Mercurial > repos > oinizan > frogs
diff 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 |
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--- a/preprocess.xml Mon Aug 23 09:25:07 2021 +0000 +++ b/preprocess.xml Thu May 12 10:44:30 2022 +0000 @@ -1,309 +1,303 @@ -<?xml version="1.0"?> -<!-- -# Copyright (C) 2015 INRA -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. ---> -<tool id="FROGS_preprocess" name="FROGS Pre-process" version="@TOOL_VERSION@+galaxy2"> - <description>merging, denoising and dereplication.</description> - +<tool id="FROGS_preprocess" name="FROGS Pre-process" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> + <description>merging, denoising and dereplication</description> <macros> <import>macros.xml</import> </macros> - - <expand macro="requirements" > + <expand macro="requirements"> <requirement type="package" version="2.17.0">vsearch</requirement> <requirement type="package" version="1.2.11">flash</requirement> <requirement type="package" version="2.10">cutadapt</requirement> </expand> - - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <command> - preprocess.py '$sequencer_type.sequencer_selected' - --output-dereplicated '$dereplicated_file' --output-count '$count_file' --summary '$summary_file' - --nb-cpus \${GALAXY_SLOTS:-1} - --min-amplicon-size $sequencer_type.min_amplicon_size --max-amplicon-size $sequencer_type.max_amplicon_size - - #if $sequencer_type.sequencer_selected == "illumina" - #if $sequencer_type.sequencing_protocol.sequencing_protocol_selected == "standard" - --five-prim-primer '$sequencer_type.sequencing_protocol.five_prim_primer' --three-prim-primer '$sequencer_type.sequencing_protocol.three_prim_primer' - #else - --without-primers - #end if - #else - --five-prim-primer '$sequencer_type.five_prim_primer' --three-prim-primer '$sequencer_type.three_prim_primer' - #end if + <command detect_errors="exit_code"> + preprocess.py '$sequencer_type.sequencer_selected' + --output-dereplicated '$dereplicated_file' --output-count '$count_file' --summary '$summary_file' + @CPUS@ + --min-amplicon-size $sequencer_type.min_amplicon_size + --max-amplicon-size $sequencer_type.max_amplicon_size + #if $sequencer_type.sequencer_selected == "illumina" + #if $sequencer_type.sequencing_protocol.sequencing_protocol_selected == "standard" + --five-prim-primer '$sequencer_type.sequencing_protocol.five_prim_primer' + --three-prim-primer '$sequencer_type.sequencing_protocol.three_prim_primer' + #else + --without-primers + #end if + #else + --five-prim-primer '$sequencer_type.five_prim_primer' + --three-prim-primer '$sequencer_type.three_prim_primer' + #end if - #if $sequencer_type.input_type.input_type_selected == "archive" - --input-archive '$sequencer_type.input_type.archive_file' - #if $sequencer_type.sequencer_selected == "illumina" and $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged" - --already-contiged - #elif $sequencer_type.sequencer_selected == "illumina" - --R1-size $sequencer_type.input_type.archive_type.R1_size --R2-size $sequencer_type.input_type.archive_type.R2_size - --mismatch-rate $sequencer_type.input_type.archive_type.mm_rate - --merge-software '$sequencer_type.input_type.archive_type.merge_software_type.merge_software_selected' - #if $sequencer_type.input_type.archive_type.merge_software_type.merge_software_selected == "flash" - --expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size - #end if - #if $sequencer_type.input_type.archive_type.keep_unmerged - --keep-unmerged - #end if - #end if - #else - #set $sep = ' ' - #if $sequencer_type.sequencer_selected == "illumina" - --samples-names - #for $current in $sequencer_type.input_type.files_by_samples_type.samples - $sep'${current.name.strip()}' - #end for - --input-R1 - #for $current in $sequencer_type.input_type.files_by_samples_type.samples - $sep'${current.R1_file}' - #end for - #if $sequencer_type.input_type.files_by_samples_type.files_by_samples_type_selected == "already_merged" - --already-contiged - #else - --input-R2 - #for $current in $sequencer_type.input_type.files_by_samples_type.samples - $sep'${current.R2_file}' - #end for - --R1-size $sequencer_type.input_type.files_by_samples_type.R1_size --R2-size $sequencer_type.input_type.files_by_samples_type.R2_size - --mismatch-rate $sequencer_type.input_type.files_by_samples_type.mm_rate - --merge-software $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software_selected - #if $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software_selected == "flash" - --expected-amplicon-size $sequencer_type.input_type.files_by_samples_type.merge_software_type.expected_amplicon_size - #end if - #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged - --keep-unmerged - #end if - #end if - #else - --input-R1 - #for $current in $sequencer_type.input_type.samples - $sep'${current.R1_file}' - #end for - --samples-names - #for $current in $sequencer_type.input_type.samples - $sep'${current.name.strip()}' - #end for - #end if - #end if - </command> - <inputs> - <conditional name="sequencer_type"> - <param name="sequencer_selected" type="select" label="Sequencer" help="Select the sequencing technology used to produce the sequences."