Added genesets as raw data files

loosolab · Jul 17, 2015 · 916de7e3f30bd24574d8d31c345931183dc2f643 · 916de7e
1 parent aa20511
commit 916de7e3f30bd24574d8d31c345931183dc2f643
diff --git a/admire.xml b/admire.xml
@@ -45,6 +45,16 @@
 	#for $custom in $customs
 	-r $custom.cr
 	#end for
+	#set $g=str($genesets).split(",")
+        #for $geneset in $g
+        #set global $gs=$geneset
+        -g ${ filter( lambda x: str( x[0] ) == str( $gs ), $__app__.tool_data_tables[ 'admire_genesets' ].get_fields() )[0][-1] }
+        #end for
+        #end if
+	#for $cugs in $cu_genesets
+	-g $cugs.cu
+	#end for
+	-i $n_images
 	-o $o_compressed > $o_log
 	</command>
 	<inputs>
@@ -102,6 +112,7 @@
 		<param name="det_p" label="Detection p-value threshold for failed probe identification" type="float" min="0" max="1" value="0.01" help="Mark a probes as failed, if it has a detection p-value higher than the given value. Failed probes can be excluded from subsequent analysis using the failed sample threshold (see below)." />
 		<param name="s_thresh" label="Failed sample threshold" type="float" min="0" max="1" value="0.4" help="Probes are excluded from subsequent analysis if the proportion of failed probes across all samples is higher than the given value." />
 		<param name="fdr" label="Q-value cutoff for multiple testing" type="float" min="0" max="1" value="0.05" help="Definde a false discovery rate to limit results after multiple testing correction." />
+		<param name="n_images" label="Number of additional plots for n best regions" type="integer" value="20" max="50" min="0" help="Prints n bubble plots for the best (i.e. most significant) regions into the visualization directory." />
 		<param name="regions" type="select" label="Select genomic regions to test" display="checkboxes" multiple="true" help="Regions will be overlapped with GC probes and significant different methylated regions will be reported.">
 			<options from_data_table="admire_regions" />
 		</param>

diff --git a/admire_genesets.loc b/admire_genesets.loc
@@ -0,0 +1,14 @@
+c1.all	c1.all	C1: Positional gene sets (by chromosome, 326) 	genesets/c1.all.v5.0.symbols.gmt
+c2.cgp	c2.cgp	C2: Chemical and genetic pertubations (3395)	genesets/c2.cpg.v5.0.symbols.gmt
+c2.cp.biocarta	c2.cp.biocarta	C2: BioCharta canonical pathways (217)	genesets/c2.cp.biocarta.v5.0.symbols.gmt
+c2.cp.kegg	c2.cp.kegg	C2: KEGG gene sets (186)	genesets/c2.cp.kegg.v5.0.symbols.gmt
+c2.cp.reactome	c2.cp.reactome	C2: Reactome gene sets (674)	genesets/c2.cp.reactome.v5.0.symbols.gmt
+c3.tft	c3.tft	C3: transcription factor targets (615)	genesets/c3.tft.v5.0.symbols.gmt
+c4.cgn	c4.cgn	C4: Cancer gene neighborhoods (427)	genesets/c4.cgn.v5.0.symbols.gmt
+c4.cm	c4.cm	C4: Cancer modules (431)	genesets/c4.cm.v5.0.symbols.gmt
+c5.bp	c5.bp	C5: GO biological process (825)	genesets/c5.bp.v5.0.symbols.gmt
+c5.cc	c5.cc	C5: GO cellular component (233)	genesets/c5.cc.v5.0.symbols.gmt
+c5.mf	c5.mf	C5: GO molecular function (396)	genesets/c5.mf.v5.0.symbols.gmt
+c6	c6	C6: Oncogenic signatures (189)	genesets/c6.all.v5.0.symbols.gmt
+c7	c7	C7: Immunologic signatures (1910)	genesets/c7.all.v5.0.symbols.gmt
+h	h	H: Hallmark gene sets (50)	genesets/h.all.v5.0.symbols.gmt
diff --git a/genesets/c1.all.v5.0.symbols.gmt b/genesets/c1.all.v5.0.symbols.gmt
diff --git a/genesets/c2.cgp.v5.0.symbols.gmt b/genesets/c2.cgp.v5.0.symbols.gmt
diff --git a/genesets/c2.cp.biocarta.v5.0.symbols.gmt b/genesets/c2.cp.biocarta.v5.0.symbols.gmt
diff --git a/genesets/c2.cp.kegg.v5.0.symbols.gmt b/genesets/c2.cp.kegg.v5.0.symbols.gmt
diff --git a/genesets/c2.cp.reactome.v5.0.symbols.gmt b/genesets/c2.cp.reactome.v5.0.symbols.gmt
diff --git a/genesets/c3.mir.v5.0.symbols.gmt b/genesets/c3.mir.v5.0.symbols.gmt
diff --git a/genesets/c3.tft.v5.0.symbols.gmt b/genesets/c3.tft.v5.0.symbols.gmt
diff --git a/genesets/c4.cgn.v5.0.symbols.gmt b/genesets/c4.cgn.v5.0.symbols.gmt
diff --git a/genesets/c4.cm.v5.0.symbols.gmt b/genesets/c4.cm.v5.0.symbols.gmt
diff --git a/genesets/c5.bp.v5.0.symbols.gmt b/genesets/c5.bp.v5.0.symbols.gmt
diff --git a/genesets/c5.cc.v5.0.symbols.gmt b/genesets/c5.cc.v5.0.symbols.gmt
diff --git a/genesets/c5.mf.v5.0.symbols.gmt b/genesets/c5.mf.v5.0.symbols.gmt
diff --git a/genesets/c6.all.v5.0.symbols.gmt b/genesets/c6.all.v5.0.symbols.gmt
diff --git a/genesets/c7.all.v5.0.symbols.gmt b/genesets/c7.all.v5.0.symbols.gmt
diff --git a/genesets/h.all.v5.0.symbols.gmt b/genesets/h.all.v5.0.symbols.gmt