# HG changeset patch # User devteam # Date 1393480820 18000 # Node ID 987dbea3b72f3c35f4ea9dc0a2b73f9a2c5621b9 # Parent 90e36e359db6cbb5d435fbb45137cca7f71e8f90 Uploaded diff -r 90e36e359db6 -r 987dbea3b72f test-data/outputrnaseqmetrics.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputrnaseqmetrics.html Thu Feb 27 01:00:20 2014 -0500 @@ -0,0 +1,59 @@ + + + + + + + + + + +
+Galaxy tool CollectRnaSeqMetrics run at 26/02/2014 22:17:36
The following output files were created (click the filename to view/download a copy):
+ + +
CollectRnaSeqMetrics.log
CollectRnaSeqMetrics.metrics.txt

+Picard on line resources

+Picard output (transposed to make it easier to see)
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
## net.sf.picard.metrics.StringHeader
# net.sf.picard.analysis.CollectRnaSeqMetrics REF_FLAT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/refFlat.txt RIBOSOMAL_INTERVALS=null STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=CollectRnaSeqMetrics.pdf RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/PICARD-in.sam OUTPUT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.metrics.txt ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## net.sf.picard.metrics.StringHeader
# Started on: Wed Feb 26 22:17:31 EST 2014
## METRICS CLASS net.sf.picard.analysis.RnaSeqMetrics
PF_BASES7321300 
PF_ALIGNED_BASES7319805 
RIBOSOMAL_BASES 
CODING_BASES0 
UTR_BASES0 
INTRONIC_BASES0 
INTERGENIC_BASES7319805 
IGNORED_READS0 
CORRECT_STRAND_READS0 
INCORRECT_STRAND_READS0 
PCT_RIBOSOMAL_BASES 
PCT_CODING_BASES0 
PCT_UTR_BASES0 
PCT_INTRONIC_BASES0 
PCT_INTERGENIC_BASES1 
PCT_MRNA_BASES0 
PCT_USABLE_BASES0 
PCT_CORRECT_STRAND_READS0 
MEDIAN_CV_COVERAGE0 
MEDIAN_5PRIME_BIAS0 
MEDIAN_3PRIME_BIAS0 
MEDIAN_5PRIME_TO_3PRIME_BIAS0 
SAMPLE 
LIBRARY 
READ_GROUP + + 
+Picard Tool Run Log
+
INFO:root:## executing java -Xmx3000m  -Djava.io.tmpdir='/home/dorine/galaxypicard/galaxy-central/database/tmp'  -jar /home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/CollectRnaSeqMetrics.jar VALIDATION_STRINGENCY=LENIENT I=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/PICARD-in.sam O=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.metrics.txt CHART_OUTPUT=CollectRnaSeqMetrics.pdf ASSUME_SORTED=true MINIMUM_LENGTH=500 REF_FLAT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/refFlat.txt STRAND_SPECIFICITY=NONE RIBOSOMAL_INTERVALS=null RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=ALL_READS returned status 0 and nothing on stderr
+
+INFO:root:Unable to find expected pdf file /home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.pdf

+
+
The freely available Picard software +generated all outputs reported here running as a Galaxy tool
+