Mercurial > repos > matthias > dada2_filterandtrim

annotate dada2_filterAndTrim.xml @ 8:e9d1e654cc9d 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 7831a1e3225240028b30ae02808bdff9babaf368-dirty
author matthias
date Mon, 27 May 2019 05:34:36 -0400
parents 37305bbf8f44
children e09edc2b553a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
ea3c356bff55 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_filterAndTrim" name="dada2: filterAndTrim" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@">
0
1d6e206b8291 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>Filters and trims an short read data</description>
1d6e206b8291 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>
1d6e206b8291 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>
1d6e206b8291 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>
1d6e206b8291 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"/>
1d6e206b8291 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"/>
1d6e206b8291 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[
3
e4b415aa4c84 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
9 Rscript '$dada2_script'
e4b415aa4c84 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
10 ## && sed -i '1!b;s/^/#dataset/' $outtab
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
11 ]]></command>
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
12 <configfiles>
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
13 <configfile name="dada2_script"><![CDATA[
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
14 truncQ <- c($trim.truncQ)
1d6e206b8291 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 truncLen <- c($trim.truncLen)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
16 trimLeft <- c($trim.trimLeft)
1d6e206b8291 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 trimRight <- c($trim.trimRight)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
18 #if str($filter.maxLen) == ""
1d6e206b8291 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 maxLen <- c(Inf)
1d6e206b8291 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 #else:
1d6e206b8291 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 maxLen <- c($filter.maxLen)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
22 #end if
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
23 minLen <- c($filter.minLen)
1d6e206b8291 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 maxN <- c($filter.maxN)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
25 minQ <- c($filter.minQ)
1d6e206b8291 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 #if str($filter.maxEE) == ""
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
27 maxEE <- c(Inf)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
28 #else:
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
29 maxEE <- c($filter.maxEE)
1d6e206b8291 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 #end if
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
31 #if $paired_cond.paired_select != "single" and $seprev_cond.seprev_select == "yes"
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
32 truncQ <- c(truncQ,$seprev_cond.trim.truncQ)
1d6e206b8291 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 truncLen <- c(truncLen,$seprev_cond.trim.truncLen)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
34 trimLeft <- c(trimLeft,$seprev_cond.trim.trimLeft)
1d6e206b8291 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 trimRight <- c(trimRight,$seprev_cond.trim.trimRight)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
36 #if str($seprev_cond.filter.maxLen) == ""
1d6e206b8291 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 maxLen <- c(maxLen,Inf)
1d6e206b8291 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 #else:
1d6e206b8291 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 maxLen <- c(maxLen,$seprev_cond.filter.maxLen)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
40 #end if
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
41 minLen <- c(minLen,$seprev_cond.filter.minLen)
1d6e206b8291 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 maxN <- c(maxN,$seprev_cond.filter.maxN)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
43 minQ <- c(minQ,$seprev_cond.filter.minQ)
1d6e206b8291 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 #if str($seprev_cond.filter.maxEE) == ""
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
45 maxEE <- c(maxEE,Inf)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
46 #else:
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
47 maxEE <- c(maxEE,$seprev_cond.filter.maxEE)
1d6e206b8291 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 #end if
1d6e206b8291 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 #end if
1d6e206b8291 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
1d6e206b8291 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 fwd <- NULL
1d6e206b8291 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 rev <- NULL
1d6e206b8291 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 filt.fwd <- NULL
1d6e206b8291 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 filt.rev <- NULL
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
55 #if $paired_cond.paired_select == "paired"
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
56 fwd <- c(fwd, '$paired_cond.paired_reads.forward')
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
57 rev <- c(rev, '$paired_cond.paired_reads.reverse')
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
58 filt.fwd <- c(filt.fwd, '$paired_output.forward')
2
ea3c356bff55 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 filt.rev <- c(filt.rev, '$paired_output.reverse')
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
60 #else if $paired_cond.paired_select == "separate"
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
61 fwd <- c(fwd, '$paired_cond.forward')
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
62 rev <- c(rev, '$paired_cond.reverse')
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
63 filt.fwd <- c(filt.fwd, '$output_fwd')
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
64 filt.rev <- c(filt.rev, '$output_rev')
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
65 #else
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
66 fwd <- c(fwd, '$paired_cond.reads')
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
67 filt.fwd <- c(filt.fwd, '$output_single')
0
1d6e206b8291 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 #end if
1d6e206b8291 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
1d6e206b8291 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 library(dada2, quietly=T)
1d6e206b8291 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
1d6e206b8291 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 ftout <- filterAndTrim(fwd, filt.fwd, rev = rev, filt.rev, compress = TRUE,
1d6e206b8291 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 truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen,
1d6e206b8291 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 minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.phix = $rmPhiX, orient.fwd = '$orientFwd')
3
e4b415aa4c84 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
75
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
76 #if $paired_cond.paired_select == "separate":
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
77 rownames(ftout) <- c( '$paired_cond.forward.element_identifier' )
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
78 #else if $paired_cond.paired_select == "paired"
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
79 rownames(ftout) <- c( '$paired_cond.paired_reads.element_identifier' )
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
80 #else:
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
81 rownames(ftout) <- c( '$paired_cond.reads.element_identifier' )
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
82 #end if
