frogs: preprocess.xml annotate

annotate preprocess.xml @ 9:7bf54edaba24 draft

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty

author	oinizan
date	Thu, 12 May 2022 10:44:30 +0000
parents	76dcbe930b1d
children	ab9e3c8ab443

rev	line source
9 7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	1 <tool id="FROGS_preprocess" name="FROGS Pre-process" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">
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>
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	3 <macros>
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>
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 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
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	17 #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	18 #if $sequencer_type.sequencing_protocol.sequencing_protocol_selected == "standard"
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	19 --five-prim-primer '$sequencer_type.sequencing_protocol.five_prim_primer'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	20 --three-prim-primer '$sequencer_type.sequencing_protocol.three_prim_primer'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	21 #else
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	22 --without-primers
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	23 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	24 #else
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	25 --five-prim-primer '$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
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	40 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	41 #if $sequencer_type.input_type.archive_type.keep_unmerged
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
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	70 #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged
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
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	75 --input-R1
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	76 #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	77 $sep'${current.R1_file}'
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	78 #end for
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	79 --samples-names
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.name.strip()}'
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>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	90 <option value="454">454</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	91 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	92 <when value="illumina">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	93 <!-- Samples -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	94 <conditional name="input_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	95 <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).">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	96 <option value="files_by_samples" selected="true">Files by samples</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	97 <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	98 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	99 <when value="archive">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	100 <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	101 <conditional name="archive_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	102 <param name="archive_type_selected" type="select" label="Are reads already merged ?" help="The archive contains 1 file by sample : R1 and R2 pair are already merged in one sequence.">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	103 <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	104 <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	105 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	106 <!-- $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	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="" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	111 <param argument="--mismatch-rate" type="float" label="Mismatch rate" help="The maximum rate of mismatch 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	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>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	122 <param argument="--keep-unmerged" type="boolean" 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)" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	123 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	124 <when value="already_merged"></when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	125 </conditional>
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="files_by_samples">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	128 <conditional name="files_by_samples_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	129 <param name="files_by_samples_type_selected" type="select" label="Are reads already merged ?" help="The inputs contain 1 file by sample : R1 and R2 pair are already merged in one sequence.">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	130 <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	131 <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	132 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	133 <when value="paired">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	134 <!-- Samples -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	135 <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	136 <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	137 <expand macro="sanitizer_validator"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	138 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	139 <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	140 <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	141 </repeat>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	142 <!-- Reads size -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	143 <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	144 <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	145 <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	146 <conditional name="merge_software_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	147 <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	148 <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	149 <option value="flash">Flash</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	150 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	151 <when value="flash">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	152 <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	153 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	154 <when value="vsearch"></when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	155 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	156 <param argument="--keep-unmerged" type="boolean" 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)" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	157 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	158 <when value="already_merged">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	159 <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	160 <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	161 <expand macro="sanitizer_validator"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	162 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	163 <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	164 </repeat>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	165 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	166 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	167 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	168 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	169 <!-- Amplicons -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	170 <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	171 <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	172 <!-- Primers -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	173 <conditional name="sequencing_protocol">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	174 <param name="sequencing_protocol_selected" type="select" label="Sequencing protocol" help="The protocol used for sequencing step: standard or custom with PCR primers as sequencing primers.">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	175 <option value="standard" selected="true">Illumina standard</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	176 <option value="without_primers">Custom protocol (Kozich et al. 2013)</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	177 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	178 <when value="standard">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	179 <param argument="--five-prim-primer" type="text" label="5' primer" help="The 5' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters' help section">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	180 <sanitizer invalid_char="">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	181 <valid initial="string.letters"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	182 </sanitizer>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	183 <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	184 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	185 <param argument="--three-prim-primer" type="text" label="3' primer" help="The 3' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters' help section">
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>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	191 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	192 <when value="without_primers"></when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	193 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	194 </when>
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	195
9 7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	196 <when value="454">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	197 <!-- Samples -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	198 <conditional name="input_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	199 <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	200 <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	201 <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	202 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	203 <when value="archive">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	204 <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	205 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	206 <when value="files_by_samples">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	207 <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	208 <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	209 <expand macro="sanitizer_validator"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	210 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	211 <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	212 </repeat>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	213 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	214 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	215 <!-- Amplicons -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	216 <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	217 <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	218 <!-- Primers -->