> - <option value="illumina" selected="true">Illumina</option> - <option value="454">454</option> - </param> - <when value="illumina"> - <!-- Samples --> - <conditional name="input_type"> - <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)."> - <option value="files_by_samples" selected="true">Files by samples</option> - <option value="archive">TAR Archive</option> - </param> - <when value="archive"> - <param name="archive_file" type="data" format="tar,tar.gz" label="TAR archive file" help="The TAR file containing the sequences file(s) for each sample." optional="false" /> - <conditional name="archive_type"> - <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."> - <option value="paired" selected="true">No</option> - <option value="already_merged">Yes</option> - </param> - <!-- $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged" --> - <when value="paired"> - <!-- Reads size --> - <param name="R1_size" type="integer" label="Reads 1 size" help="The maximum read1 size." value="" optional="false" /> - <param name="R2_size" type="integer" label="Reads 2 size" help="The maximum read2 size." value="" optional="false" /> - <param name="mm_rate" type="float" label="Mismatch rate." help="The maximum rate of mismatch in the overlap region" value="0.1" optional="false" /> - <conditional name="merge_software_type"> - <param name="merge_software_selected" type="select" label="Merge software" help="Select the software to merge paired-end reads."> - <option value="vsearch" selected="true">Vsearch</option> - <option value="flash">Flash</option> - </param> - <when value="flash"> - <param name="expected_amplicon_size" type="integer" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons." value="" /> - </when> - <when value="vsearch"></when> - </conditional> - <param name="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)" /> - </when> - <when value="already_merged"></when> - </conditional> - </when> - <when value="files_by_samples"> - <conditional name="files_by_samples_type"> - <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."> - <option value="paired" selected="true">No</option> - <option value="already_merged">Yes</option> - </param> - <when value="paired"> - <!-- Samples --> - <repeat name="samples" title="Samples" min="1"> - <param name="name" type="text" label="Name" help="The sample name." optional="false"> - <validator type="empty_field" message="This parameter is required." /> - </param> - <param format="fastq" name="R1_file" type="data" label="Reads 1" help="R1 FASTQ file of paired-end reads." /> - <param format="fastq" name="R2_file" type="data" label="Reads 2" help="R2 FASTQ file of paired-end reads." /> - </repeat> - <!-- Reads size --> - <param name="R1_size" type="integer" label="Reads 1 size" help="The maximum read1 size." value="" optional="false" /> - <param name="R2_size" type="integer" label="Reads 2 size" help="The maximum read2 size." value="" optional="false" /> - <param name="mm_rate" type="float" label="Mismatch rate." help="The maximum rate of mismatches in the overlap region" value="0.1" optional="false" /> - <conditional name="merge_software_type"> - <param name="merge_software_selected" type="select" label="Merge software" help="Select the software to merge paired-end reads."> - <option value="vsearch" selected="true">Vsearch</option> - <option value="flash">Flash</option> - </param> - <when value="flash"> - <param name="expected_amplicon_size" type="integer" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons." value="" /> - </when> - <when value="vsearch"></when> - </conditional> - <param name="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)" /> - </when> - <when value="already_merged"> - <repeat name="samples" title="Samples" min="1"> - <param name="name" type="text" label="Name" help="The sample name." optional="false"> - <validator type="empty_field" message="This parameter is required." /> - </param> - <param format="fastq" name="R1_file" type="data" label="Sequence file" help="FASTQ file of merged reads." /> - </repeat> - </when> - </conditional> - </when> - </conditional> - <!