Mercurial > repos > jjohnson > cummerbund
annotate cummerbund_wrapper.xml @ 16:a29a35968ddb default tip
Fix tool_dependencies.xml
| author | Jim Johnson <jj@umn.edu> |
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| date | Fri, 08 Nov 2013 13:37:14 -0600 |
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1 <tool id="cummerbund" name="cummeRbund" version="0.0.7"> |
| 0 | 2 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description> |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 cummerbund_wrapper.py | |
| 6 --r-script ${script_file} | |
| 7 --html-report-from-directory "${output_html}" "${output_html.files_path}" | |
| 8 </command> | |
| 9 | |
| 10 <inputs> | |
| 11 <conditional name="backend_database_source"> | |
| 12 <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?"> | |
| 13 <option value="history" selected="true">Use backend database from the history</option> | |
| 14 <option value="cuffdiff_output">Build backend database using cuffdiff output</option> | |
| 15 </param> | |
| 16 <when value="cuffdiff_output"> | |
| 17 <param format="tabular" name="isoforms_fpkm_tracking" type="data" label="Transcript FPKM tracking"/> | |
| 18 <param format="tabular" name="isoforms_exp" type="data" label="Transcript differential expression testing"/> | |
| 19 <param format="tabular" name="genes_fpkm_tracking" type="data" label="Gene FPKM tracking"/> | |
| 20 <param format="tabular" name="genes_exp" type="data" label="Gene differential expression testing"/> | |
| 21 <param format="tabular" name="tss_groups_fpkm_tracking" type="data" label="TSS groups FPKM tracking"/> | |
| 22 <param format="tabular" name="tss_groups_exp" type="data" label="TSS groups differential expression testing"/> | |
| 23 <param format="tabular" name="cds_fpkm_tracking" type="data" label="CDS FPKM tracking"/> | |
| 24 <param format="tabular" name="cds_exp_diff" type="data" label="CDS FPKM differential expression testing"/> | |
| 25 <param format="tabular" name="cds_diff" type="data" label="CDS overloading diffential expression testing"/> | |
| 26 <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/> | |
| 27 <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/> | |
| 28 <param name="rebuild" type="hidden" value="TRUE"/> | |
| 29 </when> | |
| 30 <when value="history"> | |
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31 <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/> |
| 0 | 32 </when> |
| 33 </conditional> | |
| 34 <repeat name="plots" title="Plots"> | |
| 35 <param name="width" type="text" value="1280" label="The width of the image"/> | |
| 36 <param name="height" type="text" value="960" label="The height of the image"/> | |
| 37 <conditional name="plot"> | |
| 38 <param name="type" type="select" label="Plot type"> | |
| 39 <option value="density" selected="true">Density</option> | |
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40 <option value="dispersion">Dispersion</option> |
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41 <option value="fpkmSCV">Squared Coefficient of Variation</option> |
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42 <option value="scatterMatrix">Scatter Matrix</option> |
| 0 | 43 <option value="boxplot">Boxplot</option> |
| 44 <option value="scatter">Scatter</option> | |
| 45 <option value="volcano">Volcano</option> | |
| 46 <option value="heatmap">Heatmap</option> | |
| 47 <option value="cluster">Cluster</option> | |
| 48 <option value="expressionplot">Expression Plot</option> | |
| 49 <option value="expressionbarplot">Expression Bar Plot</option> | |
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50 <option value="mds">MultiDimentional Scaling (MDS) Plot</option> |
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51 <option value="pca">Principal Component Analysis (PCA) Plot</option> |
| 9 | 52 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option> |
| 53 <option value="dendrogram">Dendrogram</option> | |
| 0 | 54 </param> |
| 55 <when value="density"> | |
| 56 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
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57 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/> |
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58 </when> |
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59 <when value="mds"> |
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60 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> |
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61 </when> |
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62 <when value="pca"> |
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63 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> |
