Mercurial > repos > jjohnson > cummerbund
comparison cummerbund_wrapper.xml @ 1:6a9bc26ab8d9
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)) |