Mercurial > repos > matthias > dada2_learnerrors

annotate notes.txt @ 0:56d5be6c03b9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
author matthias
date Fri, 08 Mar 2019 06:30:11 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
1 TODO
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
2 ====
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
3
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
4
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
5
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
6 If we make a monolithic tool:
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
7
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
8 * implement sanity checks between important compute intensive steps (user definable criteria, abort if violated)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
9
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
10 If we keep separate tools:
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
11
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
12 - make Rdata data types specific (like xmcs https://github.com/workflow4metabolomics/xcms/tree/dev/datatypes)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
13 * alternatively the data set types could be derived from tabular and the Rdata could be attached via
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
14 `.extra_files_path` this way the user could have some intermediate output that he could look at.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
15
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
16
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
17 In both cases:
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
18
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
19 * allow input of single end data, single pair, single pair in separate data sets, ...
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
20 * add mergePairsByID functionality to mergePairs tool
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
21
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
22
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
23 Datatypes:
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
24 ==========
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
25
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
26 **derep-class**: list w 3 members
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
27 - uniques: Named integer vector. Named by the unique sequence, valued by abundance.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
28 • quals: Numeric matrix of average quality scores by position for each unique. Uniques are
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
29 rows, positions are cols.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
30 * map: Integer vector of length the number of reads, and value the index (in uniques) of the
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
31 unique to which that read was assigned.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
32
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
33 **learnErrorsOutput**: A named list with three entries
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
34 - err_out: A numeric matrix with the learned error rates.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
35 - err_in: The initialization error rates (unimportant).
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
36 - trans: A feature table of observed transitions for each type (eg. A->C) and quality score.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
37
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
38 **dada-class**: A multi-item List with the following named values...
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
39 • denoised: Integer vector, named by sequence valued by abundance, of the denoised sequences.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
40 • clustering: An informative data.frame containing information on each cluster.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
41 • sequence: A character vector of each denoised sequence. Identical to names(denoised).
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
42 • quality: The average quality scores for each cluster (row) by position (col).
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
43 • map: Integer vector that maps the unique (index of derep.unique) to the denoised sequence (index of dada.denoised).
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
44 • birth_subs: A data.frame containing the substitutions at the birth of each new cluster.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
45 • trans: The matrix of transitions by type (row), eg. A2A, A2C..., and quality score (col)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
46 observed in the final output of the dada algorithm.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
47 • err_in: The err matrix used for this invocation of dada.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
48 • err_out: The err matrix estimated from the output of dada. NULL if err_function not provided.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
49 • opts: A list of the dada_opts used for this invocation of dada.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
50 • call: The function call used for this invocation of dada.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
51
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
52 **uniques**: derep, dada, mergepairs(or data frame w sequenc and abundance columns)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
53
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
54 **mergepairs**:
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
55
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
56 data.frame(s) has a row for each unique pairing of forward/reverse denoised sequences, and the following columns:
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
57 • abundance: Number of reads corresponding to this forward/reverse combination.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
58 • sequence: The merged sequence.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
59 • forward: The index of the forward denoised sequence.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
60 • reverse: The index of the reverse denoised sequence.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
61 • nmatch: Number of matches nts in the overlap region.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
62 • nmismatch: Number of mismatches in the overlap region.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
63 • nindel: Number of indels in the overlap region.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
64 • prefer: The sequence used for the overlap region. 1=forward; 2=reverse.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
65 • accept: TRUE if overlap between forward and reverse denoised sequences was at least minOverlap and had at most maxMismatch differences. FALSE otherwise.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
66 • ...: Additional columns specified in propagateCol
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
67
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
68
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
69
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
70 Tools:
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
71 ======
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
72
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
73 • Quality filtering
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
74
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
75 filterAndTrim IO=(fastq -> fastq)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
76
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
77 • Dereplication
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
78
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
79 derepFastq (fastq -> derep-class object)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
80
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
81 • Learn error rates
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
82
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
83 learnErrors + plotErrors
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
84 - in: input list, or vector, of file names (or a list of derep-class objects WHY .. learning should be done on full data)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
85 - out: named list w entries
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
86 - \$err\_out: A numeric matrix with the learned error rates.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
87 - \$err\_in: The initialization error rates (unimportant).
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
88 - \$trans: A feature table of observed transitions for each type (eg. A->C) and quality score
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
89
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
90 • Sample Inference (dada)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
91 in: (list of) derep-class object
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
92 out: (list of) dada-class object
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
93
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
94 • Chimera Removal
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
95
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
96 removeBimeraDenovo
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
97
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
98 in: A uniques-vector or any object that can be coerced into one with getUniques.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
99 out: A uniques vector, or an object of matching class if a data.frame or sequence table is provided
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
100
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
101 • Merging of Paired Reads
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
102
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
103 mergePairs
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
104 in: 2x dada-class object(s), 2x derep-class object(s)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
105 out: A data.frame, or a list of data.frames.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
106 - The return data.frame(s) has a row for each unique pairing of forward/reverse denoised sequences,
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
107 - cols
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
108 - \$abundance: Number of reads corresponding to this forward/reverse combination.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
109 - \$sequence: The merged sequence.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
110 - \$forward: The index of the forward denoised sequence.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
111 - \$reverse: The index of the reverse denoised sequence.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
112 - \$nmatch: Number of matches nts in the overlap region.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
113 - \$nmismatch: Number of mismatches in the overlap region.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
114 - \$nindel: Number of indels in the overlap region.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
115 - \$prefer: The sequence used for the overlap region. 1=forward; 2=reverse.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
116 - \$accept: TRUE if overlap between forward and reverse denoised sequences was at least minOverlap and had at most maxMismatch differences. FALSE otherwise.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
117 - \$...: Additional columns specified in propagateCol.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
118
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
119 • Taxonomic Classification (assignTaxonomy, assignSpecies)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
120
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
121 * Other
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
122
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
123 makeSequenceTable
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
124 in A list of the samples to include in the sequence table. Samples can be provided in any format that can be processed by getUniques
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
125 out Named integer matrix (row for each sample, column for each unique sequence)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
126
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
127 mergeSequenceTables
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
128
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
129 uniquesToFasta
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
130 in: A uniques-vector or any object that can be coerced into one with getUniques.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
131
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
132 getSequences
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
133
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
134 extracts the sequences from several different data objects: including including dada-class
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
135 and derep-class objects, as well as data.frame objects that have both \$sequence and \$abun-
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
136 dance columns.
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
137
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
138 getUniques
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
139
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
140 extracts the uniques-vector from several different data objects, including dada-class
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
141 and derep-class objects, as well as data.frame objects that have both \$sequence and \$abundance
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
142 columns
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
143
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
144 plotQualityProfile
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
145
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
146 seqComplexity
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
147
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
148 setDadaOpt(...)