Mercurial > repos > jjohnson > cummerbund
annotate cummerbund_wrapper.xml @ 8:b0d11fcbc3ac
cummerbund add MDS and PCA plots, handle errors from R
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 11 Oct 2012 15:14:51 -0500 |
| parents | 9d25b0fd882b |
| children | b6427cdbf6d4 |
| rev | line source |
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1 <tool id="cummerbund" name="cummeRbund" version="0.0.6"> |
| 0 | 2 |
| 3 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description> | |
| 4 | |
| 5 <command interpreter="python"> | |
| 6 cummerbund_wrapper.py | |
| 7 --r-script ${script_file} | |
| 8 --html-report-from-directory "${output_html}" "${output_html.files_path}" | |
| 9 </command> | |
| 10 | |
| 11 <inputs> | |
| 12 <conditional name="backend_database_source"> | |
| 13 <param name="backend_database_selector" type="select" label="Will you select a backend database file from the history or do you want to build a new one using cuffdiff output?"> | |
| 14 <option value="history" selected="true">Use backend database from the history</option> | |
| 15 <option value="cuffdiff_output">Build backend database using cuffdiff output</option> | |
| 16 </param> | |
| 17 <when value="cuffdiff_output"> | |
| 18 <param format="tabular" name="isoforms_fpkm_tracking" type="data" label="Transcript FPKM tracking"/> | |
| 19 <param format="tabular" name="isoforms_exp" type="data" label="Transcript differential expression testing"/> | |
| 20 <param format="tabular" name="genes_fpkm_tracking" type="data" label="Gene FPKM tracking"/> | |
| 21 <param format="tabular" name="genes_exp" type="data" label="Gene differential expression testing"/> | |
| 22 <param format="tabular" name="tss_groups_fpkm_tracking" type="data" label="TSS groups FPKM tracking"/> | |
| 23 <param format="tabular" name="tss_groups_exp" type="data" label="TSS groups differential expression testing"/> | |
| 24 <param format="tabular" name="cds_fpkm_tracking" type="data" label="CDS FPKM tracking"/> | |
| 25 <param format="tabular" name="cds_exp_diff" type="data" label="CDS FPKM differential expression testing"/> | |
| 26 <param format="tabular" name="cds_diff" type="data" label="CDS overloading diffential 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"/> | |
| 29 <param name="rebuild" type="hidden" value="TRUE"/> | |
| 30 </when> | |
| 31 <when value="history"> | |
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32 <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/> |
| 0 | 33 </when> |
| 34 </conditional> | |
| 35 <repeat name="plots" title="Plots"> | |
| 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"/> | |
| 38 <conditional name="plot"> | |
| 39 <param name="type" type="select" label="Plot type"> | |
| 40 <option value="density" selected="true">Density</option> | |
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41 <option value="dispersion">Dispersion</option> |
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42 <option value="fpkmSCV">Squared Coefficient of Variation</option> |
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43 <option value="scatterMatrix">Scatter Matrix</option> |
| 0 | 44 <option value="boxplot">Boxplot</option> |
| 45 <option value="scatter">Scatter</option> | |
| 46 <option value="volcano">Volcano</option> | |
| 47 <option value="heatmap">Heatmap</option> | |
| 48 <option value="cluster">Cluster</option> | |
| 49 <option value="expressionplot">Expression Plot</option> | |
| 50 <option value="expressionbarplot">Expression Bar Plot</option> | |
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51 <option value="mds">MultiDimentional Scaling (MDS) Plot</option> |
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52 <option value="pca">Principal Component Analysis (PCA) Plot</option> |
| 0 | 53 </param> |
| 54 <when value="density"> | |
| 55 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
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56 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/> |
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57 </when> |
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58 <when value="mds"> |
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59 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> |
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60 </when> |
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61 <when value="pca"> |
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62 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> |
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63 </when> |
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64 <when value="dispersion"> |
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65 </when> |
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66 <when value="fpkmSCV"> |
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67 </when> |
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68 <when value="scatterMatrix"> |
| 0 | 69 </when> |
| 70 <when value="boxplot"> | |
| 71 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 72 </when> | |
| 73 <when value="scatter"> | |
| 74 <param name="x" type="text" label="Sample name for x axis"/> | |
| 75 <param name="y" type="text" label="Sample name for y axis"/> | |
| 76 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 77 <param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/> | |
| 78 <conditional name="multiple_genes"> | |
| 79 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> | |
| 80 <when value="T"> | |
| 81 <param name="features" type="select" label="Expression levels to plot?"> | |
| 82 <option value="gene" selected="true">Genes</option> | |