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
83 write.table(ftout, "$outtab", quote=F, sep="\t", col.names=NA)
1d6e206b8291 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 ]]></configfile>
1d6e206b8291 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 </configfiles>
1d6e206b8291 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 <inputs>
1d6e206b8291 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 <conditional name="paired_cond">
1d6e206b8291 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 <param name="paired_select" type="select" label="Paired reads">
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
89 <option value="paired">paired - in a data set pair</option>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
90 <option value="separate">paired - in two separate data sets</option>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
91 <option value="single">single</option>
0
1d6e206b8291 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 </param>
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
93 <when value="paired">
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
94 <param name="paired_reads" argument="fwd/rev" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired short read data"/>
0
1d6e206b8291 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 </when>
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
96 <when value="separate">
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
97 <param name="forward" argument="fwd" type="data" format="fastq,fastq.gz" label="Forward read data"/>
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
98 <param name="reverse" argument="rev" type="data" format="fastq,fastq.gz" label="Reverse read data"/>
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
99 </when>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
100 <when value="single">
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
101 <param name="reads" argument="fwd" type="data" format="fastq,fastq.gz" label="Short read data"/>
0
1d6e206b8291 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 </when>
1d6e206b8291 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 </conditional>
1d6e206b8291 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 <expand macro="trimmers"/>
1d6e206b8291 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 <expand macro="filters"/>
1d6e206b8291 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 <conditional name="seprev_cond">
1d6e206b8291 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 <param name="seprev_select" type="select" label="Separate filters and trimmers for reverse reads" help="only applies to paired end data">
1d6e206b8291 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 <option value="no">no</option>
1d6e206b8291 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 <option value="yes">yes</option>
1d6e206b8291 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 </param>
1d6e206b8291 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 <when value="no"/>
1d6e206b8291 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 <when value="yes">
1d6e206b8291 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 <expand macro="trimmers"/>
1d6e206b8291 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 <expand macro="filters"/>
3
e4b415aa4c84 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
115 </when>
0
1d6e206b8291 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 </conditional>
3
e4b415aa4c84 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
117 <param argument="rmPhiX" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Discard reads matching the PhiX genome" />
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
118 <param name="orientFwd" argument="orient.fwd" type="text" value="" optional="true" label="String present at the start of valid reads" help="see below"/>
2
ea3c356bff55 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
119 <param name="output_statistics" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Output statistics" help="Create extra table with the number of reads pre and post filtering" />
0
1d6e206b8291 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 </inputs>
1d6e206b8291 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 <outputs>
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
122 <collection name="paired_output" type="paired" structured_like="paired_reads" inherit_format="true">
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
123 <filter>paired_cond['paired_select'] == "paired"</filter>
3
e4b415aa4c84 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
124 </collection>
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
125 <data name="output_single" format_source="reads" >
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
126 <filter>paired_cond['paired_select'] == "single"</filter>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
127 </data>
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
128 <data name="output_fwd" format_source="forward" label="${tool.name} on ${on_string}: Forward reads" >
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
129 <filter>paired_cond['paired_select'] == "separate"</filter>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
130 </data>
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
131 <data name="output_rev" format_source="reverse" label="${tool.name} on ${on_string}: Reverse reads" >
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
132 <filter>paired_cond['paired_select'] == "separate"</filter>
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
133 </data>
2
ea3c356bff55 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents: 0
diff changeset
134 <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
3
e4b415aa4c84 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
135 <filter>output_statistics</filter>
e4b415aa4c84 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
136 </data>
0
1d6e206b8291 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 </outputs>
2
ea3c356bff55 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
138 <tests>
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
139 <!-- paired data
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
140 currently removed `expect_num_outputs="2"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
0
1d6e206b8291 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 <test>
1d6e206b8291 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 <conditional name="paired_cond">
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
143 <param name="paired_select" value="paired"/>
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
144 <param name="paired_reads">
0
1d6e206b8291 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 <collection type="paired">
2
ea3c356bff55 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
146 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
ea3c356bff55 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
147 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
0
1d6e206b8291 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 </collection>
2
ea3c356bff55 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
149 </param>
ea3c356bff55 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
150 </conditional>
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
151 <output_collection name="paired_output" type="paired" count="2">
3
e4b415aa4c84 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
152 <element name="forward" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
e4b415aa4c84 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
153 <element name="reverse" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
154 </output_collection>
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
155 <output name="outtab" value="filterAndTrim_F3D0.tab" ftype="tabular"/>
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
