Mercurial > repos > matthias > dada2_learnerrors

annotate dada2_learnErrors.xml @ 8:af8d1ccbd153 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 977f22125c9ad5c3c5560de8946017305c5633c1
author matthias
date Mon, 27 May 2019 13:21:48 -0400
parents 382900945187
children ef3ebaa70032
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
1 <tool id="dada2_learnErrors" name="dada2: learnErrors" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@">
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
2 <description>Learn Error rates</description>
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 <macros>
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 <import>macros.xml</import>
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 </macros>
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 <expand macro="requirements"/>
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 <expand macro="version_command"/>
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 <command detect_errors="exit_code"><![CDATA[
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
9 Rscript '$dada2_script' \${GALAXY_SLOTS:-1}
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
10 ]]></command>
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 <configfiles>
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 <configfile name="dada2_script"><![CDATA[
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 library(ggplot2, quietly=T)
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 library(dada2, quietly=T)
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 args <- commandArgs(trailingOnly = TRUE)
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 nthreads <- as.integer(args[1])
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 files <- c()
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
20 #for $read in $fls:
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
21 files <- c(files, '$read')
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
22 #end for
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
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
24 err <- learnErrors(files, nbases = 10**$nbases,
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
25 errorEstimationFunction = $advanced.errfoo, multithread = nthreads,
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 randomize = $advanced.randomize, MAX_CONSIST = $advanced.maxconsist, OMEGA_C = $advanced.omegac)
56d5be6c03b9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
27
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
28 ## write.table(err\$err_out, file = '$errors', quote = F, sep = "\t", row.names = T, col.names = F)
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
29 saveRDS(err, file='$errors')
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
30
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 ## generate error plots
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
32 plot <- plotErrors(err, obs = $plotopt.obs, err_out = $plotopt.err_out, err_in = $plotopt.err_in, nominalQ = $plotopt.nominalQ)
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
33 ggsave('plot.pdf', plot, width = 20,height = 15,units = c("cm"))
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
34 ]]></configfile>
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 </configfiles>
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 <inputs>
7
382900945187 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 5
diff changeset
37 <param argument="fls" type="data" multiple="true" format="fastq,fastq.gz" label="Short read data" help="forward or reverse reads should be processed separately"/>
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
38 <param argument="nbases" type="integer" value="8" min="0" label="Magnitide of number of bases to use for learning"/>
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
39 <section name="advanced" title="Advanced Option">
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
40 <expand macro="errorEstimationFunction"/>
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
41 <param argument="randomize" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Randomize samples" help="Pick samples at random, otherwise samples are read in the provided order until enough reads are obtained (default)."/>
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
42 <param name="maxconsist" argument="MAX_CONSIST" type="integer" value="10" min="0" label="Maximum number of times to step through the selfconsistency loop" help="If convergence was not reached in MAX_CONSIST steps, the estimated error rates in the last step are returned."/>
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
43 <param name="omegac" argument="OMEGA_C" type="float" value="0" min="0" label="Threshold at which unique sequences inferred to contain errors are corrected" help="For reasons of convergence, and because it is
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
44 more conservative, it is recommended to set this value to 0, which means that
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
45 all reads are counted and contribute to estimating the error rates."/>
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
46 </section>
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
47 <section name="plotopt" title="Plotting Option">
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
48 <param argument="obs" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Plot observed error rates"/>
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
49 <param argument="err_out" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Plot output error rates"/>
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
50 <param argument="err_in" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Plot input error rates"/>
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
51 <param argument="nominalQ" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Plot expected error rates"/>
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
52 </section>
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 </inputs>
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 <outputs>
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 <data name="errors" format="dada2_errorrates" label="${tool.name} on ${on_string}"/>
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
56 <data name="plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}: error rates plot"/>
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
57 </outputs>
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
58 <tests>
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
59 <test>
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
60 <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz"/>
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
61 <output name="errors" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates"/>
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
62 <output name="plot" value="learnErrors_F3D0_R1.pdf" ftype="pdf" />
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
63 </test>
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
64 <!-- test for creating input for dada results for reverse, not needed for testing -->
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
65 <test>
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
66 <param name="fls" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz"/>
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
67 <output name="errors" value="learnErrors_F3D0_R2.Rdata" ftype="dada2_errorrates"/>
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
68 <output name="plot" value="learnErrors_F3D0_R2.pdf" ftype="pdf" />
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
69 </test>
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
70 <!-- test w non-default parameters -->
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
71 <test>
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
72 <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz"/>
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
73 <param name="nbases" value="6" />
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
74 <param name="advanced|errfoo" value="noqualErrfun" />
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
75 <param name="advanced|randomize" value="TRUE" />
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
76 <param name="advanced|maxconsist" value="5" />
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
77 <param name="advanced|omegac" value="1e-10" />
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
78 <param name="plotopt|obs" value="FALSE" />
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
79 <param name="plotopt|err_out" value="FALSE" />
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
80 <param name="plotopt|err_in" value="TRUE" />
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
81 <param name="plotopt|nominalQ" value="FALSE"/>
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
82 <output name="errors" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" compare="sim_size" delta="14000"/>
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
83 <output name="plot" value="learnErrors_F3D0_R1.pdf" ftype="pdf" compare="sim_size" />
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
84 </test>
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
85 <!-- TODO test w multiple inputs -->
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
86 </tests>
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
87 <help><![CDATA[
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
88 Description
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
89 ...........
