Mercurial > repos > oinizan > frogs

annotate preprocess.xml @ 24:48a1ff3045e2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
author oinizan
date Mon, 22 May 2023 08:34:12 +0000
parents 5cd82f533de6
children 646bee69560f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
d73e09b3bc26 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 58dbb2c93ec7f854929ed4f5a294d6eeaaed467a-dirty
oinizan
parents: 14
diff changeset
1 <tool id="FROGS_preprocess" name="FROGS_1 Pre-process" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
2 <description>merging, denoising and dereplication</description>
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
3 <macros>
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
4 <import>macros.xml</import>
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
5 </macros>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
6 <expand macro="requirements">
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
7 <requirement type="package" version="2.17.0">vsearch</requirement>
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
8 <requirement type="package" version="1.2.11">flash</requirement>
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
9 <requirement type="package" version="2.10">cutadapt</requirement>
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
10 </expand>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
11 <command detect_errors="exit_code">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
12 preprocess.py '$sequencer_type.sequencer_selected'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
13 --output-dereplicated '$dereplicated_file' --output-count '$count_file' --summary '$summary_file'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
14 @CPUS@
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
15 --min-amplicon-size $sequencer_type.min_amplicon_size
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
16 --max-amplicon-size $sequencer_type.max_amplicon_size
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
17 #if $sequencer_type.sequencer_selected in ('illumina', 'longreads')
21
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
18 #if $sequencer_type.is_primer_in_seq.primer_choice == "true"
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
19 --five-prim-primer '$sequencer_type.is_primer_in_seq.five_prim_primer'
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
20 --three-prim-primer '$sequencer_type.is_primer_in_seq.three_prim_primer'
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
21 #else
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
22 --without-primers
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
23 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
24 #else
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
25 --five-prim-primer '$sequencer_type.five_prim_primer'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
26 --three-prim-primer '$sequencer_type.three_prim_primer'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
27 #end if
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
28
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
29 #if $sequencer_type.input_type.input_type_selected == "archive"
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
30 --input-archive '$sequencer_type.input_type.archive_file'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
31 #if $sequencer_type.sequencer_selected == "illumina" and $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged"
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
32 --already-contiged
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
33 #elif $sequencer_type.sequencer_selected == "illumina"
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
34 --R1-size $sequencer_type.input_type.archive_type.R1_size
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
35 --R2-size $sequencer_type.input_type.archive_type.R2_size
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
36 --mismatch-rate $sequencer_type.input_type.archive_type.mismatch_rate
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
37 --merge-software $sequencer_type.input_type.archive_type.merge_software_type.merge_software
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
38 #if $sequencer_type.input_type.archive_type.merge_software_type.merge_software == "flash"
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
39 --expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
40 #end if
21
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
41 #if $sequencer_type.input_type.archive_type.keep_unmerged == "Yes"
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
42 --keep-unmerged
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
43 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
44 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
45 #else
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
46 #set $sep = ' '
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
47 #if $sequencer_type.sequencer_selected == "illumina"
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
48 --samples-names
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
49 #for $current in $sequencer_type.input_type.files_by_samples_type.samples
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
50 $sep'${current.name.strip()}'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
51 #end for
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
52 --input-R1
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
53 #for $current in $sequencer_type.input_type.files_by_samples_type.samples
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
54 $sep'${current.R1_file}'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
55 #end for
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
56 #if $sequencer_type.input_type.files_by_samples_type.files_by_samples_type_selected == "already_merged"
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
57 --already-contiged
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
58 #else
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
59 --input-R2
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
60 #for $current in $sequencer_type.input_type.files_by_samples_type.samples
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
61 $sep'${current.R2_file}'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
62 #end for
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
63 --R1-size $sequencer_type.input_type.files_by_samples_type.R1_size
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
64 --R2-size $sequencer_type.input_type.files_by_samples_type.R2_size
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
65 --mismatch-rate $sequencer_type.input_type.files_by_samples_type.mismatch_rate
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
66 --merge-software $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
67 #if $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software == "flash"
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
68 --expected-amplicon-size $sequencer_type.input_type.files_by_samples_type.merge_software_type.expected_amplicon_size
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
69 #end if
21
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
70 #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged == "Yes"
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
71 --keep-unmerged
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
72 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
73 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
74 #else
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
75 --samples-names
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
76 #for $current in $sequencer_type.input_type.samples
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