156 </test>
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
157 <!-- separate paired data -->
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
158 <test>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
159 <conditional name="paired_cond">
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
160 <param name="paired_select" value="separate"/>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
161 <param name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
162 <param name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
163 </conditional>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
164 <output name="output_fwd" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
165 <output name="output_rev" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
166 <output name="outtab" value="filterAndTrim_F3D0.tab" ftype="tabular" compare="sim_size"/>
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
167 </test>
2
ea3c356bff55 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
168 <!-- single end data -->
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
169 <test expect_num_outputs="1">
2
ea3c356bff55 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
170 <conditional name="paired_cond">
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
171 <param name="paired_select" value="single"/>
2
ea3c356bff55 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
172 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
ea3c356bff55 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
173 </conditional>
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
174 <param name="output_statistics" value="FALSE" />
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
175 <output name="output_fwd" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
2
ea3c356bff55 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
176 </test>
ea3c356bff55 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
177 <!-- single end data trimming -->
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
178 <test expect_num_outputs="1">
2
ea3c356bff55 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
179 <conditional name="paired_cond">
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
180 <param name="paired_select" value="single"/>
2
ea3c356bff55 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
181 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
ea3c356bff55 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
182 </conditional>
ea3c356bff55 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
183 <param name="trim|truncQ" value="30" />
ea3c356bff55 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
184 <param name="trim|trimLeft" value="150" />
ea3c356bff55 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
185 <param name="trim|trimRight" value="2" />
ea3c356bff55 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
186 <param name="trim|truncLen" value="2" />
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
187 <param name="output_statistics" value="FALSE" />
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
188 <output name="output_fwd" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
2
ea3c356bff55 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
189 </test>
ea3c356bff55 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
190 <!-- single end data filtering -->
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
191 <test expect_num_outputs="1">
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
192 <conditional name="paired_cond">
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
193 <param name="paired_select" value="single"/>
2
ea3c356bff55 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
194 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
ea3c356bff55 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
195 </conditional>
ea3c356bff55 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
196 <param name="filter|maxLen" value="255" />
ea3c356bff55 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
197 <param name="filter|minLen" value="60" />
ea3c356bff55 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
198 <param name="filter|maxN" value="100" />
ea3c356bff55 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
199 <param name="filter|minQ" value="13" />
ea3c356bff55 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
200 <param name="filter|maxEE" value="1" />
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
201 <param name="output_statistics" value="FALSE" />
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
202 <output name="output_fwd" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
2
ea3c356bff55 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
203 </test>
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
204 <!-- paired data w separate filters and trimmers for reverse
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
205 currently removed `expect_num_outputs="1"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
206 <test>
2
ea3c356bff55 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
207 <conditional name="paired_cond">
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
208 <param name="paired_select" value="paired"/>
8
e9d1e654cc9d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty
matthias
parents: 6
diff changeset
209 <param name="paired_reads">
2
ea3c356bff55 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
210 <collection type="paired">
ea3c356bff55 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
211 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
ea3c356bff55 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
212 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
ea3c356bff55 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
213 </collection>
ea3c356bff55 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
214 </param>
ea3c356bff55 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
215 </conditional>
ea3c356bff55 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
216 <param name="seprev_cond|seprev_select" value="yes"/>
ea3c356bff55 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
217 <param name="seprev_cond|trim|truncQ" value="30" />
ea3c356bff55 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
218 <param name="seprev_cond|trim|trimLeft" value="150" />
ea3c356bff55 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
219 <param name="seprev_cond|trim|trimRight" value="2" />
ea3c356bff55 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
220 <param name="seprev_cond|trim|truncLen" value="2" />
ea3c356bff55 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
221 <param name="seprev_cond|filter|maxLen" value="255" />
ea3c356bff55 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
222 <param name="seprev_cond|filter|minLen" value="60" />
ea3c356bff55 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
223 <param name="seprev_cond|filter|maxN" value="100" />
ea3c356bff55 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
224 <param name="seprev_cond|filter|minQ" value="13" />
ea3c356bff55 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
225 <param name="seprev_cond|filter|maxEE" value="1" />
5
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
226 <param name="output_statistics" value="FALSE" />
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents: 3
diff changeset
227 <output_collection name="paired_output" type="paired" count="2"/>
2
ea3c356bff55 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
228 </test>
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
229 </tests>
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
230
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
231 <help><![CDATA[
2
ea3c356bff55 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
232 Description
ea3c356bff55 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
233 ...........
