Mercurial > repos > iuc > dada2_learnerrors

annotate README.rst @ 6:0776d824d896 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
author iuc
date Fri, 30 Jun 2023 07:59:02 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
1 Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html.
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
2
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
3 - assignTaxonomyAddspecies
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
4 - filterAndTrim
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
5 - learnErrors
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
6 - dada
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
7 - mergePairs
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
8 - makeSequenceTable
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
9 - plotComplexity
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
10 - plotQualityProfile
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
11 - removeBimeraDenovo
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
12 - seqCounts
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
13
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
14 Installation
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
15 ============
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
16
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
17 A conda release >=4.6 is needed so that the bioconductor-dada2 conda environment can be installed correctly.
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
18
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
19 The dada2 wrappers can be installed via the toolshed. Since they use datatypes that have been introduced with Galaxy release 19.09 they won't work out of the box for older Galaxy releases.
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
20 In order to run the tools you may either upgrade Galaxy or execute the following two steps:
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
21
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
22
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
23 1. ``find GALAXY_ROOT/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/ -name "dada2_*xml" -exec sed -i -e 's/profile="19.09"/profile="YOUR_RELEASE"/' {} ;`` (replace GALAXY_ROOT and YOUR_RELEASE appropriately)
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
24
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
25 2. insert the following lines in ``config/datatypes.xml`` (just before the line ``</registration>``):
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
26 .. code-block::
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
27
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
28 <datatype extension="dada2_dada" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
29 <datatype extension="dada2_errorrates" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
30 <datatype extension="dada2_mergepairs" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
31 <datatype extension="dada2_sequencetable" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
32 <datatype extension="dada2_uniques" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
33
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
34
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
35 Datatypes
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
36 =========
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
37
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
38 The dada2 Galaxy wrappers use a few extra data types to ensure that only inputs of the correct type can be used, these datatypes are available from Galaxy release 19.05, for earlier releases they need to be added manually.
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
39
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
40 For the outputs of dada, learnErrors, and mergePairs the following datatypes are used that derive from Rdata (which contains the named list that is returned from the corresponding dada function):
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
41
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
42 - dada2_dada (Rdata: named list, see docs for dada-class)
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
43 - dada2_errorrates (Rdata: named list, see docs for learnErrors)
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
44 - dada2_mergepairs (Rdata: named list, see docs for mergePairs)
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
45
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
46
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
47 For the outputs of makeSequenceTable and removeBimeraDenovo the following data types are used which derive from tabular:
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
48
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
49 - dada2_uniques
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
50 - in R a named integer vector (names are the unique sequences)
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
51 - in Galaxy written as a table (each row corresponding to a unique sequence, column 1: the sequence, column 2: the count)
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
52 - dada2_sequencetable
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
53 - in R a named integer matrix (rows = samples, columns = unique sequences)
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
54 - in Galaxy written as a table (rows = unique sequences, columns = samples)
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
55
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
56
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
57 Note the difference between the R and Galaxy representations! The main motivation is that the dada2_sequencetable is analogous to OTU tables as produced for instance by qiime (and it seemed natural to extend this to the uniques which are essentially a sequencetables of single samples).
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
58
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
59 Test data
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
60 =========
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
61
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
62 Test data for ``dada2_seqCounts`` is generated using planemo's ``--update_test_data`` argument and manual
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
63 inspection of the test files. In addition a run of the pipeline (using collections) is executed
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
64 manually using ``planemo serve`` making sure that the entries of the tables are generated in a useful way.
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
65
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
66 In order to have the Collection unzip tool available use ``planemo s --galaxy_root GALAXY_ROOT --extra_tools GALAXY_ROOT/lib/galaxy/tools/``
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
67
0776d824d896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
diff changeset
68 All test other test data is generated using the shell script (``gentest.sh``) in test-data