77 $sep'${current.name.strip()}'
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
78 #end for
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
79 --input-R1
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
80 #for $current in $sequencer_type.input_type.samples
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
81 $sep'${current.R1_file}'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
82 #end for
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
83 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
84 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
85 </command>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
86 <inputs>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
87 <conditional name="sequencer_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
88 <param name="sequencer_selected" type="select" label="Sequencer" help="Select the sequencing technology used to produce the sequences.">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
89 <option value="illumina" selected="true">Illumina</option>
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
90 <option value="longreads">Longreads (PACBIO, ONT)</option>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
91 <option value="454">454</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
92 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
93 <when value="illumina">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
94 <!-- Samples -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
95 <conditional name="input_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
96 <param name="input_type_selected" type="select" label="Input type" help="Samples files can be provided in a single TAR archive or sample by sample (with one or two files each).">
13
4dd70eba5941 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 38a21bfbbb70a5752ea12898bce9c5601dfcca65-dirty"
oinizan
parents: 12
diff changeset
97 <option value="files_by_samples" >Files by samples</option>
4dd70eba5941 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 38a21bfbbb70a5752ea12898bce9c5601dfcca65-dirty"
oinizan
parents: 12
diff changeset
98 <option value="archive" selected="true">TAR Archive</option>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
99 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
100 <when value="archive">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
101 <param name="archive_file" type="data" format="tar,tgz" label="TAR archive file" help="The TAR file containing the sequences file(s) for each sample." />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
102 <conditional name="archive_type">
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
103 <param name="archive_type_selected" type="select" label="Are reads already merged ?" help="Yes = The archive contains 1 file by sample : R1 and R2 pairs are already merged in one sequence.">
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
104 <option value="paired" selected="true">No</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
105 <option value="already_merged">Yes</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
106 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
107 <when value="paired">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
108 <!-- Reads size -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
109 <param name="R1_size" type="integer" label="Reads 1 size" help="The maximum read1 size." value="" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
110 <param name="R2_size" type="integer" label="Reads 2 size" help="The maximum read2 size." value="" />
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
111 <param argument="--mismatch-rate" type="float" label="Mismatch rate" help="The maximum rate of mismatches in the overlap region" value="0.1" />
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
112 <conditional name="merge_software_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
113 <param argument="--merge-software" type="select" label="Merge software" help="Select the software to merge paired-end reads">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
114 <option value="vsearch" selected="true">Vsearch</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
115 <option value="flash">Flash</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
116 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
117 <when value="flash">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
118 <param argument="--expected-amplicon-size" type="integer" min="0" value="" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
119 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
120 <when value="vsearch"></when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
121 </conditional>
21
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
122 <param argument="--keep-unmerged" type="select" label="Would you like to keep unmerged reads?" help="No = Unmerged reads will be excluded; Yes = unmerged reads will be artificially combined with 100 N. (default No)" display="radio">
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
123 <option value="No" selected="true">No, unmerged reads will be excluded.</option>
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
124 <option value="Yes">Yes, unmerged reads will be artificially combined.</option>
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
125 </param>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
126 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
127 <when value="already_merged"></when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
128 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
129 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
130 <when value="files_by_samples">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
131 <conditional name="files_by_samples_type">
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
132 <param name="files_by_samples_type_selected" type="select" label="Are reads already merged ?" help="Yes = The inputs contain 1 file by sample : R1 and R2 pairq are already merged in one sequence.">
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
133 <option value="paired" selected="true">No</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
134 <option value="already_merged">Yes</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
135 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
136 <when value="paired">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
137 <!-- Samples -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
138 <repeat name="samples" title="Samples" min="1">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
139 <param name="name" type="text" label="Name" help="The sample name.">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
140 <expand macro="sanitizer_validator"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
141 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
142 <param format="fastq" name="R1_file" type="data" label="Reads 1" help="R1 FASTQ file of paired-end reads." />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
143 <param format="fastq" name="R2_file" type="data" label="Reads 2" help="R2 FASTQ file of paired-end reads." />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
144 </repeat>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
145 <!-- Reads size -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
146 <param name="R1_size" type="integer" label="Reads 1 size" help="The maximum read1 size." value="" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
147 <param name="R2_size" type="integer" label="Reads 2 size" help="The maximum read2 size." value="" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
