
119 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
120 </when>
121 <when value="gff3">
122 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
123 </when>
124 <when value="sam">
125 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
126 </when>
127 <when value="gtf">
128 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
129 </when>
130 </conditional>
131
132 <conditional name="optionRef">
133 <param name="Ref" type="select" label="reference sequence file">
134 <option value="Yes">Yes</option>
135 <option value="No" selected="true">No</option>
136 </param>
137 <when value="Yes">
138 <param name="inputSequenceFile" format="fasta" type="data" value="None"/>
139 </when>
140 <when value="No">
141 </when>
142 </conditional>
143
144
145
146
147 <conditional name="optionwidth">
148 <param name="width" type="select" label="width of the plots (in px)">
149 <option value="Yes">Yes</option>
150 <option value="No" selected="true">No</option>
151 </param>
152 <when value="Yes">
153 <param name="widthVal" type="integer" value="1500" />
154 </when>
155 <when value="No">
156 </when>
157 </conditional>
158
159 <conditional name="optionheight">
160 <param name="height" type="select" label="height of the plots (in px)">
161 <option value="Yes">Yes</option>
162 <option value="No" selected="true">No</option>
163 </param>
164 <when value="Yes">
165 <param name="heightVal" type="integer" value="1000" />
166 </when>
167 <when value="No">
168 </when>
169 </conditional>
170
171 <conditional name="optiontitle">
172 <param name="title" type="select" label="title of the plots ">
173 <option value="Yes">Yes</option>
174 <option value="No" selected="true">No</option>
175 </param>
176 <when value="Yes">
177 <param name="titleVal" type="text" value=" " />
178 </when>
179 <when value="No">
180 </when>
181 </conditional>
182
183 <conditional name="optionXlab">
184 <param name="Xlab" type="select" label="label on the x-axis">
185 <option value="Yes">Yes</option>
186 <option value="No" selected="true">No</option>
187 </param>
188 <when value="Yes">
189 <param name="XlabVal" type="text" value=" "/>
190 </when>
191 <when value="No">
192 </when>
193 </conditional>
194
195 <conditional name="optionYlab">
196 <param name="Ylab" type="select" label="label on the y-axis">
197 <option value="Yes">Yes</option>
198 <option value="No" selected="true">No</option>
199 </param>
200 <when value="Yes">
201 <param name="YlabVal" type="text" value=" " />
202 </when>
203 <when value="No">
204 </when>
205 </conditional>
206
207 <conditional name="optionplusColor">
208 <param name="plusColor" type="select" label="color for the elements on the plus strand">
209 <option value="Yes">Yes</option>
210 <option value="No" selected="true">No</option>
211 </param>
212 <when value="Yes">
213 <param name="plusColorVal" type="text" value="red"/>
214 </when>
215 <when value="No">
216 </when>
217 </conditional>
218
219 <conditional name="optionminusColor">
220 <param name="minusColor" type="select" label="color for the elements on the minus strand">
221 <option value="Yes">Yes</option>
222 <option value="No" selected="true">No</option>
223 </param>
224 <when value="Yes">
225 <param name="minusColorVal" type="text" value="blue"/>
226 </when>
227 <when value="No">
228 </when>
229 </conditional>
230
231 <conditional name="optionsumColor">
232 <param name="sumColor" type="select" label="color for 2 strands coverage line">
233 <option value="Yes">Yes</option>
234 <option value="No" selected="true">No</option>
235 </param>
236 <when value="Yes">
237 <param name="sumColorVal" type="text" value="black"/>
238 </when>
239 <when value="No">
240 </when>
241 </conditional>
242
243 <conditional name="optionlineColor">
244 <param name="lineColor" type="select" label="color for the lines">
245 <option value="Yes">Yes</option>
246 <option value="No" selected="true">No</option>
247 </param>
248 <when value="Yes">
249 <param name="lineColorVal" type="text" value="black"/>
250 </when>
251 <when value="No">
252 </when>
253 </conditional>
254
255 <param name="merge" type="boolean" truevalue="-1" falsevalue="" checked="false" label="merge the 2 plots in 1"/>
256 </inputs>
257
258 <outputs>
259 <data name="outputFile" format="tar" label="[plotCoverage] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
260 </outputs>
261
262 <help>
263 This script gives a .tar out file, if you want to take look at the results, you have to download it.
264 </help>
265 </tool>