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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
author iuc
date Thu, 05 Dec 2019 18:01:18 -0500
parents d26cea4b4cc4
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d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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1 Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html.
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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4cc834cce4fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
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3 - assignTaxonomyAddspecies
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4 - filterAndTrim
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5 - learnErrors
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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6 - dada
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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7 - mergePairs
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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8 - makeSequenceTable
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4cc834cce4fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
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9 - plotComplexity
4cc834cce4fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
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10 - plotQualityProfile
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11 - removeBimeraDenovo
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4cc834cce4fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
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12 - seqCounts
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d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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14 Installation
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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15 ============
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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4cc834cce4fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
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17 A conda release >=4.6 is needed so that the bioconductor-dada2 conda environment can be installed correctly.
4cc834cce4fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
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d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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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.
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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20 In order to run the tools you may either upgrade Galaxy or execute the following two steps:
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d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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22 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)
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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23 2. insert the following lines in `config/datatypes.xml` (just before the line `</registration>`):
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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24 ```
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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25 <datatype extension="dada2_dada" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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26 <datatype extension="dada2_errorrates" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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27 <datatype extension="dada2_mergepairs" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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28 <datatype extension="dada2_sequencetable" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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29 <datatype extension="dada2_uniques" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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30 ```
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32 Datatypes
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33 =========
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d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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35 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.
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d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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37 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):
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39 - dada2_dada (Rdata: named list, see docs for dada-class)
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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40 - dada2_errorrates (Rdata: named list, see docs for learnErrors)
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41 - dada2_mergepairs (Rdata: named list, see docs for mergePairs)
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43 For the outputs of makeSequenceTable and removeBimeraDenovo the following data types are used which derive from tabular:
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45 - dada2_uniques
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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46 -- in R a named integer vector (names are the unique sequences)
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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47 -- in Galaxy written as a table (each row corresponding to a unique sequence, column 1: the sequence, column 2: the count)
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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48 - dada2_sequencetable
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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49 -- in R a named integer matrix (rows = samples, columns = unique sequences)
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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50 -- in Galaxy written as a table (rows = unique sequences, columns = samples)
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52 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).
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54 Test data
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55 =========
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57 Test data for `dada2_seqCounts` is generated using planemo's `--update_test_data` argument and manual
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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58 inspection of the test files. In addition a run of the pipeline (using collections) is executed
d26cea4b4cc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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59 manually using `planemo serve` making sure that the entries of the tables are generated in a useful way.
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61 In order to have the Collection unzip tool available use `planemo s --galaxy_root GALAXY_ROOT --extra_tools GALAXY_ROOT/lib/galaxy/tools/`
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63 All test other test data is generated using the shell script (`gentest.sh`) in test-data