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64 </when> |
| 9 | 65 <when value="maplot"> |
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66 <param name="x" type="text" label="Sample name 1" help="Condition1 name used in cuffdiff"> |
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67 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/> |
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68 </param> |
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69 <param name="y" type="text" label="Sample name 2" help="Condition2 name used in cuffdiff"> |
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70 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/> |
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71 </param> |
| 9 | 72 <param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/> |
| 73 </when> | |
| 74 <when value="dendrogram"> | |
| 75 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> | |
| 76 </when> | |
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77 <when value="dispersion"> |
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78 </when> |
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79 <when value="fpkmSCV"> |
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80 </when> |
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81 <when value="scatterMatrix"> |
| 0 | 82 </when> |
| 83 <when value="boxplot"> | |
| 84 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 85 </when> | |
| 86 <when value="scatter"> | |
| 87 <param name="x" type="text" label="Sample name for x axis"/> | |
| 88 <param name="y" type="text" label="Sample name for y axis"/> | |
| 89 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 90 <param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/> | |
| 91 <conditional name="multiple_genes"> | |
| 92 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> | |
| 93 <when value="T"> | |
| 94 <param name="features" type="select" label="Expression levels to plot?"> | |
| 95 <option value="gene" selected="true">Genes</option> | |
| 96 <option value="isoforms">Isoforms</option> | |
| 97 <option value="tss">TSS</option> | |
| 98 <option value="cds">CDS</option> | |
| 99 </param> | |
| 100 <repeat name="genes" title="Genes"> | |
| 101 <param name="gene_id" type="text" label="Gene ID"/> | |
| 102 </repeat> | |
| 103 </when> | |
| 104 <when value="F"/> | |
| 105 </conditional> | |
| 106 </when> | |
| 107 <when value="volcano"> | |
| 108 <param name="x" type="text" label="First sample name for comparison"/> | |
| 109 <param name="y" type="text" label="Second sample name for comparison"/> | |
| 110 <conditional name="multiple_genes"> | |
| 111 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> | |
| 112 <when value="T"> | |
| 113 <param name="features" type="select" label="Expression levels to plot?"> | |
| 114 <option value="gene" selected="true">Genes</option> | |
| 115 <option value="isoforms">Isoforms</option> | |
| 116 <option value="tss">TSS</option> | |
| 117 <option value="cds">CDS</option> | |
| 118 </param> | |
| 119 <repeat name="genes" title="Genes"> | |
| 120 <param name="gene_id" type="text" label="Gene ID"/> | |
| 121 </repeat> | |
| 122 </when> | |
| 123 <when value="F"/> | |
| 124 </conditional> | |
| 125 </when> | |
| 126 <when value="heatmap"> | |
| 127 <param name="features" type="select" label="Expression levels to plot?"> | |
| 128 <option value="gene" selected="true">Genes</option> | |
| 129 <option value="isoforms">Isoforms</option> | |
| 130 <option value="tss">TSS</option> | |
| 131 <option value="cds">CDS</option> | |
| 132 </param> | |
| 133 <repeat name="genes" title="Genes"> | |
| 134 <param name="gene_id" type="text" label="Gene ID"/> | |
| 135 </repeat> | |
| 136 <param name="clustering" type="select" label="Cluster by"> | |
| 137 <option value="row">Row</option> | |
| 138 <option value="column">Column</option> | |
| 139 <option value="both" selected="true">Both</option> | |
| 140 <option value="none">None</option> | |
| 141 </param> | |
| 142 <param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
| 143 <param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
| 144 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 145 <param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/> | |
| 146 </when> | |
| 147 <when value="cluster"> | |
| 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 <repeat name="genes" title="Genes"> | |
| 155 <param name="gene_id" type="text" label="Gene ID"/> | |
| 156 </repeat> | |
| 157 <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/> | |
| 158 <param name="iter_max" type="text" value="100" label="Max iterations"/> | |