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	219 <param argument="--five-prim-primer" type="text" label="5' primer" help="The 5' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters' help section">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	220 <sanitizer invalid_char="">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	221 <valid initial="string.letters"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	222 </sanitizer>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	223 <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	224 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	225 <param argument="--three-prim-primer" type="text" label="3' primer" help="The 3' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters' help section">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	226 <sanitizer invalid_char="">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	227 <valid initial="string.letters"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	228 </sanitizer>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	229 <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	230 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	231 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	232 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	233 </inputs>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	234 <outputs>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	235 <data format="fasta" name="dereplicated_file" label="${tool.name}: dereplicated.fasta" from_work_dir="dereplicated.fasta" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	236 <data format="tabular" name="count_file" label="${tool.name}: count.tsv" from_work_dir="count.tsv" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	237 <data format="html" name="summary_file" label="${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	238 </outputs>
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	239 <tests>
9 7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	240 <test>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	241 <conditional name="sequencer_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	242 <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	243 <conditional name="input_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	244 <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	245 <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	246 <conditional name="archive_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	247 <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	248 <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	249 <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	250 <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	251 <conditional name="merge_software_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	252 <param name="merge_software" value="flash" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	253 <param name="expected_amplicon_size" value="420" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	254 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	255 <param name="keep_unmerged" value="true" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	256 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	257 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	258 <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	259 <param name="max_amplicon_size" value="490" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	260 <conditional name="sequencing_protocol">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	261 <param name="sequencing_protocol_selected" value="standard" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	262 <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	263 <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	264 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	265 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	266 <output name="dereplicated_file" file="references/01-prepro-flash.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	267 <output name="count_file" file="references/01-prepro-flash.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	268 <output name="summary_file" file="references/01-prepro-flash.html" compare="sim_size" delta="0" />
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	269 </test>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	270 <test>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	271 <conditional name="sequencer_type">
9 7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	272 <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	273 <conditional name="input_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	274 <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	275 <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	276 <conditional name="archive_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	277 <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	278 <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	279 <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	280 <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	281 <conditional name="merge_software_type">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	282 <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	283 </conditional>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	284 <param name="keep_unmerged" value="true" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	285 </conditional>
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 <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	288 <param name="max_amplicon_size" value="490" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	289 <conditional name="sequencing_protocol">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	290 <param name="sequencing_protocol_selected" value="standard" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	291 <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	292 <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	293 </conditional>
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	294 </conditional>
9 7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	295 <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	296 <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	297 <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	298 </test>
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	299 </tests>
9 7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	300 <help>
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	301
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	302 @HELP_LOGO@
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	303
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	304 .. class:: infomark page-header h2
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	305
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	306 What it does
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	307
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	308 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	309
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	310 .. class:: infomark page-header h2
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	311
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	312 Inputs/Outputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	313
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	314 .. class:: h3
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	315
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	316 Inputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	317
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	318 Sample files added one after another or provide in an archive file (tar or tar.gz).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	319
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	320 .. container:: row
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	321
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	322 .. container:: col-md-6
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	323
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	324 Illumina inputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	325
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	326 :Usage: For samples sequenced in paired-end. In case of overlapping pair, 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.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	327 :Files: One R1 and R2 by sample (format `FASTQ <https://en.wikipedia.org/wiki/FASTA_format>`_)
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	328 :Example: splA_R1.fastq.gz, splA_R2.fastq.gz, splB_R1.fastq.gz, splB_R2.fastq.gz
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	329
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	330 OR
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	331
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	332 :Usage: For samples sequenced in single-ends or when R1 and R2 reads are already merged.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	333 :Files: One sequence file by sample (format `FASTQ <https://en.wikipedia.org/wiki/FASTA_format>`_).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	334 :Example: splA.fastq.gz, splB.fastq.gz
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	335
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	336 .. container:: col-md-6
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	337
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	338 454 inputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	339
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	340 :Files: One sequence file by sample (format `FASTQ <https://en.wikipedia.org/wiki/FASTA_format>`_)
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	341 :Example: splA.fastq.gz, splB.fastq.gz
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	342
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	343 Remark: In an archive if you use R1 and R2 files their names must end with _R1 and _R2. The part upstram from this tag (_R1 and _R2) will be consider as sample name.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	344
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	345 .. class:: h3
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	346
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	347 Outputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	348
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	349 Sequence file (dereplicated.fasta):
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	350
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	351 Only one file with all samples sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). These sequences are dereplicated: strictly identical sequence are represented only once, the initial count by sample is kept in count file (see bellowà) and the total count is added in the sequence header. A "FROGS_combined" suffix will be added to un-merged pair sequence if you want to keep them.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	352
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	353 Count file (count.tsv):