148 <param name="mismatch_rate" type="float" label="Mismatch rate." help="The maximum rate of mismatches in the overlap region" value="0.1" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
149 <conditional name="merge_software_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
150 <param argument="--merge-software" type="select" label="Merge software" help="Select the software to merge paired-end reads">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
151 <option value="vsearch" selected="true">Vsearch</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
152 <option value="flash">Flash</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
153 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
154 <when value="flash">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
155 <param argument="--expected-amplicon-size" type="integer" min="0" value="" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
156 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
157 <when value="vsearch"></when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
158 </conditional>
21
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
159 <param argument="--keep-unmerged" type="select" label="Would you like to keep unmerged reads?" help="No = Unmerged reads will be excluded; Yes = unmerged reads will be artificially combined with 100 N. (default No)" display="radio">
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
160 <option value="No" selected="true">No, unmerged reads will be excluded</option>
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
161 <option value="Yes">Yes, unmerged reads will be artificially combined.</option>
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
162 </param>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
163 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
164 <when value="already_merged">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
165 <repeat name="samples" title="Samples" min="1">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
166 <param name="name" type="text" label="Name" help="The sample name.">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
167 <expand macro="sanitizer_validator"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
168 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
169 <param format="fastq" name="R1_file" type="data" label="Sequence file" help="FASTQ file of merged reads." />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
170 </repeat>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
171 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
172 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
173 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
174 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
175 <!-- Amplicons -->
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
176 <param argument="--min-amplicon-size" type="integer" value="" label="Minimum amplicon size" help="The minimum size of the amplicons (with primers)"/>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
177 <param argument="--max-amplicon-size" type="integer" value="" label="Maximum amplicon size" help="The maximum size of the amplicons (with primers)"/>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
178 <!-- Primers -->
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
179 <conditional name="is_primer_in_seq">
21
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
180 <param name="primer_choice" type="select" label="Do the sequences have PCR primers?" help="" display="radio">
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
181 <option value="true" selected="true">Yes</option>
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
182 <option value="false">No</option>
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
183 </param>
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
184 <when value="true">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
185 <param argument="--five-prim-primer" type="text" label="5' primer" help="The 5' primer sequence (wildcards are accepted). This primer must be written in 5' to 3' orientation (see details in 'Primers parameters' help section)">
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
186 <sanitizer invalid_char="">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
187 <valid initial="string.letters"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
188 </sanitizer>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
189 <validator type="regex">[A-Za-z]+</validator>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
190 </param>
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
191 <param argument="--three-prim-primer" type="text" label="3' primer" help="The 3' primer sequence (wildcards are accepted). This primer must be written in 5' to 3' orientation (see details in 'Primers parameters' help section)">
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
192 <sanitizer invalid_char="">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
193 <valid initial="string.letters"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
194 </sanitizer>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
195 <validator type="regex">[A-Za-z]+</validator>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
196 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
197 </when>
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
198 <when value="false"></when>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
199 </conditional>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
200 </when>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
201
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
202 <when value="longreads">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
203 <!-- Samples -->
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
204 <conditional name="input_type">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
205 <param name="input_type_selected" type="select" label="Input type" help="Samples files can be provided in single archive or with one file by sample.">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
206 <option value="files_by_samples">One file by sample</option>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
207 <option value="archive" selected="true">TAR Archive</option>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
208 </param>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
209 <when value="archive">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
210 <param name="archive_file" type="data" format="tar,tgz" label="TAR archive file" help="The TAR file containing the sequences file for each sample." />
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
211 </when>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
212 <when value="files_by_samples">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
213 <repeat name="samples" title="Samples" min="1">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
214 <param name="name" type="text" label="Name" help="The sample name.">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
215 <expand macro="sanitizer_validator"/>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
216 </param>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
217 <param format="fastq" name="R1_file" type="data" label="Sequence file" help="FASTQ file of sample." />
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
218 </repeat>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
219 </when>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
220 </conditional>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
221
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
222 <!-- Amplicons -->
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