| 159 </when> | |
| 160 <when value="expressionplot"> | |
| 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="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM | |
| 170 values for each condition?"/> | |
| 171 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> | |
| 172 </when> | |
| 173 <when value="expressionbarplot"> | |
| 174 <param name="features" type="select" label="Expression levels to plot?"> | |
| 175 <option value="gene" selected="true">Genes</option> | |
| 176 <option value="isoforms">Isoforms</option> | |
| 177 <option value="tss">TSS</option> | |
| 178 <option value="cds">CDS</option> | |
| 179 </param> | |
| 180 <param name="gene_id" type="text" label="Gene ID"/> | |
| 181 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 182 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> | |
| 183 </when> | |
| 184 </conditional> | |
| 185 </repeat> | |
| 186 </inputs> | |
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187 <stdio> |
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188 <exit_code range="1:" level="fatal" description="CummerBund Error" /> |
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189 </stdio> |
| 0 | 190 <outputs> |
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191 <data format="cuffdatadb" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)"> |
| 0 | 192 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter> |
| 193 </data> | |
| 194 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/> | |
| 195 </outputs> | |
| 196 | |
| 197 <requirements> | |
| 198 <requirement type="binary">R</requirement> | |
| 199 </requirements> | |
| 200 | |
| 201 <!--> | |
| 202 <tests> | |
| 203 <test> | |
| 204 <param name="" value=""/> | |
| 205 <output name="" file=""/> | |
| 206 </test> | |
| 207 </tests> | |
| 208 --> | |
| 209 <configfiles> | |
| 210 <configfile name="script_file"> | |
| 211 | |
| 212 ## Feature Selection ## | |
| 213 get_features <- function(myGenes, f="gene") { | |
| 214 if (f == "isoforms") | |
| 215 return(isoforms(myGenes)) | |
| 216 else if (f == "tss") | |
| 217 return(TSS(myGenes)) | |
| 218 else if (f == "cds") | |
| 219 return(CDS(myGenes)) | |
| 220 else | |
| 221 return(myGenes) | |
| 222 } | |
| 223 | |
| 224 ## Main Function ## | |
| 225 | |
| 226 ## Load cummeRbund library | |
| 227 library("cummeRbund") | |
| 228 | |
| 229 ## Initialize cuff object | |
| 230 cuff <- readCufflinks(dir = "", | |
| 231 #if $backend_database_source.backend_database_selector == "cuffdiff_output": | |
| 232 dbFile = "${output_database}", | |
| 233 geneFPKM = "${genes_fpkm_tracking}", | |
| 234 geneDiff = "${genes_exp}", | |
| 235 isoformFPKM = "${isoforms_fpkm_tracking}", | |
| 236 isoformDiff = "${isoforms_exp}", | |
| 237 TSSFPKM = "${tss_groups_fpkm_tracking}", | |
| 238 TSSDiff = "${tss_groups_exp}", | |
| 239 CDSFPKM = "${cds_fpkm_tracking}", | |
| 240 CDSExpDiff = "${cds_exp_diff}", | |
| 241 CDSDiff = "${cds_diff}", | |
| 242 promoterFile = "${promoters_diff}", | |
| 243 splicingFile = "${splicing_diff}", | |
| 244 rebuild = T) | |
| 245 #else: | |
| 246 dbFile = "${backend_database_source.input_database}", | |
| 247 rebuild = F) | |
| 248 #end if | |
| 249 | |
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250 ## Print out info |
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251 print(cuff) |
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252 sink("cuffdb_info.txt") |
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253 print(cuff) |
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254 print("SAMPLES:") |
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255 samples(cuff) |
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256 print("REPLICATES:") |
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257 replicates(cuff) |
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258 print("FEATURES:") |
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259 print(annotation(genes(cuff))) |
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260 sink() |
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261 |
| 0 | 262 #for $i, $p in enumerate($plots, start=1): |
| 263 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) | |
| 264 png(filename = "${filename}", width = ${p.width}, height = ${p.height}) | |
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265 tryCatch({ |
| 0 | 266 ## Density plot ## |
| 267 #if $p.plot['type'] == "density": | |
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268 csDensity(genes(cuff),replicates=$p.plot.replicates) |
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269 |
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270 ## Dispersion plot ## |