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	354
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	355 This file contains the count of all unique sequences in each sample (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	356
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	357 Summary file (report.html):
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 This file reports the number of remaining sequences after each filter (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). 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	360
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	361 .. image:: static/images/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	362 :height: 850
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	363 :width: 831
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 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	366
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	367 .. image:: static/images/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	368 :height: 379
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	369 :width: 364
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	370
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	371 .. class:: infomark page-header h2
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	372
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	373 How it works
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	374
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	375 .. csv-table::
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	376 :header: "Steps", "Illumina", "454"
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	377 :widths: 5, 150, 150
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	378 :class: table table-striped
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	379
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	380 "1", "For un-merged data: Merges R1 and R2 with a maximum of M% mismatch in the overlaped region(`VSEARCH <https://github.com/torognes/vsearch/>`_ or `FLASH <http://ccb.jhu.edu/software/FLASH/>`_ or optionnaly `PEAR <https://sco.h-its.org/exelixis/web/software/pear/>`_) with a minimum of 10 bp in the overlap region. Resulting un-merged reads may optionnaly be artificially combined by adding 100 N between the reads", "/"
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	381 "2", "If sequencing protocol is the illumina standard protocol : Removes sequences where the two primers are not present and removes primers in the remaining sequence (`cutadapt <http://cutadapt.readthedocs.org/en/latest/guide.html>`_). The primer search accepts 10% of differences", "Removes sequences where the two primers are not present, removes primers sequence from amplicon sequence and reverse complement the sequences on strand - (`cutadapt <http://cutadapt.readthedocs.org/en/latest/guide.html>`_). The primer search accepts 10% of differences"
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	382 "3", "Filters sequences with ambiguous nucleotides and for merged sequences filters on their length which must be range between 'Minimum amplicon size - primer length' and 'Maximum amplicon size - primer length'", "Removes sequences with at least one homopolymer with more than seven nucleotides and with a distance of less than or equal to 10 nucleo-tides between two poor quality positions, i.e. with a Phred quality score lesser than 10"
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	383 "4", "Dereplicates sequences", "Dereplicates sequences"
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	384
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	385
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	386 .. class:: infomark page-header h2
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	387
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	388 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	389
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	390 .. class:: h3
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	391
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	392 Keeping or not un-merged paired reads
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	393
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	394 This option is usefull when and only when, targeted amplicon is longer than the sequencing technology can provide (ITS amplicon for example). In other case, carefully, you will only keep noise in your analysis.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	395
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	396 .. class:: h3
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	397
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	398 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	399
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	400 - Case of a sequencing of overlapping sequences: case of 16S V3-V4 amplicon MiSeq sequencing
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	401
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	402 .. image:: static/images/FROGS_preprocess_overlapped_sequence.png
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	403 :height: 261
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	404 :width: 531
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	405
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	406 - Case of a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing
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 .. image:: static/images/FROGS_preprocess_combined_sequence1.png
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	409 :height: 279
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	410 :width: 797
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	411
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	412 .. class:: warningmark
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	413
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	414 “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	415
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	416 Reads pair are not merged because:
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	417
9 7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	418 - 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	419 - 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	420
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	421 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	422 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	423
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	424 .. image:: static/images/FROGS_preprocess_combined_sequence2.png
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	425 :height: 357
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	426 :width: 798
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	427
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	428 .. class:: h3
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	429
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	430 Primers parameters
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	431
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	432 The (`Kozich et al. 2013 <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/>`_ ) protocol uses custom sequencing primers which are also the PCR primers. In this case the reads do not contain the PCR primers.
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 In case of Illumina 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	435
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	436 .. role:: alert-info
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	437
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	438 Example:
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	439
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	440 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	441
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	442 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	443
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	444 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	445
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	446 .. class:: h3
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	447
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	448 FLASH : Amplicons sizes parameters
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	449
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	450 .. class:: infomark
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	451
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	452 We now recommend to use PEAR if availbale (only for accademic user) or Vsearch.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	453
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	454 The two following images show two examples of perfect values fors sizes parameters.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	455
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	456 .. image:: static/images/FROGS_preprocess_ampliconSize_unimodal_v3.png
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	457 :height: 415
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	458 :width: 676
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	459
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	460 .. image:: static/images/FROGS_preprocess_ampliconSize_multimodal_v3.png
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	461 :height: 415
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	462 :width: 676
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	463
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	464 Don't worry the "Expected amplicon size" does not need to be very accurate, and only necessary for sequences merging with FLASH.
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 .. class:: h3
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	467
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	468 If the filter 'merged' reduce drasticaly the number of sequences:
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	469
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	470 In un-merged Illumina data, and targeted amplicon size in the range of R1+R2-10, the reduction of dataset by the merged filter is classicaly inferior than 20%. A loss of more than 20% in all samples can highlight a quality problem.
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	471
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	472 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 <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_) 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!
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	473
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	474
7 76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty" oinizan parents: 6 diff changeset	475 @HELP_CONTACT@
0 27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811" oinizan parents: diff changeset	476
9 7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	477 </help>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty oinizan parents: 7 diff changeset	478 <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	479 </tool>

Mercurial > repos > oinizan > frogs

annotate preprocess.xml @ 9:7bf54edaba24 draft