223 <param argument="--min-amplicon-size" type="integer" value="" label="Minimum amplicon size" help="The minimum size for the amplicons (with primers)"/>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
224 <param argument="--max_amplicon-size" type="integer" value="" label="Maximum amplicon size" help="The maximum size for the amplicons (with primers)"/>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
225
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
226 <!-- Primers -->
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
227 <conditional name="is_primer_in_seq">
21
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
228 <param name="primer_choice" type="select" label="Do the sequences have PCR primers?" help="" display="radio">
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
229 <option value="true" selected="true">Yes</option>
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
230 <option value="false">No</option>
74a9b83110a7 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
oinizan
parents: 16
diff changeset
231 </param>
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
232 <when value="true">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
233 <param argument="--five-prim-primer" type="text" label="5' primer" help="The 5' primer sequence (wildcards are accepted). This primer must be written in 5' to 3' orientation (see details in 'Primers parameters' help section)">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
234 <sanitizer invalid_char="">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
235 <valid initial="string.letters"/>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
236 </sanitizer>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
237 <validator type="regex">[A-Za-z]+</validator>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
238 </param>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
239 <param argument="--three-prim-primer" type="text" label="3' primer" help="The 3' primer sequence (wildcards are accepted). This primer must be written in 5' to 3' orientation (see details in 'Primers parameters' help section)">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
240 <sanitizer invalid_char="">
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
241 <valid initial="string.letters"/>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
242 </sanitizer>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
243 <validator type="regex">[A-Za-z]+</validator>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
244 </param>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
245 </when>
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
246 <when value="false"></when>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
247 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
248 </when>
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
249
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
250 <when value="454">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
251 <!-- Samples -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
252 <conditional name="input_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
253 <param name="input_type_selected" type="select" label="Input type" help="Samples files can be provided in single archive or with one file by sample.">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
254 <option value="files_by_samples" selected="true">One file by sample</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
255 <option value="archive">TAR Archive</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
256 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
257 <when value="archive">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
258 <param name="archive_file" type="data" format="tar,tgz" label="TAR archive file" help="The TAR file containing the sequences file for each sample." />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
259 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
260 <when value="files_by_samples">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
261 <repeat name="samples" title="Samples" min="1">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
262 <param name="name" type="text" label="Name" help="The sample name.">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
263 <expand macro="sanitizer_validator"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
264 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
265 <param format="fastq" name="R1_file" type="data" label="Sequence file" help="FASTQ file of sample." />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
266 </repeat>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
267 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
268 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
269 <!-- Amplicons -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
270 <param argument="--min-amplicon-size" type="integer" value="" label="Minimum amplicon size" help="The minimum size for the amplicons (with primers)"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
271 <param argument="--max_amplicon-size" type="integer" value="" label="Maximum amplicon size" help="The maximum size for the amplicons (with primers)"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
272 <!-- Primers -->
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
273 <param argument="--five-prim-primer" type="text" label="5' primer" help="The 5' primer sequence (wildcards are accepted). This primer must be written in 5' to 3' orientation (see details in 'Primers parameters' help section)">
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
274 <sanitizer invalid_char="">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
275 <valid initial="string.letters"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
276 </sanitizer>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
277 <validator type="regex">[A-Za-z]+</validator>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
278 </param>
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
279 <param argument="--three-prim-primer" type="text" label="3' primer" help="The 3' primer sequence (wildcards are accepted). This primer must be written in 5' to 3' orientation (see details in 'Primers parameters' help section)">
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
280 <sanitizer invalid_char="">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
281 <valid initial="string.letters"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
282 </sanitizer>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
283 <validator type="regex">[A-Za-z]+</validator>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
284 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
285 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
286 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
287 </inputs>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
288 <outputs>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
289 <data format="fasta" name="dereplicated_file" label="${tool.name}: dereplicated.fasta" from_work_dir="dereplicated.fasta" />
12
613b7551f28b planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0c3aee486a7e9b369ad4c037c2f588236acad117-dirty
oinizan
parents: 11
diff changeset
290 <data format="tsv" name="count_file" label="${tool.name}: count.tsv" from_work_dir="count.tsv" />
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
291 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
292 </outputs>
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
293 <tests>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
294 <test>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
295 <conditional name="sequencer_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
