Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Differential_Gene_Expression.xml @ 53:b89788eead3c draft

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author yhoogstrate
date Fri, 13 Jun 2014 09:11:42 -0400
parents f710e5ed7cea
children 8c63794c3d3e
comparison
equal deleted inserted replaced
52:7fc17dc83777 53:b89788eead3c
77 > $output_R 77 > $output_R
78 #else: 78 #else:
79 > /dev/null 79 > /dev/null
80 #end if 80 #end if
81 81
82 2> stderr.txt 82 2> stderr.txt ;
83 ; 83
84 grep -v 'Calculating library sizes from column' stderr.txt 1>&2 84 grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
85
86 ## Locale error messages:
87 grep -v 'During startup - Warning messages' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
88 grep -v 'Setting LC_TIME failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
89 grep -v 'Setting LC_MONETARY failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
90 grep -v 'Setting LC_PAPER failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
91 grep -v 'Setting LC_MEASUREMENT failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
92 grep -v 'Setting LC_CTYPE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
93 grep -v 'Setting LC_COLLATE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
94
95 cat stderr.txt >&2
85 96
86 </command> 97 </command>
87 98
88 <inputs> 99 <inputs>
89 <param name="expression_matrix" type="data" format="tabular" label="Expression (read count) matrix" /> 100 <param name="expression_matrix" type="data" format="tabular" label="Expression (read count) matrix" />
304 } 315 }
305 </configfile> 316 </configfile>
306 </configfiles> 317 </configfiles>
307 318
308 <outputs> 319 <outputs>
309 <data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differtially expressed genes" /> 320 <data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differentially expressed genes" />
310 <data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" /> 321 <data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" />
311 322
312 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts"> 323 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts">
313 <filter>("make_output_raw_counts" in outputs)</filter> 324 <filter>outputs and ("make_output_raw_counts" in outputs)</filter>
314 </data> 325 </data>
315 326
316 <data format="pdf" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot"> 327 <data format="pdf" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot">
317 <filter>("make_output_MDSplot" in outputs)</filter> 328 <filter>outputs and ("make_output_MDSplot" in outputs)</filter>
318 </data> 329 </data>
319 330
320 <data format="pdf" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot"> 331 <data format="pdf" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
321 <filter>("make_output_BCVplot" in outputs)</filter> 332 <filter>outputs and ("make_output_BCVplot" in outputs)</filter>
322 </data> 333 </data>
323 334
324 <data format="pdf" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot"> 335 <data format="pdf" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
325 <filter>("make_output_MAplot" in outputs)</filter> 336 <filter>outputs and ("make_output_MAplot" in outputs)</filter>
326 </data> 337 </data>
327 338
328 <data format="pdf" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution"> 339 <data format="pdf" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution">
329 <filter>("make_output_PValue_distribution_plot" in outputs)</filter> 340 <filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter>
330 </data> 341 </data>
331 342
332 <data format="pdf" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering"> 343 <data format="pdf" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering">
333 <filter>("make_output_hierarchical_clustering_plot" in outputs)</filter> 344 <filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter>
334 </data> 345 </data>
335 346
336 <data format="pdf" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap"> 347 <data format="pdf" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap">
337 <filter>("make_output_heatmap_plot" in outputs)</filter> 348 <filter>outputs and ("make_output_heatmap_plot" in outputs)</filter>
338 </data> 349 </data>
339 350
340 <data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object"> 351 <data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object">
341 <filter>("make_output_RData_obj" in outputs)</filter> 352 <filter>outputs and ("make_output_RData_obj" in outputs)</filter>
342 </data> 353 </data>
343 354
344 <data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" > 355 <data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" >
345 <filter>("make_output_R_stdout" in outputs)</filter> 356 <filter>outputs and ("make_output_R_stdout" in outputs)</filter>
346 </data> 357 </data>
347 </outputs> 358 </outputs>
348 359
349 <help> 360 <help>
350 edgeR: Differential Gene(Expression) Analysis 361 edgeR: Differential Gene(Expression) Analysis