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comparison cummerbund_wrapper.xml @ 1:6a9bc26ab8d9

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Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
author Jim Johnson <jj@umn.edu>
date Mon, 08 Oct 2012 15:26:47 -0500
parents 8ba5f0460b1e
children 9d25b0fd882b
comparison
equal deleted inserted replaced
0:8ba5f0460b1e 1:6a9bc26ab8d9
27 <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/> 27 <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/>
28 <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/> 28 <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/>
29 <param name="rebuild" type="hidden" value="TRUE"/> 29 <param name="rebuild" type="hidden" value="TRUE"/>
30 </when> 30 </when>
31 <when value="history"> 31 <when value="history">
32 <param name="input_database" type="data" format="data" label="Select backend database (sqlite)"/> 32 <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/>
33 </when> 33 </when>
34 </conditional> 34 </conditional>
35 <repeat name="plots" title="Plots"> 35 <repeat name="plots" title="Plots">
36 <param name="width" type="text" value="1280" label="The width of the image"/> 36 <param name="width" type="text" value="1280" label="The width of the image"/>
37 <param name="height" type="text" value="960" label="The height of the image"/> 37 <param name="height" type="text" value="960" label="The height of the image"/>
38 <conditional name="plot"> 38 <conditional name="plot">
39 <param name="type" type="select" label="Plot type"> 39 <param name="type" type="select" label="Plot type">
40 <option value="density" selected="true">Density</option> 40 <option value="density" selected="true">Density</option>
41 <option value="dispersion">Dispersion</option>
42 <option value="fpkmSCV">Squared Coefficient of Variation</option>
43 <option value="scatterMatrix">Scatter Matrix</option>
41 <option value="boxplot">Boxplot</option> 44 <option value="boxplot">Boxplot</option>
42 <option value="scatter">Scatter</option> 45 <option value="scatter">Scatter</option>
43 <option value="volcano">Volcano</option> 46 <option value="volcano">Volcano</option>
44 <option value="heatmap">Heatmap</option> 47 <option value="heatmap">Heatmap</option>
45 <option value="cluster">Cluster</option> 48 <option value="cluster">Cluster</option>
46 <option value="expressionplot">Expression Plot</option> 49 <option value="expressionplot">Expression Plot</option>
47 <option value="expressionbarplot">Expression Bar Plot</option> 50 <option value="expressionbarplot">Expression Bar Plot</option>
48 </param> 51 </param>
49 <when value="density"> 52 <when value="density">
50 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> 53 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
54 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/>
55 </when>
56 <when value="dispersion">
57 </when>
58 <when value="fpkmSCV">
59 </when>
60 <when value="scatterMatrix">
51 </when> 61 </when>
52 <when value="boxplot"> 62 <when value="boxplot">
53 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> 63 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
54 </when> 64 </when>
55 <when value="scatter"> 65 <when value="scatter">
218 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) 228 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type'])
219 png(filename = "${filename}", width = ${p.width}, height = ${p.height}) 229 png(filename = "${filename}", width = ${p.width}, height = ${p.height})
220 230
221 ## Density plot ## 231 ## Density plot ##
222 #if $p.plot['type'] == "density": 232 #if $p.plot['type'] == "density":
223 csDensity(genes(cuff)) 233 csDensity(genes(cuff),replicates=$p.plot.replicates)
234 devname = dev.off()
235
236 ## Dispersion plot ##
237 #elif $p.plot['type'] == "dispersion":
238 dispersionPlot(genes(cuff))
239 devname = dev.off()
240
241 ## Squared Coefficient of Variation plot ##
242 #elif $p.plot['type'] == "fpkmSCV":
243 fpkmSCVPlot(genes(cuff))
244 devname = dev.off()
245
246 ## Scatter Matrix ##
247 #elif $p.plot['type'] == "scatterMatrix":
248 csScatterMatrix(genes(cuff))
224 devname = dev.off() 249 devname = dev.off()
225 250
226 ## Boxplot ## 251 ## Boxplot ##
227 #elif $p.plot['type'] == "boxplot": 252 #elif $p.plot['type'] == "boxplot":
228 csBoxplot(genes(cuff)) 253 csBoxplot(genes(cuff))