296 <param name="sequencer_selected" value="illumina" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
297 <conditional name="input_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
298 <param name="input_type_selected" value="archive" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
299 <param name="archive_file" ftype="tgz" value="input/test_dataset.tar.gz" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
300 <conditional name="archive_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
301 <param name="archive_type_selected" value="paired" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
302 <param name="R1_size" value="267" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
303 <param name="R2_size" value="266" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
304 <param name="mismatch_rate" value="0.15" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
305 <conditional name="merge_software_type">
24
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
306 <param name="merge_software" value="flash" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
307 <param name="expected_amplicon_size" value="420" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
308 </conditional>
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
309 <param name="keep_unmerged" value="Yes" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
310 </conditional>
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
311 </conditional>
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
312 <param name="min_amplicon_size" value="44" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
313 <param name="max_amplicon_size" value="490" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
314 <conditional name="is_primer_in_seq">
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
315 <param name="primer_choice" value="true" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
316 <param name="five_prim_primer" value="GGCGVACGGGTGAGTAA" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
317 <param name="three_prim_primer" value="GTGCCAGCNGCNGCGG" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
318 </conditional>
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
319 </conditional>
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
320 <output name="count_file" file="references/01-prepro-flash.tsv" compare="diff" lines_diff="0" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
321 <output name="summary_file" file="references/01-prepro-flash.html" compare="sim_size" delta="0" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
322 </test>
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
323 <test>
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
324 <conditional name="sequencer_type">
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
325 <param name="sequencer_selected" value="illumina" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
326 <conditional name="input_type">
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
327 <param name="input_type_selected" value="archive" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
328 <param name="archive_file" ftype="tgz" value="input/test_dataset.tar.gz" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
329 <conditional name="archive_type">
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
330 <param name="archive_type_selected" value="paired" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
331 <param name="R1_size" value="267" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
332 <param name="R2_size" value="266" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
333 <param name="mismatch_rate" value="0.15" />
48a1ff3045e2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 23
diff changeset
334 <conditional name="merge_software_type">
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
335 <param name="merge_software" value="vsearch" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
336 </conditional>
22
57824202c333 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 21
diff changeset
337 <param name="keep_unmerged" value="Yes" />
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
338 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
339 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
340 <param name="min_amplicon_size" value="44" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
341 <param name="max_amplicon_size" value="490" />
22
57824202c333 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 21
diff changeset
342 <conditional name="is_primer_in_seq">
57824202c333 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
oinizan
parents: 21
diff changeset
343 <param name="primer_choice" value="true" />
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
344 <param name="five_prim_primer" value="GGCGVACGGGTGAGTAA" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
345 <param name="three_prim_primer" value="GTGCCAGCNGCNGCGG" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
346 </conditional>
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
347 </conditional>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
348 <output name="dereplicated_file" file="references/01-prepro-vsearch.fasta" compare="diff" lines_diff="0" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
349 <output name="count_file" file="references/01-prepro-vsearch.tsv" compare="diff" lines_diff="0" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
350 <output name="summary_file" file="references/01-prepro-vsearch.html" compare="sim_size" delta="0" />
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
351 </test>
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
352 </tests>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
353 <help>
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
354
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
355 @HELP_LOGO@
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
356
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
357 .. class:: h2
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
358
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
359 What it does
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
360
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
361 FROGS Pre-process filters and dereplicates amplicons for use in diversity analysis.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
362
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
363 .. class:: h2
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
364
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
365 Inputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
366
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
367 Sequencer (methods used to sequence data):
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
368 - short reads : Illumnia Miseq , Hiseq (paired-ends or single-ends)
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
369 - long reads : PACBIO or Oxford Nanopore Technology (single-ends)
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
370 - short reads : 454 (single-ends)
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
371
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
372 Input file to submit and *"Are reads already merged ?"* parameter:
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
373 - a .tar archive (option Archive TAR) containing one file *_R1* and one file *_R2* per sample if the sequences are paired and not merged. ex: samplesA-B-C-D.tar(.gz)
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
374 - or a .tar archive (option Archive TAR) containing one file per sample (i) if the sequences are paired-end and already merged or (ii) if the sequences are single-end. ex: samplesA-B.tar(.gz) in this case reply *Yes* at *"Are reads already merged ?"*.
