Mercurial > repos > cjav > cummerbund
annotate cummerbund_wrapper.xml @ 3:f4e2d805434c
adds R requirement
| author | Carlos Borroto <carlos.borroto@gmail.com> |
|---|---|
| date | Tue, 14 Feb 2012 13:28:04 -0500 |
| parents | 5de9fff7ccf7 |
| children | a9f216cf02f5 |
| rev | line source |
|---|---|
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5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
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diff
changeset
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1 <tool id="cummerbund" name="cummeRbund" version="0.0.2"> |
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5de9fff7ccf7
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Carlos Borroto <carlos.borroto@gmail.com>
parents:
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changeset
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2 |
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5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
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3 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description> |
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Carlos Borroto <carlos.borroto@gmail.com>
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4 |
| 0 | 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> | |
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parents:
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diff
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10 |
| 0 | 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"> | |
| 32 <param name="input_database" type="data" format="data" label="Select backend database (sqlite)"/> | |
| 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> | |
| 41 <option value="boxplot">Boxplot</option> | |
| 42 <option value="scatter">Scatter</option> | |
| 43 <option value="volcano">Volcano</option> | |
| 44 <option value="heatmap">Heatmap</option> | |
| 45 <option value="cluster">Cluster</option> | |
| 46 <option value="expressionplot">Expression Plot</option> | |
| 47 <option value="expressionbarplot">Expression Bar Plot</option> | |
| 48 </param> | |
| 49 <when value="density"> | |
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2
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
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50 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> |
| 0 | 51 </when> |
| 52 <when value="boxplot"> | |
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2
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
53 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> |
| 0 | 54 </when> |
| 55 <when value="scatter"> | |
| 56 <param name="x" type="text" label="Sample name for x axis"/> | |
| 57 <param name="y" type="text" label="Sample name for y axis"/> | |
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2
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
58 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> |
| 0 | 59 <param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/> |
| 60 <conditional name="multiple_genes"> | |
| 61 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> | |
| 62 <when value="T"> | |
| 63 <param name="features" type="select" label="Expression levels to plot?"> | |
| 64 <option value="gene" selected="true">Genes</option> | |
| 65 <option value="isoforms">Isoforms</option> | |
| 66 <option value="tss">TSS</option> | |
| 67 <option value="cds">CDS</option> | |
| 68 </param> | |
| 69 <repeat name="genes" title="Genes"> | |
| 70 <param name="gene_id" type="text" label="Gene ID"/> | |
| 71 </repeat> | |
| 72 </when> | |
| 73 </conditional> | |
| 74 </when> | |
| 75 <when value="volcano"> | |
| 76 <param name="x" type="text" label="First sample name for comparison"/> | |
| 77 <param name="y" type="text" label="Second sample name for comparison"/> | |
| 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 </conditional> | |
| 92 </when> | |
| 93 <when value="heatmap"> | |
| 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> | |
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2
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
100 <repeat name="genes" title="Genes"> |
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5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
101 <param name="gene_id" type="text" label="Gene ID"/> |
|
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
102 </repeat> |
| 0 | 103 <param name="clustering" type="select" label="Cluster by"> |
| 104 <option value="row">Row</option> | |
| 105 <option value="column">Column</option> | |
| 106 <option value="both" selected="true">Both</option> | |
| 107 <option value="none">None</option> | |
| 108 </param> | |
| 109 <param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
| 110 <param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
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2
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
111 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> |
| 0 | 112 <param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/> |
| 113 </when> | |
| 114 <when value="cluster"> | |
| 115 <param name="features" type="select" label="Expression levels to plot?"> | |
| 116 <option value="gene" selected="true">Genes</option> | |
| 117 <option value="isoforms">Isoforms</option> | |
| 118 <option value="tss">TSS</option> | |
| 119 <option value="cds">CDS</option> | |
| 120 </param> | |
| 121 <repeat name="genes" title="Genes"> | |
| 122 <param name="gene_id" type="text" label="Gene ID"/> | |
| 123 </repeat> | |
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2
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
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124 <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/> |
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5de9fff7ccf7
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Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
125 <param name="iter_max" type="text" value="100" label="Max iterations"/> |
| 0 | 126 </when> |
| 127 <when value="expressionplot"> | |
| 128 <param name="features" type="select" label="Expression levels to plot?"> | |
| 129 <option value="gene" selected="true">Genes</option> | |
| 130 <option value="isoforms">Isoforms</option> | |
| 131 <option value="tss">TSS</option> | |
| 132 <option value="cds">CDS</option> | |
| 133 </param> | |
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2
