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diff test-data/picard_CASM_test1.tab @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents 5053a18d9bc8
children
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--- a/test-data/picard_CASM_test1.tab	Mon Sep 25 08:32:17 2023 +0000
+++ b/test-data/picard_CASM_test1.tab	Sun Mar 03 16:06:11 2024 +0000
@@ -1,12 +1,83 @@
 ## htsjdk.samtools.metrics.StringHeader
-# CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false INPUT=picard_CASM_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_10.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
+# CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, METRIC_ACCUMULATION_LEVEL=ALL_READS] IS_BISULFITE_SEQUENCED=false INPUT=picard_CASM_bam OUTPUT=/tmp/tmpjhdz2g17/job_working_directory/000/3/outputs/dataset_4d6599a2-4dca-4fa0-8d6b-b676800fb9a8.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    EXPECTED_PAIR_ORIENTATIONS=[FR] METRIC_ACCUMULATION_LEVEL=[ALL_READS] COLLECT_ALIGNMENT_INFORMATION=true STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
 ## htsjdk.samtools.metrics.StringHeader
-# Started on: Sat Apr 14 09:27:21 CEST 2018
+# Started on: Sat Mar 02 17:42:27 GMT 2024
 
 ## METRICS CLASS	picard.analysis.AlignmentSummaryMetrics
-CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_ALIGNED_BASES	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_MISMATCH_RATE	PF_HQ_ERROR_RATE	PF_INDEL_RATE	MEAN_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	PF_READS_IMPROPER_PAIRS	PCT_PF_READS_IMPROPER_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER	SAMPLE	LIBRARY	READ_GROUP
-FIRST_OF_PAIR	100	100	1	0	100	1	17831	100	17831	16865	1	0.008188	0.008188	0	251	99	0.99	1	0.01	0	0.46	0.74	0			
-SECOND_OF_PAIR	100	100	1	0	99	0.99	17907	99	17907	16887	1	0.008879	0.008879	0	251	99	1	0	0	0	0.545455	0.676768	0			
-PAIR	200	200	1	0	199	0.995	35738	199	35738	33752	1	0.008534	0.008534	0	251	198	0.994975	1	0.005025	0	0.502513	0.708543	0			
+CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_ALIGNED_BASES	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_MISMATCH_RATE	PF_HQ_ERROR_RATE	PF_INDEL_RATE	MEAN_READ_LENGTH	SD_READ_LENGTH	MEDIAN_READ_LENGTH	MAD_READ_LENGTH	MIN_READ_LENGTH	MAX_READ_LENGTH	MEAN_ALIGNED_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	PF_READS_IMPROPER_PAIRS	PCT_PF_READS_IMPROPER_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER	PCT_SOFTCLIP	PCT_HARDCLIP	AVG_POS_3PRIME_SOFTCLIP_LENGTH	SAMPLE	LIBRARY	READ_GROUP
+FIRST_OF_PAIR	100	100	1	0	100	1	17831	100	17831	16865	1	0.008188	0.008188	0	251	0	251	0	251	251	178.31	99	0.99	1	0.01	0	0.46	0.74	0	0.289602	0	57.985294			
+SECOND_OF_PAIR	100	100	1	0	99	0.99	17907	99	17907	16887	1	0.008879	0.008879	0	251	0	251	0	251	251	179.07	99	1	0	0	0	0.545455	0.676768	0	0.276574	0	48.307692			
+PAIR	200	200	1	0	199	0.995	35738	199	35738	33752	1	0.008534	0.008534	0	251	0	251	0	251	251	178.69	198	0.994975	1	0.005025	0	0.502513	0.708543	0	0.283088	0	53.255639			
 
+## HISTOGRAM	java.lang.Integer
+READ_LENGTH	PAIRED_TOTAL_LENGTH_COUNT	PAIRED_ALIGNED_LENGTH_COUNT
+0	0	1
+112	0	1
+113	0	1
+120	0	2
+124	0	1
+127	0	1
+130	0	2
+131	0	1
+132	0	5
+133	0	2
+134	0	3
+137	0	2
+138	0	12
+139	0	1
+140	0	3
+141	0	3
+143	0	3
+144	0	1
+146	0	4
+147	0	1
+151	0	4
+152	0	1
+155	0	1
+156	0	9
+157	0	4
+158	0	1
+159	0	2
+161	0	4
+162	0	1
+167	0	2
+169	0	1
+170	0	1
+171	0	10
+172	0	1
+173	0	3
+176	0	2
+177	0	3
+179	0	5
+180	0	1
+181	0	1
+182	0	5
+184	0	9
+185	0	2
+186	0	2
+187	0	4
+192	0	2
+193	0	1
+194	0	3
+200	0	2
+201	0	6
+203	0	8
+205	0	1
+206	0	1
+208	0	3
+213	0	7
+216	0	3
+222	0	1
+228	0	6
+229	0	2
+230	0	1
+231	0	5
+232	0	1
+233	0	1
+236	0	2
+238	0	2
+241	0	5
+242	0	3
+250	0	2
+251	200	3