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
375 - or one file by sample (option One file by sample). ex: sampleA_R1.fastq(.gz) + sampleA_R2.fastq(.gz) + sampleB_R1.fastq(.gz) + sampleB_R2.fastq(.gz) if you have 2 samples A and B and sequences are paired and not merged
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
376 - or one file by sample (option One file by sample). ex: sampleA.fastq(.gz) + sampleB.fastq(.gz) if sequences are paired-end and already merged. Iin this case reply *Yes* at *"Are reads already merged ?"*.
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
377
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
378 Remark:
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
379 - The sample name must be of R1 and R2 files must be end with *_R1* and *_R2*. The upstream part from this tag (_R1 and _R2) will be consider as sample name. ex: sampleA_R1.fastq + sampleA_R2.fastq, the kept name will be sampleA
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
380 - sample files (alone or inside an archive) must be in `FASTQ &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_ format or fastq.gz.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
381
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
382
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
383 .. class:: h4
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
384
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
385 For paired-end reads:
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
386
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
387 **read size:** The maximum size of read R1 and of read R2. It is common to find read sizes of 150, 250 or 300 for Illumina sequencers.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
388
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
389 **Mismatch rate:** The allowed maximum rate of mismatches during the merging between overlap sections of R1 and R2 reads. By default, the mismatch rate is 10%.
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
390
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
391 **Merge software:** For read merging it is possible to choose between 2 software `VSEARCH &lt;https://github.com/torognes/vsearch/&gt;`_ (by default) or `FLASH &lt;http://ccb.jhu.edu/software/FLASH/&gt;`_.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
392
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
393 **Would you like to keep unmerged reads?:** In some cases, it is necessary to keep unmergeable reads (ITS, non-mergeable reads *i.e.* V1V4 of 16S rRNA). *No* (by default) = Unmerged reads will be excluded; *Yes* = unmerged reads will be artificially combined and kept for following process.
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
394
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
395
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
396 .. class:: h4
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
397
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
398 For paired-end and single-ends reads:
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
399
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
400 **Minimum amplicon length:** The minimum size of the amplicons after read (R1, R2) pair merging.
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
401
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
402 **Maximum amplicon length:** The maximum size of the amplicons after read (R1, R2) pair merging. In case of overlapping pairs, the maximum amplicon length (including primers) must be inferior or equal to the length of the R1 plus R2 length minus 10. R1 and R2 are merged by the common region with a minimum length of 10.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
403
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
404 Do the sequences have PCR primers?:
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
405 - Yes (By default), after processing, the sequences will be returned without the PCR primers.
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
406 - No, the sequences do not contain PCR primer (`Kozich et al. 2013 &lt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/&gt;`_)
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
407
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
408
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
409 .. class:: h2
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
410
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
411 Outputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
412
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
413 **Sequence file** (dereplicated.fasta): Only one file with all samples sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_). These sequences are dereplicated: strictly identical sequences are represented only once, the initial count by sample is kept in count file (see bellow) and the total count is added in the sequence header. A "FROGS_combined" suffix will be added to unmerged paired sequences if you want to keep them.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
414
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
415 **Count file** (count.tsv): This file contains the count of all unique sequences in each sample (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
416
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
417 **Report file** (report.html): This file reports the number of remaining sequences after each filter (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_). Depending of the tool configuration there will be more or less filtering steps so more or less bars in the barplot.