ea3c356bff55 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
234
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
235 Filters and trims a FASTQ dataset (can be compressed) based on several user-definable criteria, and outputs a compressed FASTQ data set containing those trimmed reads which passed the filters. For paired end data forward and reverse FASTQ datasets can be provided as pair of FASTQ datasets (or two separate data sets), in which case filtering is performed on the forward and reverse reads independently, and both reads must pass for the read pair to be in the output.
2
ea3c356bff55 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
236
ea3c356bff55 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
237 Usage
3
e4b415aa4c84 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
238 .....
2
ea3c356bff55 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
239
6
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
240 **Input** is a FASTQ dataset (or a pair in case of paired end data) containing all reads of a sample. It is suggested to organize them in a (paired) collection (in particular if you have multiple samples).
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
241
37305bbf8f44 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 72e787011111e0262b8161c3834a6258d7b667bc
matthias
parents: 5
diff changeset
242 **Output** is a (paired) collection of filtered and trimmed paired FASTQ datasets (again one data set or pair per sample).
2
ea3c356bff55 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
243
ea3c356bff55 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
244 Upstream dada2 tools are *dada2: derepFastq* and *dada2: learnErrorRates*. Note that these tools do not work on paired end data. So, if you have paired end data you need to split the generated paired collection into one containing the forward reads and one containing the reverse reads. This can be done by the *unzip collection* tool.
ea3c356bff55 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
245
ea3c356bff55 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
246 An additional tabular output gives the number of reads before and after trimming. This can data set can be used as input for *dada2: sequence counts* to track the sequence counts for each sample through all dada2 pipeline step.
ea3c356bff55 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
247
ea3c356bff55 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
248 Details
ea3c356bff55 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
249 .......
ea3c356bff55 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
250
ea3c356bff55 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
251 *Trimming and filtering*:
ea3c356bff55 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
252
ea3c356bff55 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
253 - Truncation of the read length is enforced after trimming of the right end.
3
e4b415aa4c84 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
254 - The long read filter is applied before trimming and the short read filter after trimming.
2
ea3c356bff55 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
255 - For details on the calculation of the number of expected errors see also https://doi.org/10.1093/bioinformatics/btv401
ea3c356bff55 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
256
ea3c356bff55 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
257
ea3c356bff55 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
258 *String present at the start of valid reads*:
ea3c356bff55 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
259
ea3c356bff55 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
260 This string is compared to the start of each read, and the reverse complement of each read. If it exactly matches the start of the read, the read is kept. If it exactly matches the start of the reverse complement read, the read is reverse-complemented and kept. Otherwise the read if filtered out. For paired reads, the string is compared to the start of the forward and reverse reads, and if it matches the start of the reverse read the reads are swapped and kept. The primary use of this parameter is to unify the orientation of amplicon sequencing libraries that are a mixture of forward and reverse orientations, and that include the forward primer on the reads.
ea3c356bff55 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
261
ea3c356bff55 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
262 Notes
ea3c356bff55 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
263 .....
ea3c356bff55 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
264
ea3c356bff55 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
265 This step may be replaced by alternative tools to filter and trim short read data if the following is ensured:
ea3c356bff55 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
266
ea3c356bff55 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
267 - For paired end data unpaired reads must be removed.
3
e4b415aa4c84 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
268 - There must not be a read containing a non-canonical nucleotide (N).
e4b415aa4c84 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
269
e4b415aa4c84 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
270 @HELP_OVERVIEW@
0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
271 ]]></help>
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
272 <expand macro="citations"/>
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
273 </tool>