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271 #elif $p.plot['type'] == "dispersion": |
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272 dispersionPlot(genes(cuff)) |
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273 |
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274 ## Squared Coefficient of Variation plot ## |
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275 #elif $p.plot['type'] == "fpkmSCV": |
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276 fpkmSCVPlot(genes(cuff)) |
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277 |
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278 ## Scatter Matrix ## |
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279 #elif $p.plot['type'] == "scatterMatrix": |
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280 csScatterMatrix(genes(cuff)) |
| 0 | 281 |
| 282 ## Boxplot ## | |
| 283 #elif $p.plot['type'] == "boxplot": | |
| 284 csBoxplot(genes(cuff)) | |
| 285 | |
| 286 ## Scatter ## | |
| 287 #elif $p.plot['type'] == "scatter": | |
| 288 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
| 289 myGeneIds <- c() | |
| 290 #for $g in $p.plot.multiple_genes['genes']: | |
| 291 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 292 #end for | |
| 293 myGenes <- getGenes(cuff, myGeneIds) | |
| 294 csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
| 295 #else | |
| 296 csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
| 297 #end if | |
| 298 | |
| 299 ## Volcano ## | |
| 300 #elif $p.plot['type'] == "volcano": | |
| 301 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
| 302 myGeneIds <- c() | |
| 303 #for $g in $p.plot.multiple_genes['genes']: | |
| 304 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 305 #end for | |
| 306 myGenes <- getGenes(cuff, myGeneIds) | |
| 307 csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}") | |
| 308 #else | |
| 309 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}") | |
| 310 #end if | |
| 311 | |
| 312 ## Heatmap ## | |
| 313 #elif $p.plot['type'] == "heatmap": | |
| 314 myGeneIds <- c() | |
| 315 #for $g in $p.plot.genes: | |
| 316 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 317 #end for | |
| 318 myGenes <- getGenes(cuff, myGeneIds) | |
| 319 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}") | |
| 320 | |
| 321 ## Cluster ## | |
| 322 #elif $p.plot['type'] == "cluster": | |
| 323 myGeneIds <- c() | |
| 324 #for $g in $p.plot.genes: | |
| 325 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 326 #end for | |
| 327 myGenes <- getGenes(cuff, myGeneIds) | |
| 328 csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}") | |
| 329 | |
| 330 ## Expression Plot ## | |
| 331 #elif $p.plot['type'] == "expressionplot": | |
| 332 myGeneId <- "$p.plot.gene_id" | |
| 333 myGenes <- getGenes(cuff, myGeneId) | |
| 334 expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}") | |
| 335 | |
| 336 ## Expression Bar Plot ## | |
| 337 #elif $p.plot['type'] == "expressionbarplot": | |
| 338 myGeneId <- "$p.plot.gene_id" | |
| 339 myGenes <- getGenes(cuff, myGeneId) | |
| 340 expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}") | |
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341 |
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342 ## MDS plot ## |
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343 #elif $p.plot['type'] == "mds": |
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344 MDSplot(genes(cuff),replicates=$p.plot.replicates) |
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345 |
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346 ## PCA plot ## |
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347 #elif $p.plot['type'] == "pca": |
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348 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates) |
| 9 | 349 |
| 350 ## MAplot plot ## | |
| 351 #elif $p.plot['type'] == "maplot": | |
| 352 MAplot(genes(cuff), "${p.plot.x}", "${p.plot.y}", useCount=${p.plot.use_count}) | |
| 353 | |
| 354 ## Dendogram plot ## | |
| 355 #elif $p.plot['type'] == "dendrogram": | |
| 356 csDendro(genes(cuff),replicates=$p.plot.replicates) | |
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357 #end if |
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358 |
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359 },error = function(e) {paste("$p.plot['type'] failed: ", e)}) |
| 0 | 360 devname = dev.off() |
| 361 | |
| 362 #end for | |
| 363 </configfile> | |
| 364 </configfiles> | |
| 365 | |
| 366 <help> | |
| 367 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. | |
| 368 </help> | |
| 369 | |
| 370 </tool> |