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
134 <param name="gene_id" type="text" label="Gene ID"/> |
|
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
135 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> |
| 0 | 136 <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM |
| 137 values for each condition?"/> | |
| 138 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> | |
| 139 </when> | |
| 140 <when value="expressionbarplot"> | |
| 141 <param name="features" type="select" label="Expression levels to plot?"> | |
| 142 <option value="gene" selected="true">Genes</option> | |
| 143 <option value="isoforms">Isoforms</option> | |
| 144 <option value="tss">TSS</option> | |
| 145 <option value="cds">CDS</option> | |
| 146 </param> | |
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2
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
147 <param name="gene_id" type="text" label="Gene ID"/> |
|
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
148 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> |
| 0 | 149 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> |
| 150 </when> | |
| 151 </conditional> | |
| 152 </repeat> | |
| 153 </inputs> | |
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2
5de9fff7ccf7
fix for warnings on empty conditional inputs
Carlos Borroto <carlos.borroto@gmail.com>
parents:
0
diff
changeset
|
154 |
| 0 | 155 <outputs> |
| 156 <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)"> | |
| 157 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter> | |
| 158 </data> | |
| 159 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/> | |
| 160 </outputs> | |
| 161 | |
| 3 | 162 <requirements> |
| 163 <requirement type="binary">R</requirement> | |
| 164 </requirements> | |
| 165 | |
| 0 | 166 <!--> |
| 167 <tests> | |
| 168 <test> | |
| 169 <param name="" value=""/> | |
| 170 <output name="" file=""/> | |
| 171 </test> | |
| 172 </tests> | |
| 173 --> | |
| 174 <configfiles> | |
| 175 <configfile name="script_file"> | |
| 176 | |
| 177 ## Feature Selection ## | |
| 178 get_features <- function(myGenes, f="gene") { | |
| 179 if (f == "isoforms") | |
| 180 return(isoforms(myGenes)) | |
| 181 else if (f == "tss") | |
| 182 return(TSS(myGenes)) | |
| 183 else if (f == "cds") | |
| 184 return(CDS(myGenes)) | |
| 185 else | |
| 186 return(myGenes) | |
| 187 } | |
| 188 | |
| 189 ## Main Function ## | |
| 190 | |
| 191 ## Load cummeRbund library | |
| 192 library("cummeRbund") | |
| 193 | |
| 194 ## Initialize cuff object | |
| 195 cuff <- readCufflinks(dir = "", | |
| 196 #if $backend_database_source.backend_database_selector == "cuffdiff_output": | |
| 197 dbFile = "${output_database}", | |
| 198 geneFPKM = "${genes_fpkm_tracking}", | |
| 199 geneDiff = "${genes_exp}", | |
| 200 isoformFPKM = "${isoforms_fpkm_tracking}", | |
| 201 isoformDiff = "${isoforms_exp}", | |
| 202 TSSFPKM = "${tss_groups_fpkm_tracking}", | |
| 203 TSSDiff = "${tss_groups_exp}", | |
| 204 CDSFPKM = "${cds_fpkm_tracking}", | |
| 205 CDSExpDiff = "${cds_exp_diff}", | |
| 206 CDSDiff = "${cds_diff}", | |
| 207 promoterFile = "${promoters_diff}", | |
| 208 splicingFile = "${splicing_diff}", | |
| 209 rebuild = T) | |
| 210 #else: | |
| 211 dbFile = "${backend_database_source.input_database}", | |
| 212 rebuild = F) | |
| 213 #end if | |
| 214 | |
| 215 #for $i, $p in enumerate($plots, start=1): | |
| 216 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) | |
| 217 png(filename = "${filename}", width = ${p.width}, height = ${p.height}) | |
| 218 | |
| 219 ## Density plot ## | |
| 220 #if $p.plot['type'] == "density": | |
| 221 csDensity(genes(cuff)) | |
| 222 devname = dev.off() | |
| 223 | |
| 224 ## Boxplot ## | |
| 225 #elif $p.plot['type'] == "boxplot": | |
| 226 csBoxplot(genes(cuff)) | |
| 227 devname = dev.off() | |
| 228 | |
| 229 ## Scatter ## | |
| 230 #elif $p.plot['type'] == "scatter": | |
| 231 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
| 232 myGeneIds <- c() | |
| 233 #for $g in $p.plot.multiple_genes['genes']: | |
| 234 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 235 #end for | |
| 236 myGenes <- getGenes(cuff, myGeneIds) | |
| 237 csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
| 238 #else | |
| 239 csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
| 240 #end if | |
| 241 devname = dev.off() | |
| 242 | |
| 243 ## Volcano ## | |
| 244 #elif $p.plot['type'] == "volcano": | |
| 245 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
| 246 myGeneIds <- c() | |
| 247 #for $g in $p.plot.multiple_genes['genes']: | |
| 248 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 249 #end for | |
| 250 myGenes <- getGenes(cuff, myGeneIds) | |
| 251 csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}") | |
| 252 #else | |
| 253 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}") | |
| 254 #end if | |
| 255 devname = dev.off() | |
| 256 | |
| 257 ## Heatmap ## | |
| 258 #elif $p.plot['type'] == "heatmap": | |
| 259 myGeneIds <- c() | |
| 260 #for $g in $p.plot.genes: | |
| 261 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 262 #end for | |
| 263 myGenes <- getGenes(cuff, myGeneIds) | |
| 264 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}") | |
| 265 devname = dev.off() | |
| 266 | |
| 267 ## Cluster ## | |
| 268 #elif $p.plot['type'] == "cluster": | |
| 269 myGeneIds <- c() | |
| 270 #for $g in $p.plot.genes: | |
| 271 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 272 #end for | |
| 273 myGenes <- getGenes(cuff, myGeneIds) | |
| 274 csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}") | |
| 275 devname = dev.off() | |
| 276 | |
| 277 ## Expression Plot ## | |
| 278 #elif $p.plot['type'] == "expressionplot": | |
| 279 myGeneId <- "$p.plot.gene_id" | |
| 280 myGenes <- getGenes(cuff, myGeneId) | |
| 281 expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}") | |
| 282 devname = dev.off() | |
| 283 | |
| 284 ## Expression Bar Plot ## | |
| 285 #elif $p.plot['type'] == "expressionbarplot": | |
| 286 myGeneId <- "$p.plot.gene_id" | |
| 287 myGenes <- getGenes(cuff, myGeneId) | |
| 288 expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}") | |
| 289 devname = dev.off() | |
| 290 #end if | |
| 291 | |
| 292 #end for | |
| 293 </configfile> | |
| 294 </configfiles> | |
| 295 | |
| 296 <help> | |
| 297 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. | |
| 298 </help> | |
| 299 | |
| 300 </tool> |