| 83 <option value="isoforms">Isoforms</option> | |
| 84 <option value="tss">TSS</option> | |
| 85 <option value="cds">CDS</option> | |
| 86 </param> | |
| 87 <repeat name="genes" title="Genes"> | |
| 88 <param name="gene_id" type="text" label="Gene ID"/> | |
| 89 </repeat> | |
| 90 </when> | |
| 91 <when value="F"/> | |
| 92 </conditional> | |
| 93 </when> | |
| 94 <when value="volcano"> | |
| 95 <param name="x" type="text" label="First sample name for comparison"/> | |
| 96 <param name="y" type="text" label="Second sample name for comparison"/> | |
| 97 <conditional name="multiple_genes"> | |
| 98 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> | |
| 99 <when value="T"> | |
| 100 <param name="features" type="select" label="Expression levels to plot?"> | |
| 101 <option value="gene" selected="true">Genes</option> | |
| 102 <option value="isoforms">Isoforms</option> | |
| 103 <option value="tss">TSS</option> | |
| 104 <option value="cds">CDS</option> | |
| 105 </param> | |
| 106 <repeat name="genes" title="Genes"> | |
| 107 <param name="gene_id" type="text" label="Gene ID"/> | |
| 108 </repeat> | |
| 109 </when> | |
| 110 <when value="F"/> | |
| 111 </conditional> | |
| 112 </when> | |
| 113 <when value="heatmap"> | |
| 114 <param name="features" type="select" label="Expression levels to plot?"> | |
| 115 <option value="gene" selected="true">Genes</option> | |
| 116 <option value="isoforms">Isoforms</option> | |
| 117 <option value="tss">TSS</option> | |
| 118 <option value="cds">CDS</option> | |
| 119 </param> | |
| 120 <repeat name="genes" title="Genes"> | |
| 121 <param name="gene_id" type="text" label="Gene ID"/> | |
| 122 </repeat> | |
| 123 <param name="clustering" type="select" label="Cluster by"> | |
| 124 <option value="row">Row</option> | |
| 125 <option value="column">Column</option> | |
| 126 <option value="both" selected="true">Both</option> | |
| 127 <option value="none">None</option> | |
| 128 </param> | |
| 129 <param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
| 130 <param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
| 131 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 132 <param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/> | |
| 133 </when> | |
| 134 <when value="cluster"> | |
| 135 <param name="features" type="select" label="Expression levels to plot?"> | |
| 136 <option value="gene" selected="true">Genes</option> | |
| 137 <option value="isoforms">Isoforms</option> | |
| 138 <option value="tss">TSS</option> | |
| 139 <option value="cds">CDS</option> | |
| 140 </param> | |
| 141 <repeat name="genes" title="Genes"> | |
| 142 <param name="gene_id" type="text" label="Gene ID"/> | |
| 143 </repeat> | |
| 144 <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/> | |
| 145 <param name="iter_max" type="text" value="100" label="Max iterations"/> | |
| 146 </when> | |
| 147 <when value="expressionplot"> | |
| 148 <param name="features" type="select" label="Expression levels to plot?"> | |
| 149 <option value="gene" selected="true">Genes</option> | |
| 150 <option value="isoforms">Isoforms</option> | |
| 151 <option value="tss">TSS</option> | |
| 152 <option value="cds">CDS</option> | |
| 153 </param> | |
| 154 <param name="gene_id" type="text" label="Gene ID"/> | |
| 155 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 156 <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM | |
| 157 values for each condition?"/> | |
| 158 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> | |
| 159 </when> | |
| 160 <when value="expressionbarplot"> | |
| 161 <param name="features" type="select" label="Expression levels to plot?"> | |
| 162 <option value="gene" selected="true">Genes</option> | |
| 163 <option value="isoforms">Isoforms</option> | |
| 164 <option value="tss">TSS</option> | |
| 165 <option value="cds">CDS</option> | |
| 166 </param> | |
| 167 <param name="gene_id" type="text" label="Gene ID"/> | |
| 168 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 169 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> | |
| 170 </when> | |
| 171 </conditional> | |
| 172 </repeat> | |
| 173 </inputs> | |
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174 <stdio> |
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175 <exit_code range="1:" level="fatal" description="CummerBund Error" /> |
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176 </stdio> |
| 0 | 177 <outputs> |
| 178 <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)"> | |
| 179 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter> | |
| 180 </data> | |
| 181 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/> | |
| 182 </outputs> | |
| 183 | |
| 184 <requirements> | |
| 185 <requirement type="binary">R</requirement> | |
| 186 </requirements> | |
| 187 | |
| 188 <!--> | |
| 189 <tests> | |
| 190 <test> | |
| 191 <param name="" value=""/> | |
| 192 <output name="" file=""/> | |
| 193 </test> | |
| 194 </tests> | |
| 195 --> | |
| 196 <configfiles> | |
| 197 <configfile name="script_file"> | |
| 198 | |
| 199 ## Feature Selection ## | |
| 200 get_features <- function(myGenes, f="gene") { | |
| 201 if (f == "isoforms") | |
| 202 return(isoforms(myGenes)) | |
| 203 else if (f == "tss") | |
| 204 return(TSS(myGenes)) | |
| 205 else if (f == "cds") | |
| 206 return(CDS(myGenes)) | |
| 207 else | |
| 208 return(myGenes) | |
| 209 } | |
| 210 | |
| 211 ## Main Function ## | |
| 212 | |
| 213 ## Load cummeRbund library | |
| 214 library("cummeRbund") | |
| 215 | |
| 216 ## Initialize cuff object | |
| 217 cuff <- readCufflinks(dir = "", | |
| 218 #if $backend_database_source.backend_database_selector == "cuffdiff_output": | |
