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annotate test-data/sortmerna.txt @ 29:ef6bd40a30d2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
author iuc
date Fri, 10 Oct 2025 20:11:35 +0000
parents b437798cb165
children
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b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
1 Tue Jan 31 17:04:24 2017
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
2
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
3 Command: /home/lina/sortmerna/sortmerna --ref /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta,/home/lina/sortmerna/index/silva-bac-16s-db:/home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta,/home/lina/sortmerna/index/silva-bac-23s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta,/home/lina/sortmerna/index/silva-arc-16s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta,/home/lina/sortmerna/index/silva-arc-23s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta,/home/lina/sortmerna/index/silva-euk-18s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta,/home/lina/sortmerna/index/silva-euk-28s:/home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5s-db:/home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5.8s-db --reads 25839_merged.fastq --num_alignments 1 --fastx --aligned Sample_2055324_ribo/sortmerna_out/2055324_ribo_rrna_reads --other Sample_2055324_ribo/sortmerna_out/2055324_ribo_rrna_free_reads.fastq fastq tq --log -v --blast 1
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
4 Process pid = 27736
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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5 Parameters summary:
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
6 Index: /home/lina/sortmerna/index/silva-bac-16s-db
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
7 Seed length = 18
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
8 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
9 Gumbel lambda = 0.602725
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
10 Gumbel K = 0.329559
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
11 Minimal SW score based on E-value = 57
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
12 Index: /home/lina/sortmerna/index/silva-bac-23s-db
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
13 Seed length = 18
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
14 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
15 Gumbel lambda = 0.602436
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
16 Gumbel K = 0.335011
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
17 Minimal SW score based on E-value = 57
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
18 Index: /home/lina/sortmerna/index/silva-arc-16s-db
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
19 Seed length = 18
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
20 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
21 Gumbel lambda = 0.596286
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
22 Gumbel K = 0.322254
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
23 Minimal SW score based on E-value = 55
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
24 Index: /home/lina/sortmerna/index/silva-arc-23s-db
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
25 Seed length = 18
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
26 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
27 Gumbel lambda = 0.597507
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
28 Gumbel K = 0.331576
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
29 Minimal SW score based on E-value = 53
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
30 Index: /home/lina/sortmerna/index/silva-euk-18s-db
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
31 Seed length = 18
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
32 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
33 Gumbel lambda = 0.612551
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
34 Gumbel K = 0.339810
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
35 Minimal SW score based on E-value = 56
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
36 Index: /home/lina/sortmerna/index/silva-euk-28s
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
37 Seed length = 18
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
38 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
39 Gumbel lambda = 0.612082
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
40 Gumbel K = 0.345772
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
41 Minimal SW score based on E-value = 56
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
42 Index: /home/lina/sortmerna/index/rfam-5s-db
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
43 Seed length = 18
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
44 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
45 Gumbel lambda = 0.616694
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
46 Gumbel K = 0.342032
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
47 Minimal SW score based on E-value = 54
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
48 Index: /home/lina/sortmerna/index/rfam-5.8s-db
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
49 Seed length = 18
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
50 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
51 Gumbel lambda = 0.617555
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
52 Gumbel K = 0.343861
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
53 Minimal SW score based on E-value = 52
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
54 Number of seeds = 2
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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55 Edges = 4 (as integer)
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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56 SW match = 2
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
57 SW mismatch = -3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
58 SW gap open penalty = 5
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
59 SW gap extend penalty = 2
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
60 SW ambiguous nucleotide = -3
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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61 SQ tags are not output
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
62 Number of threads = 20
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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63 Reads file = 25839_merged.fastq
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
64
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
65 Results:
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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66 Total reads = 4443556
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
67 Total reads passing E-value threshold = 48848 (1.10%)
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
68 Total reads failing E-value threshold = 4394708 (98.90%)
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
69 Minimum read length = 35
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
70 Maximum read length = 76
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
71 Mean read length = 74
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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72 By database:
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
73 /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta 0.59%
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
74 /home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta 0.24%
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
75 /home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta 0.00%
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
76 /home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta 0.00%
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
77 /home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta 0.25%
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
78 /home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta 0.01%
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
79 /home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta 0.00%
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
80 /home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta 0.00%
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
81
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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82 Tue Jan 31 17:08:40 2017
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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83