-- Amplicons --> - <param name="min_amplicon_size" type="integer" label="Minimum amplicon size" help="The minimum size for the amplicons (with primers)." value="" optional="false" /> - <param name="max_amplicon_size" type="integer" label="Maximum amplicon size" help="The maximum size for the amplicons (with primers)." value="" optional="false" /> - <!-- Primers --> - <conditional name="sequencing_protocol"> - <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."> - <option value="standard" selected="true">Illumina standard</option> - <option value="without_primers">Custom protocol (Kozich et al. 2013)</option> - </param> - <when value="standard"> - <param name="five_prim_primer" type="text" size="20" label="5' primer" help="The 5' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters' help section." optional="false"> - <validator type="empty_field" message="This parameter is required." /> - </param> - <param name="three_prim_primer" type="text" size="20" label="3' primer" help="The 3' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters' help section." optional="false"> - <validator type="empty_field" message="This parameter is required." /> - </param> - </when> - <when value="without_primers"></when> - </conditional> - </when> + #if $sequencer_type.input_type.input_type_selected == "archive" + --input-archive '$sequencer_type.input_type.archive_file' + #if $sequencer_type.sequencer_selected == "illumina" and $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged" + --already-contiged + #elif $sequencer_type.sequencer_selected == "illumina" + --R1-size $sequencer_type.input_type.archive_type.R1_size + --R2-size $sequencer_type.input_type.archive_type.R2_size + --mismatch-rate $sequencer_type.input_type.archive_type.mismatch_rate + --merge-software $sequencer_type.input_type.archive_type.merge_software_type.merge_software + #if $sequencer_type.input_type.archive_type.merge_software_type.merge_software == "flash" + --expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size + #end if + #if $sequencer_type.input_type.archive_type.keep_unmerged + --keep-unmerged + #end if + #end if + #else + #set $sep = ' ' + #if $sequencer_type.sequencer_selected == "illumina" + --samples-names + #for $current in $sequencer_type.input_type.files_by_samples_type.samples + $sep'${current.name.strip()}' + #end for + --input-R1 + #for $current in $sequencer_type.input_type.files_by_samples_type.samples + $sep'${current.R1_file}' + #end for + #if $sequencer_type.input_type.files_by_samples_type.files_by_samples_type_selected == "already_merged" + --already-contiged + #else + --input-R2 + #for $current in $sequencer_type.input_type.files_by_samples_type.samples + $sep'${current.R2_file}' + #end for + --R1-size $sequencer_type.input_type.files_by_samples_type.R1_size + --R2-size $sequencer_type.input_type.files_by_samples_type.R2_size + --mismatch-rate $sequencer_type.input_type.files_by_samples_type.mismatch_rate + --merge-software $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software + #if $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software == "flash" + --expected-amplicon-size $sequencer_type.input_type.files_by_samples_type.merge_software_type.expected_amplicon_size + #end if + #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged + --keep-unmerged + #end if + #end if + #else + --input-R1 + #for $current in $sequencer_type.input_type.samples + $sep'${current.R1_file}' + #end for + --samples-names + #for $current in $sequencer_type.input_type.samples + $sep'${current.name.strip()}' + #end for + #end if + #end if + </command> + <inputs> + <conditional name="sequencer_type"> + <param name="sequencer_selected" type="select" label="Sequencer" help="Select the sequencing technology used to produce the sequences."> + <option value="illumina" selected="true">Illumina</option> + <option value="454">454</option> + </param> + <when value="illumina"> + <!-- Samples --> + <conditional name="input_type"> + <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)."> + <option value="files_by_samples" selected="true">Files by samples</option> + <option value="archive">TAR Archive</option> + </param> + <when value="archive"> + <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." /> + <conditional name="archive_type"> + <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."> + <option value="paired" selected="true">No</option> + <option value="already_merged">Yes</option> + </param> + <!-- $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged" --> + <when value="paired"> + <!