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
418
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
419 .. image:: FROGS_preprocess_summary_v3.png
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
420 :height: 850
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
421 :width: 831
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
422
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
423 It also presents the length distribution of the full amplicon sequences after merging step and after filtering steps.
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
424
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
425 .. image:: FROGS_preprocess_lengthsSamples_v3.png
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
426 :height: 379
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
427 :width: 364
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
428
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
429
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
430 .. class:: h2
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
431
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
432 How it works ?
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
433
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
434 .. csv-table::
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
435 :header: "Steps", "Illumina"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
436 :widths: 10, 150
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
437 :class: table table-hover
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
438
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
439 "1", "For unmerged data: Merges R1 and R2 with a maximum of M% mismatch in the overlaped region(`VSEARCH &lt;https://github.com/torognes/vsearch/&gt;`_ or `FLASH &lt;http://ccb.jhu.edu/software/FLASH/&gt;`_ or optionnaly `PEAR &lt;https://sco.h-its.org/exelixis/web/software/pear/&gt;`_) with a minimum of 10 bp in the overlap region. Resulting unmerged reads may optionnaly be artificially combined by adding 100 N between the reads"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
440 "2", "If reads contains after sequencing the PCR primers: process removes sequences where the two primers are not present and removes primers in the kept sequences (`cutadapt &lt;http://cutadapt.readthedocs.org/en/latest/guide.html&gt;`_). The primer search accepts 10% of differences."
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
441 "3", "Process filters sequences with ambiguous nucleotides and for *merged* sequences filters on their length that must be ranged between 'Minimum amplicon size minus primer length' and 'Maximum amplicon size minus primer length'"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
442 "4", "Dereplicates sequences"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
443
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
444 .. csv-table::
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
445 :header: "Steps", "Longreads"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
446 :widths: 10, 150
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
447 :class: table table-hover
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
448
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
449 "1", "Non merging process, longreads from PACBIO or ONT are single-end reads"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
450 "2", "If reads contains after sequencing the PCR primers: process searches 5' primer on reads, then for all reads without 5' primer found the process (`cutadapt &lt;http://cutadapt.readthedocs.org/en/latest/guide.html&gt;`_) reverse-transcripts reads and searches again 5' primer (in dereplicates.fasta output, sequences have *rc* tag in the header when they have been reverse-complemented by cutadapt). Remark, after this step all reads are in same sens (5' -> 3'). Last step consists to search 3' primer on all theses reads. Process removes reads if 5' primer or 3' primer are not find at the end of process. When primers are found, reads are trimmed. The primer search accepts 10% of differences"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
451 "3", "Process filters sequences with ambiguous nucleotides and on their length that must be range between 'Minimum amplicon size minus primer length' and 'Maximum amplicon size minus primer length'"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
452 "4", "Dereplicates sequences"
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
453
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
454 .. csv-table::
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
455 :header: "Steps", "454"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
456 :widths: 10, 150
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
457 :class: table table-hover
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
458
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
459 "1", "Non merging process, 454 reads are single-end reads"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
460 "2", "Removes sequences where the two primers are not present, removes primers sequence from amplicon sequence and reverse complement the sequences on strand - (`cutadapt &lt;http://cutadapt.readthedocs.org/en/latest/guide.html&gt;`_). The primer search accepts 10% of differences"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
461 "3", "Removes sequences with at least one homopolymer with more than seven nucleotides and with a distance of less than or equal to 10 nucleotides between two poor quality positions, *i.e.* with a Phred quality score lesser than 10"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
462 "4", "Dereplicates sequences"
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
463
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
464 .. class:: h2
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
465
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
466 Advices/details on parameters
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
467
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
468 .. class:: h4
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
469
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
470 Keeping or not unmerged paired-end reads
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
471
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
472 .. class:: warningmark
12
613b7551f28b planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0c3aee486a7e9b369ad4c037c2f588236acad117-dirty
oinizan
parents: 11
diff changeset
473
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
474 This option is usefull when and only when, **targeted amplicon is longer than the sequencing technology** can provide (ITS amplicons, V1-V4 region of 16S for example). In other case, carefully, you will only keep noise in your analysis.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