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
90
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
91 Error rates are learned by alternating between sample inference and error rate estimation until convergence. Additionally a plot is generated that shows the observed frequency of each transition (eg. A->C) as a function of the associated quality score, the final estimated error rates (if they exist), the initial input rates, and the expected error rates under the nominal definition of quality scores.
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
92
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
93 In addition a plot is generated (with plotErrors) that shows the observed frequency of each transition (eg. A->C) as a function of the associated quality score. Also the final estimated error rates (if they exist) are shown. Optionally also the initial input rates and the expected error rates under the nominal definition of quality scores can be added to the plot.
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
94
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
95 Usage
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
96 .....
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
97
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
98 **Input** are the FASTQ dataset containing the filtered and trimmed reads of the samples.
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
99
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
100 **Output** a dataset with type *dada2_errorrates* (which is a RData file containing the output of dada2's learnErrors function) and a **plot** showing the error rates for each possible transition (A→C, A→G,...)
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
101
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
102 - Points are the observed error rates for each consensus quality score.
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
103 - The black line shows the estimated error rates after convergence of the machine-learning algorithm.
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
104 - The red line shows the error rates expected under the nominal definition of the Q-score.
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
105
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
106 The learned error rates are input the the *dada2: dada* tool.
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
107
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
108 Details
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
109 .......
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
110
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
111 The learnErrors method learns a parametric error model from the data, by alternating estimation of the error rates and inference of sample composition until they converge on a jointly consistent solution. As in many machine-learning problems, the algorithm must begin with an initial guess, for which the maximum possible error rates in this data are used (the error rates if only the most abundant sequence is correct and all the rest are errors).
2
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
112
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
113 It is expected that the estimated error rates (black lines in the plot) are in a good fit to the observed rates (points in the plot), and that the error rates drop with increased quality. Try to increase the **number of bases to use for learning** if this is not the case.
57eb7437f646 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
114
5
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
115 Error functions:
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
116
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
117 - loessErrfun: accepts a matrix of observed transitions, with each transition corresponding to a row (eg. row 2 = A->C) and each column to a quality score (eg. col 31 = Q30). It returns a matrix of estimated error rates of the same shape. Error rates are estimates by a loess fit of the observed rates of each transition as a function of the quality score. Self-transitions (i.e. A->A) are taken to be the left-over probability.
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
118 - noqualErrfun: accepts a matrix of observed transitions, groups together all observed transitions regardless of quality scores, and estimates the error rate for that transition as the observed fraction of those transitions. The effect is that quality scores will be effectively ignored.
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
119 - PacBioErrfun: This function accepts a matrix of observed transitions from PacBio CCS amplicon sequencing data, with each transition corresponding to a row (eg. row 2 = A->C) and each column to a quality score (eg. col 31 = Q30). It returns a matrix of estimated error rates of the same shape. Error rates are estimates by loessErrfun for quality scores 0-92, and individually by the maximum likelihood estimate for the maximum quality score of 93.
9aeea74a1fc9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
120
3
10141f4eaae9 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 2
diff changeset
121 @HELP_OVERVIEW@
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
122 ]]></help>
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 <expand macro="citations"/>
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 </tool>