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comparison 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
comparison
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32:f9242e01365a 33:3f254c5ced1d
1 ## htsjdk.samtools.metrics.StringHeader 1 ## htsjdk.samtools.metrics.StringHeader
2 # 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 2 # 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
3 ## htsjdk.samtools.metrics.StringHeader 3 ## htsjdk.samtools.metrics.StringHeader
4 # Started on: Sat Apr 14 09:27:21 CEST 2018 4 # Started on: Sat Mar 02 17:42:27 GMT 2024
5 5
6 ## METRICS CLASS picard.analysis.AlignmentSummaryMetrics 6 ## METRICS CLASS picard.analysis.AlignmentSummaryMetrics
7 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 7 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
8 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 8 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
9 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 9 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
10 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 10 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
11 11
12 ## HISTOGRAM java.lang.Integer
13 READ_LENGTH PAIRED_TOTAL_LENGTH_COUNT PAIRED_ALIGNED_LENGTH_COUNT
14 0 0 1
15 112 0 1
16 113 0 1
17 120 0 2
18 124 0 1
19 127 0 1
20 130 0 2
21 131 0 1
22 132 0 5
23 133 0 2
24 134 0 3
25 137 0 2
26 138 0 12
27 139 0 1
28 140 0 3
29 141 0 3
30 143 0 3
31 144 0 1
32 146 0 4
33 147 0 1
34 151 0 4
35 152 0 1
36 155 0 1
37 156 0 9
38 157 0 4
39 158 0 1
40 159 0 2
41 161 0 4
42 162 0 1
43 167 0 2
44 169 0 1
45 170 0 1
46 171 0 10
47 172 0 1
48 173 0 3
49 176 0 2
50 177 0 3
51 179 0 5
52 180 0 1
53 181 0 1
54 182 0 5
55 184 0 9
56 185 0 2
57 186 0 2
58 187 0 4
59 192 0 2
60 193 0 1
61 194 0 3
62 200 0 2
63 201 0 6
64 203 0 8
65 205 0 1
66 206 0 1
67 208 0 3
68 213 0 7
69 216 0 3
70 222 0 1
71 228 0 6
72 229 0 2
73 230 0 1
74 231 0 5
75 232 0 1
76 233 0 1
77 236 0 2
78 238 0 2
79 241 0 5
80 242 0 3
81 250 0 2
82 251 200 3
12 83