-- Reads size --> + <param name="R1_size" type="integer" label="Reads 1 size" help="The maximum read1 size." value="" /> + <param name="R2_size" type="integer" label="Reads 2 size" help="The maximum read2 size." value="" /> + <param argument="--mismatch-rate" type="float" label="Mismatch rate" help="The maximum rate of mismatch in the overlap region" value="0.1" /> + <conditional name="merge_software_type"> + <param argument="--merge-software" type="select" label="Merge software" help="Select the software to merge paired-end reads"> + <option value="vsearch" selected="true">Vsearch</option> + <option value="flash">Flash</option> + </param> + <when value="flash"> + <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"/> + </when> + <when value="vsearch"></when> + </conditional> + <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)" /> + </when> + <when value="already_merged"></when> + </conditional> + </when> + <when value="files_by_samples"> + <conditional name="files_by_samples_type"> + <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."> + <option value="paired" selected="true">No</option> + <option value="already_merged">Yes</option> + </param> + <when value="paired"> + <!-- Samples --> + <repeat name="samples" title="Samples" min="1"> + <param name="name" type="text" label="Name" help="The sample name."> + <expand macro="sanitizer_validator"/> + </param> + <param format="fastq" name="R1_file" type="data" label="Reads 1" help="R1 FASTQ file of paired-end reads." /> + <param format="fastq" name="R2_file" type="data" label="Reads 2" help="R2 FASTQ file of paired-end reads." /> + </repeat> + <!-- Reads size --> + <param name="R1_size" type="integer" label="Reads 1 size" help="The maximum read1 size." value="" /> + <param name="R2_size" type="integer" label="Reads 2 size" help="The maximum read2 size." value="" /> + <param name="mismatch_rate" type="float" label="Mismatch rate." help="The maximum rate of mismatches in the overlap region" value="0.1" /> + <conditional name="merge_software_type"> + <param argument="--merge-software" type="select" label="Merge software" help="Select the software to merge paired-end reads"> + <option value="vsearch" selected="true">Vsearch</option> + <option value="flash">Flash</option> + </param> + <when value="flash"> + <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"/> + </when> + <when value="vsearch"></when> + </conditional> + <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)" /> + </when> + <when value="already_merged"> + <repeat name="samples" title="Samples" min="1"> + <param name="name" type="text" label="Name" help="The sample name."> + <expand macro="sanitizer_validator"/> + </param> + <param format="fastq" name="R1_file" type="data" label="Sequence file" help="FASTQ file of merged reads." /> + </repeat> + </when> + </conditional> + </when> + </conditional> + <!-- Amplicons --> + <param argument="--min-amplicon-size" type="integer" value="" label="Minimum amplicon size" help="The minimum size for the amplicons (with primers)"/> + <param argument="--max-amplicon-size" type="integer" value="" label="Maximum amplicon size" help="The maximum size for the amplicons (with primers)"/> + <!-- Primers --> + <conditional name="sequencing_protocol"> + <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."> + <option value="standard" selected="true">Illumina standard</option> + <option value="without_primers">Custom protocol (Kozich et al. 2013)</option> + </param> + <when value="standard"> + <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"> + <sanitizer invalid_char=""> + <valid initial="string.letters"/> + </sanitizer> + <validator type="regex">[A-Za-z]+</validator> + </param> + <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"> + <sanitizer invalid_char=""> + <valid initial="string.letters"/> + </sanitizer> + <validator type="regex">[A-Za-z]+</validator> + </param> + </when> + <when value="without_primers"></when> + </conditional> + </when> - <when value="454"> - <!-- Samples --> - <conditional name="input_type"> - <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."> - <option value="files_by_samples" selected="true">One file by sample</option> - <option value="archive">TAR Archive</option> - </param> - <when value="archive"> - <param name="archive_file" type="data" format="tar,tar.gz" label="TAR archive file" help="The TAR file containing the sequences file for each sample." optional="false" /> - </when> - <when value="files_by_samples"> - <repeat name="samples" title="Samples" min="1"> - <param name="name" type="text" label="Name" help="The sample name." optional="false" /> - <param format="fastq" name="R1_file" type="data" label="Sequence file" help="FASTQ file of sample." /> - </repeat> - </when> - </conditional> - <!