comparison edgeR_Differential_Gene_Expression.xml @ 115:f06dceb5b966 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689-dirty
author yhoogstrate
date Tue, 01 Sep 2015 08:01:02 -0400
parents 5d7efbca6c75
children ed809072dc95
comparison
equal deleted inserted replaced
114:5d7efbca6c75 115:f06dceb5b966
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.a"> 2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.b">
3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description> 3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
4 4
5 <macros> 5 <macros>
6 <import>edgeR_macros.xml</import> 6 <import>edgeR_macros.xml</import>
7 </macros> 7 </macros>
99 /dev/null 99 /dev/null
100 #end if 100 #end if
101 101
102 $output_format_images 102 $output_format_images
103 ' 103 '
104 #if $output_R:
105 > $output_R
106 #end if
107 </command> 104 </command>
108 105
109 <configfiles> 106 <configfiles>
110 <configfile name="R_script"> 107 <configfile name="R_script">
111 <![CDATA[ 108 <![CDATA[
236 } 233 }
237 234
238 diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x)) 235 diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x))
239 diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y)) 236 diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y))
240 plot(c(min(mds_distance_logFC\$x),max(mds_distance_logFC\$x) + 0.45 * diff_x), c(min(mds_distance_logFC\$y) - 0.05 * diff_y,max(mds_distance_logFC\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2") 237 plot(c(min(mds_distance_logFC\$x),max(mds_distance_logFC\$x) + 0.45 * diff_x), c(min(mds_distance_logFC\$y) - 0.05 * diff_y,max(mds_distance_logFC\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2")
241 mds_distance_logFC(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20) 238 points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20)
242 text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) 239 text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
243 rm(diff_x,diff_y) 240 rm(diff_x,diff_y)
244 241
245 dev.off() 242 dev.off()
246 } 243 }
268 } 265 }
269 266
270 diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x)) 267 diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x))
271 diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y)) 268 diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y))
272 plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2") 269 plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2")
273 mds_distance_BCV(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20) 270 points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
274 text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) 271 text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
275 rm(diff_x,diff_y) 272 rm(diff_x,diff_y)
276 273
277 dev.off() 274 dev.off()
278 } 275 }
430 <option value="make_output_BCVplot">BCV-plot</option> 427 <option value="make_output_BCVplot">BCV-plot</option>
431 <option value="make_output_MAplot">MA-plot</option> 428 <option value="make_output_MAplot">MA-plot</option>
432 <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option> 429 <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option>
433 <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option> 430 <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option>
434 <option value="make_output_heatmap_plot">Heatmap</option> 431 <option value="make_output_heatmap_plot">Heatmap</option>
435
436 <option value="make_output_R_stdout">R stdout</option>
437 <option value="make_output_RData_obj">R Data object</option> 432 <option value="make_output_RData_obj">R Data object</option>
438 </param> 433 </param>
439 434
440 <param name="output_format_images" type="select" label="Output format of images" display="radio"> 435 <param name="output_format_images" type="select" label="Output format of images" display="radio">
441 <option value="png">Portable network graphics (.png)</option> 436 <option value="png">Portable network graphics (.png)</option>