# HG changeset patch
# User iuc
# Date 1515629401 18000
# Node ID d1015c2516b7ae09bcdd440f54f887a86c54cf13
# Parent  79436b3019e9164f0e387134bab7646e6e770177
planemo upload commit eea727c3bdfe36d9d16036d5ab79fb8b27c4e82e

diff -r 79436b3019e9 -r d1015c2516b7 macros.xml
--- a/macros.xml	Tue Aug 29 17:37:07 2017 -0400
+++ b/macros.xml	Wed Jan 10 19:10:01 2018 -0500
@@ -19,5 +19,5 @@
             <yield />
         </requirements>
     </xml>
-    <token name="@VERSION@">0.5.0</token>
+    <token name="@VERSION@">0.5.3</token>
 </macros>
diff -r 79436b3019e9 -r d1015c2516b7 test-data/dedup_out1.bam
Binary file test-data/dedup_out1.bam has changed
diff -r 79436b3019e9 -r d1015c2516b7 test-data/dedup_out2.bam
Binary file test-data/dedup_out2.bam has changed
diff -r 79436b3019e9 -r d1015c2516b7 test-data/dedup_out3.bam
Binary file test-data/dedup_out3.bam has changed
diff -r 79436b3019e9 -r d1015c2516b7 test-data/dedup_out4.bam
Binary file test-data/dedup_out4.bam has changed
diff -r 79436b3019e9 -r d1015c2516b7 test-data/dedup_out5.bam
Binary file test-data/dedup_out5.bam has changed
diff -r 79436b3019e9 -r d1015c2516b7 test-data/dedup_out6.bam
Binary file test-data/dedup_out6.bam has changed
diff -r 79436b3019e9 -r d1015c2516b7 test-data/group_out1.bam
Binary file test-data/group_out1.bam has changed
diff -r 79436b3019e9 -r d1015c2516b7 test-data/group_out4.bam
Binary file test-data/group_out4.bam has changed
diff -r 79436b3019e9 -r d1015c2516b7 test-data/out_paired.log
--- a/test-data/out_paired.log	Tue Aug 29 17:37:07 2017 -0400
+++ b/test-data/out_paired.log	Wed Jan 10 19:10:01 2018 -0500
@@ -1,6 +1,6 @@
-# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/tmp/tmpREDhtd/files/003/dataset_3773.dat
-# job started at Tue Aug 29 14:20:44 2017 on gaius -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd
-# pid: 21437, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64
+# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/tmp/tmpAvWtMd/files/000/dataset_20.dat
+# job started at Wed Jan  3 17:06:39 2018 on tzk-ThinkPad-T450s -- 9eecaab6-9562-4b29-8a2e-ae6c1034a14c
+# pid: 22903, system: Linux 4.10.0-42-generic #46~16.04.1-Ubuntu SMP Mon Dec 4 15:57:59 UTC 2017 x86_64
 # blacklist                               : None
 # compresslevel                           : 6
 # error_correct_cell                      : False
@@ -21,16 +21,17 @@
 # read2_stdout                            : False
 # reads_subset                            : None
 # reconcile                               : False
+# retain_umi                              : None
 # short_help                              : None
 # stderr                                  : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'>
 # stdin                                   : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>
-# stdlog                                  : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3773.dat' mode='a' encoding='UTF-8'>
+# stdlog                                  : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_20.dat' mode='a' encoding='UTF-8'>
 # stdout                                  : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>
 # timeit_file                             : None
 # timeit_header                           : None
 # timeit_name                             : all
 # whitelist                               : None
-2017-08-29 14:20:44,451 INFO Starting barcode extraction
-2017-08-29 14:20:44,461 INFO Input Reads: 100
-2017-08-29 14:20:44,461 INFO Reads output: 100
-# job finished in 0 seconds at Tue Aug 29 14:20:44 2017 --  0.73  0.05  0.00  0.00 -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd
+2018-01-03 17:06:39,365 INFO Starting barcode extraction
+2018-01-03 17:06:39,377 INFO Input Reads: 100
+2018-01-03 17:06:39,377 INFO Reads output: 100
+# job finished in 0 seconds at Wed Jan  3 17:06:39 2018 --  0.60  0.05  0.00  0.00 -- 9eecaab6-9562-4b29-8a2e-ae6c1034a14c
diff -r 79436b3019e9 -r d1015c2516b7 test-data/out_single.log
--- a/test-data/out_single.log	Tue Aug 29 17:37:07 2017 -0400
+++ b/test-data/out_single.log	Wed Jan 10 19:10:01 2018 -0500
@@ -1,6 +1,6 @@
-# output generated by extract --bc-pattern=XXXNNN --stdin=/tmp/tmpREDhtd/files/003/dataset_3766.dat --stdout /tmp/tmpREDhtd/files/003/dataset_3767.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/tmp/tmpREDhtd/files/003/dataset_3768.dat
-# job started at Tue Aug 29 14:20:26 2017 on gaius -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393
-# pid: 21338, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64
+# output generated by extract --bc-pattern=XXXNNN --stdin=/tmp/tmpAvWtMd/files/000/dataset_13.dat --stdout /tmp/tmpAvWtMd/files/000/dataset_14.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/tmp/tmpAvWtMd/files/000/dataset_15.dat
+# job started at Wed Jan  3 17:06:20 2018 on tzk-ThinkPad-T450s -- 8897b3b4-c6e2-4ee3-b6c0-71044a63b7e1
+# pid: 22794, system: Linux 4.10.0-42-generic #46~16.04.1-Ubuntu SMP Mon Dec 4 15:57:59 UTC 2017 x86_64
 # blacklist                               : None
 # compresslevel                           : 6
 # error_correct_cell                      : False
@@ -21,17 +21,18 @@
 # read2_stdout                            : False
 # reads_subset                            : None
 # reconcile                               : False
+# retain_umi                              : None
 # short_help                              : None
 # stderr                                  : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'>
-# stdin                                   : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3766.dat' mode='r' encoding='UTF-8'>
-# stdlog                                  : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3768.dat' mode='a' encoding='UTF-8'>
-# stdout                                  : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3767.dat' mode='w' encoding='UTF-8'>
+# stdin                                   : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_13.dat' mode='r' encoding='UTF-8'>
+# stdlog                                  : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_15.dat' mode='a' encoding='UTF-8'>
+# stdout                                  : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_14.dat' mode='w' encoding='UTF-8'>
 # timeit_file                             : None
 # timeit_header                           : None
 # timeit_name                             : all
 # whitelist                               : None
-2017-08-29 14:20:26,493 INFO Starting barcode extraction
-2017-08-29 14:20:26,495 INFO Input Reads: 100
-2017-08-29 14:20:26,495 INFO Reads output: 72
-2017-08-29 14:20:26,495 INFO filtered: umi quality: 28
-# job finished in 0 seconds at Tue Aug 29 14:20:26 2017 --  0.75  0.02  0.00  0.00 -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393
+2018-01-03 17:06:20,360 INFO Starting barcode extraction
+2018-01-03 17:06:20,362 INFO Input Reads: 100
+2018-01-03 17:06:20,362 INFO Reads output: 72
+2018-01-03 17:06:20,362 INFO filtered: umi quality: 28
+# job finished in 0 seconds at Wed Jan  3 17:06:20 2018 --  0.58  0.06  0.00  0.00 -- 8897b3b4-c6e2-4ee3-b6c0-71044a63b7e1