# HG changeset patch
# User geert-vandeweyer
# Date 1406988778 14400
# Node ID e6ac542a288ee51af33b036413706824f53621fe
# Parent  c668946e25d1b81a56e162551a0af78bb3058b8f
Updated Test Data

diff -r c668946e25d1 -r e6ac542a288e cufflinks_wrapper.xml
--- a/cufflinks_wrapper.xml	Fri Aug 01 09:27:09 2014 -0400
+++ b/cufflinks_wrapper.xml	Sat Aug 02 10:12:58 2014 -0400
@@ -189,7 +189,7 @@
         <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/>
         <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/>
         <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/>
-	<data format="gtf" name="skipped.gtf" label="${tool.name} on ${on_string}: Skipped Transcripts" from_working_dir="genes.fpkm_tracking"/>
+	<data format="gtf" name="skipped" label="${tool.name} on ${on_string}: Skipped Transcripts" from_working_dir="skipped.gtf"/>
     </outputs>
 
     <trackster_conf>
@@ -206,16 +206,15 @@
             <param name="min_isoform_fraction" value="0.05"/>
             <param name="pre_mrna_fraction" value="0.05"/>
             <param name="use_ref" value="No"/>
-            <param name="do_normalization" value="No" />
             <param name="do_bias_correction" value="No"/>
             <param name="multiread_correct" value="No"/>
-            <param name="length_correction" value=""/>
+            <param name="length_correction" value="Cufflinks Effective Length Correction"/>
 	    <param name="use_advanced_settings" value="No" />
             <output name="genes_expression" format="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/>
             <output name="transcripts_expression" format="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/>
             <output name="assembled_isoforms" file="cufflinks_out1.gtf"/>
             <output name="global_model" file="cufflinks_out4.txt"/>
-	   
+	    <output name="skipped" file="cufflinks_out4.gtf"/> 
         </test>
     </tests>
 
diff -r c668946e25d1 -r e6ac542a288e test-data/cufflinks_in.bam
Binary file test-data/cufflinks_in.bam has changed
diff -r c668946e25d1 -r e6ac542a288e test-data/cufflinks_out1.gtf
--- a/test-data/cufflinks_out1.gtf	Fri Aug 01 09:27:09 2014 -0400
+++ b/test-data/cufflinks_out1.gtf	Sat Aug 02 10:12:58 2014 -0400
@@ -1,4 +1,2 @@
-test_chromosome	Cufflinks	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
-test_chromosome	Cufflinks	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
-test_chromosome	Cufflinks	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
-test_chromosome	Cufflinks	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
+tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	FPKM	FPKM_conf_lo	FPKM_conf_hi	FPKM_status
+CUFF.1	-	-	CUFF.1	-	-	test_chromosome:52-550	-	-	1.06791e+07	8.5427e+06	1.28156e+07	OK
diff -r c668946e25d1 -r e6ac542a288e test-data/cufflinks_out2.fpkm_tracking
--- a/test-data/cufflinks_out2.fpkm_tracking	Fri Aug 01 09:27:09 2014 -0400
+++ b/test-data/cufflinks_out2.fpkm_tracking	Sat Aug 02 10:12:58 2014 -0400
@@ -1,2 +1,2 @@
 tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	FPKM	FPKM_conf_lo	FPKM_conf_hi	FPKM_status
-CUFF.1.1	-	-	CUFF.1	-	-	test_chromosome:52-550	298	142.855	1.04656e+07	8.35119e+06	1.25799e+07	OK
+CUFF.1.1	-	-	CUFF.1	-	-	test_chromosome:52-550	298	145.77	1.06791e+07	8.5427e+06	1.28156e+07	OK
diff -r c668946e25d1 -r e6ac542a288e test-data/cufflinks_out3.fpkm_tracking
--- a/test-data/cufflinks_out3.fpkm_tracking	Fri Aug 01 09:27:09 2014 -0400
+++ b/test-data/cufflinks_out3.fpkm_tracking	Sat Aug 02 10:12:58 2014 -0400
@@ -1,2 +1,4 @@
-tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	FPKM	FPKM_conf_lo	FPKM_conf_hi	FPKM_status
-CUFF.1	-	-	CUFF.1	-	-	test_chromosome:52-550	-	-	1.04656e+07	8.35119e+06	1.25799e+07	OK
+test_chromosome	Cufflinks	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185";
+test_chromosome	Cufflinks	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185";
+test_chromosome	Cufflinks	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185";
+test_chromosome	Cufflinks	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185";
diff -r c668946e25d1 -r e6ac542a288e test-data/cufflinks_out5.gtf