475
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
476 .. class:: h4
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
477
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
478 What is the difference between overlapped sequences and combined sequences?
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
479
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
480 **Case of a sequencing of overlapping sequences: case of 16S V3-V4 amplicon MiSeq sequencing**
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
481
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
482 .. image:: FROGS_preprocess_overlapped_sequence.png
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
483 :height: 261
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
484 :width: 531
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
485
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
486 **Case of a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing**
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
487
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
488 .. image:: FROGS_preprocess_combined_sequence1.png
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
489 :height: 279
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
490 :width: 797
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
491
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
492 .. class:: warningmark
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
493
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
494 **“FROGS combined” warning points**
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
495
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
496 Read pairs are not merged because:
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
497
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
498 - the real amplicon length is greater than de number of base sequences (490 bp for MiSeq 2x250bp, remember of the minimum 10 bp overlap)
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
499 - the overlapped region is smaller than 10 (fixed parameter in FROGS).
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
500
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
501 Thus, “FROGS combined” sequences are artificial and present particular features especially on size.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
502 Imagine a MiSeq sequencing of 2x250pb with sequences that cannot overlap, the resulting “FROGS combined” sequences length will be fixed to 600 bp.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
503
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
504 .. image:: FROGS_preprocess_combined_sequence2.png
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
505 :height: 357
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
506 :width: 798
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
507
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
508 .. class:: h4
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
509
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
510 Primers parameters
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
511
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
512 The `Kozich et al. 2013 &lt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/&gt;`_ protocol uses custom sequencing primers that are also the PCR primers. In this case, the reads do not contain the PCR primers.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
513
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
514 In case of standard protocol, the primers must be provided in 5' to 3' orientation.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
515
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
516 .. role:: alert-info
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
517
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
518 Example:
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
519
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
520 5' :alert-info:`ATGCCC` GTCGTCGTAAAATGC :alert-info:`ATTTCAG` 3'
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
521
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
522 Value for parameter 5' primer: ATGCCC
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
523
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
524 Value for parameter 3' primer: ATTTCAG
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
525
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
526
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
527 .. class:: h4
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
528
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
529 What happens if the 'merged' filter drasticaly reduces the number of sequences ?:
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
530
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
531 After merging step with VSEARCH, PEAR or FLASH, if you observe a loss of more than 20% in all samples, this can highlight a quality problem (see `FastQC &lt;http://www.bioinformatics.babraham.ac.uk/projects/fastqc/&gt;`_).
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
532
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
533 If the overlap between R1 and R2 is superior to 50 nucleotides and the quality of the end of the sequences is poor (see `FastQC &lt;http://www.bioinformatics.babraham.ac.uk/projects/fastqc/&gt;`_) you can try to cut the end of your sequences and relaunch the preprocess tool. You can either raise the mismatch percent in the overlapped region, but not too much!
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
534
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
535
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
536 .. class:: h4
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
537
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
538 FLASH : Amplicon size parameters
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
539
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
540 The two following images show two examples of perfect values for sizes parameters.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
541
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
542 .. image:: FROGS_preprocess_ampliconSize_unimodal_v3.png
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
543 :height: 415
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
544 :width: 676
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
545
11
ab9e3c8ab443 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
oinizan
parents: 9
diff changeset
546 .. image:: FROGS_preprocess_ampliconSize_multimodal_v3.png
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
547 :height: 415
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
548 :width: 676
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
549
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
550 Don't worry, the "Expected amplicon size" does not need to be very accurate, and only necessary for sequences merging with FLASH.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
551
14
ca1e9adbde51 "planemo upload commit c12b0878cb91bdeee5b3a2c873bc9905df1fc95d-dirty"
oinizan
parents: 13
diff changeset
552 **Remark :** We recommend to use PEAR if availbale (only for `academic user &lt;https://www.h-its.org/software/pear-paired-end-read-merger/&gt;`_) or Vsearch (by default on Galaxy interface). PEAR is available only in command line.
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
553
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
554
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
555
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
556 @HELP_CONTACT@
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
557
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
558 </help>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
559 <expand macro="citations" />
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
560 </tool>