annotate test-data/picard_CollectInsertSizeMetrics_test1.tab @ 23:1cd1cf786389 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
author iuc
date Thu, 16 May 2019 07:13:32 -0400
parents 5053a18d9bc8
children 3f254c5ced1d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
1 ## htsjdk.samtools.metrics.StringHeader
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 5
diff changeset
2 # CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/tmpYRm8q4/files/000/dataset_25.dat DEVIATIONS=10.0 HISTOGRAM_WIDTH=500 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectInsertSizeMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_24.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa INCLUDE_DUPLICATES=false 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
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 ## htsjdk.samtools.metrics.StringHeader
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 5
diff changeset
4 # Started on: Sat Apr 14 09:28:38 CEST 2018
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
6 ## METRICS CLASS picard.analysis.InsertSizeMetrics
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 5
diff changeset
7 MEDIAN_INSERT_SIZE MODE_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_95_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 5
diff changeset
8 200 203 28 112 251 193.969697 36.171207 99 FR 7 15 33 43 57 73 83 99 125 133 177
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10 ## HISTOGRAM java.lang.Integer
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 insert_size All_Reads.fr_count
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 112 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 120 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 132 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 134 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 138 5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 139 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 140 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 141 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 151 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 156 4
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 157 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 159 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 161 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 169 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 172 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 173 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 177 3
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 179 3
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 182 3
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 184 4
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 185 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 187 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 192 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 193 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 194 3
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 200 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 201 5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 203 8
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 205 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 208 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 213 4
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 216 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 222 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 228 5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 229 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 230 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 231 3
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 233 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 236 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 238 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 241 4
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 242 3
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 250 2
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 251 3
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56