| 219 dbFile = "${output_database}", | |
| 220 geneFPKM = "${genes_fpkm_tracking}", | |
| 221 geneDiff = "${genes_exp}", | |
| 222 isoformFPKM = "${isoforms_fpkm_tracking}", | |
| 223 isoformDiff = "${isoforms_exp}", | |
| 224 TSSFPKM = "${tss_groups_fpkm_tracking}", | |
| 225 TSSDiff = "${tss_groups_exp}", | |
| 226 CDSFPKM = "${cds_fpkm_tracking}", | |
| 227 CDSExpDiff = "${cds_exp_diff}", | |
| 228 CDSDiff = "${cds_diff}", | |
| 229 promoterFile = "${promoters_diff}", | |
| 230 splicingFile = "${splicing_diff}", | |
| 231 rebuild = T) | |
| 232 #else: | |
| 233 dbFile = "${backend_database_source.input_database}", | |
| 234 rebuild = F) | |
| 235 #end if | |
| 236 | |
| 237 #for $i, $p in enumerate($plots, start=1): | |
| 238 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) | |
| 239 png(filename = "${filename}", width = ${p.width}, height = ${p.height}) | |
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240 tryCatch({ |
| 0 | 241 ## Density plot ## |
| 242 #if $p.plot['type'] == "density": | |
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243 csDensity(genes(cuff),replicates=$p.plot.replicates) |
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244 |
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245 ## Dispersion plot ## |
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246 #elif $p.plot['type'] == "dispersion": |
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247 dispersionPlot(genes(cuff)) |
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248 |
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249 ## Squared Coefficient of Variation plot ## |
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250 #elif $p.plot['type'] == "fpkmSCV": |
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251 fpkmSCVPlot(genes(cuff)) |
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252 |
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253 ## Scatter Matrix ## |
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254 #elif $p.plot['type'] == "scatterMatrix": |
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255 csScatterMatrix(genes(cuff)) |
| 0 | 256 |
| 257 ## Boxplot ## | |
| 258 #elif $p.plot['type'] == "boxplot": | |
| 259 csBoxplot(genes(cuff)) | |
| 260 | |
| 261 ## Scatter ## | |
| 262 #elif $p.plot['type'] == "scatter": | |
| 263 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
| 264 myGeneIds <- c() | |
| 265 #for $g in $p.plot.multiple_genes['genes']: | |
| 266 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 267 #end for | |
| 268 myGenes <- getGenes(cuff, myGeneIds) | |
| 269 csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
| 270 #else | |
| 271 csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
| 272 #end if | |
| 273 | |
| 274 ## Volcano ## | |
| 275 #elif $p.plot['type'] == "volcano": | |
| 276 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
| 277 myGeneIds <- c() | |
| 278 #for $g in $p.plot.multiple_genes['genes']: | |
| 279 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 280 #end for | |
| 281 myGenes <- getGenes(cuff, myGeneIds) | |
| 282 csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}") | |
| 283 #else | |
| 284 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}") | |
| 285 #end if | |
| 286 | |
| 287 ## Heatmap ## | |
| 288 #elif $p.plot['type'] == "heatmap": | |
| 289 myGeneIds <- c() | |
| 290 #for $g in $p.plot.genes: | |
| 291 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 292 #end for | |
| 293 myGenes <- getGenes(cuff, myGeneIds) | |
| 294 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}") | |
| 295 | |
| 296 ## Cluster ## | |
| 297 #elif $p.plot['type'] == "cluster": | |
| 298 myGeneIds <- c() | |
| 299 #for $g in $p.plot.genes: | |
| 300 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 301 #end for | |
| 302 myGenes <- getGenes(cuff, myGeneIds) | |
| 303 csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}") | |
| 304 | |
| 305 ## Expression Plot ## | |
| 306 #elif $p.plot['type'] == "expressionplot": | |
| 307 myGeneId <- "$p.plot.gene_id" | |
| 308 myGenes <- getGenes(cuff, myGeneId) | |
| 309 expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}") | |
| 310 | |
| 311 ## Expression Bar Plot ## | |
| 312 #elif $p.plot['type'] == "expressionbarplot": | |
| 313 myGeneId <- "$p.plot.gene_id" | |
| 314 myGenes <- getGenes(cuff, myGeneId) | |
| 315 expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}") | |
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316 |
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317 ## MDS plot ## |
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318 #elif $p.plot['type'] == "mds": |
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319 MDSplot(genes(cuff),replicates=$p.plot.replicates) |
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320 |
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321 ## PCA plot ## |
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322 #elif $p.plot['type'] == "pca": |
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323 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates) |
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324 #end if |
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325 |
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326 },error = function(e) {paste("$p.plot['type'] failed: ", e)}) |
| 0 | 327 devname = dev.off() |
| 328 | |
| 329 #end for | |
| 330 </configfile> | |
| 331 </configfiles> | |
| 332 | |
| 333 <help> | |
| 334 This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. | |
| 335 </help> | |
| 336 | |
| 337 </tool> |