-- Amplicons --> - <param name="min_amplicon_size" type="integer" label="Minimum amplicon size" help="The minimum size for the amplicons (with primers)." value="" optional="false" /> - <param name="max_amplicon_size" type="integer" label="Maximum amplicon size" help="The maximum size for the amplicons (with primers)." value="" optional="false" /> - <!-- Primers --> - <param name="five_prim_primer" type="text" size="20" label="5' primer" help="The 5' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters' help section." optional="false"> - <validator type="empty_field" message="This parameter is required." /> - </param> - <param name="three_prim_primer" type="text" size="20" label="3' primer" help="The 3' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters' help section." optional="false"> - <validator type="empty_field" message="This parameter is required." /> - </param> - </when> - </conditional> - </inputs> - <outputs> - <data format="fasta" name="dereplicated_file" label="${tool.name}: dereplicated.fasta" from_work_dir="dereplicated.fasta" /> - <data format="tabular" name="count_file" label="${tool.name}: count.tsv" from_work_dir="count.tsv" /> - <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" /> - </outputs> + <when value="454"> + <!-- Samples --> + <conditional name="input_type"> + <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."> + <option value="files_by_samples" selected="true">One file by sample</option> + <option value="archive">TAR Archive</option> + </param> + <when value="archive"> + <param name="archive_file" type="data" format="tar,tgz" label="TAR archive file" help="The TAR file containing the sequences file for each sample." /> + </when> + <when value="files_by_samples"> + <repeat name="samples" title="Samples" min="1"> + <param name="name" type="text" label="Name" help="The sample name."> + <expand macro="sanitizer_validator"/> + </param> + <param format="fastq" name="R1_file" type="data" label="Sequence file" help="FASTQ file of sample." /> + </repeat> + </when> + </conditional> + <!-- Amplicons --> + <param argument="--min-amplicon-size" type="integer" value="" label="Minimum amplicon size" help="The minimum size for the amplicons (with primers)"/> + <param argument="--max_amplicon-size" type="integer" value="" label="Maximum amplicon size" help="The maximum size for the amplicons (with primers)"/> + <!-- Primers --> + <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"> + <sanitizer invalid_char=""> + <valid initial="string.letters"/> + </sanitizer> + <validator type="regex">[A-Za-z]+</validator> + </param> + <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"> + <sanitizer invalid_char=""> + <valid initial="string.letters"/> + </sanitizer> + <validator type="regex">[A-Za-z]+</validator> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="fasta" name="dereplicated_file" label="${tool.name}: dereplicated.fasta" from_work_dir="dereplicated.fasta" /> + <data format="tabular" name="count_file" label="${tool.name}: count.tsv" from_work_dir="count.tsv" /> + <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" /> + </outputs> <tests> - <test> - <conditional name="sequencer_type"> - <param name="sequencer_selected" value="illumina"/> - <conditional name="input_type"> - <param name="input_type_selected" value="archive"/> - <param name="archive_file" ftype="tar" value="input/test_dataset.tar.gz"/> - <conditional name="archive_type"> - <param name="archive_type_selected" value="paired"/> - <param name="R1_size" value="267"/> - <param name="R2_size" value="266"/> - <param name="mm_rate" value="0.15"/> - <conditional name="merge_software_type"> - <param name="merge_software_selected" value="flash" /> - <param name="expected_amplicon_size" value="420"/> - </conditional> - <param name="keep_unmerged" value="true"/> - </conditional> - </conditional> - <param name="min_amplicon_size" value="44"/> - <param name="max_amplicon_size" value="490"/> - <conditional name="sequencing_protocol"> - <param name="sequencing_protocol_selected" value="standard"/> - <param name="five_prim_primer" value="GGCGVACGGGTGAGTAA"/> - <param name="three_prim_primer" value="GTGCCAGCNGCNGCGG"/> - </conditional> - </conditional> - <output name="dereplicated_file" file="references/01-prepro-flash.fasta" compare="diff" lines_diff="0" /> - <output name="count_file" file="references/01-prepro-flash.tsv" compare="diff" lines_diff="0" /> - <output name="summary_file" file="references/01-prepro-flash.html" compare="sim_size" delta="0"/> + <test> + <conditional name="sequencer_type"> + <param name="sequencer_selected" value="illumina" /> + <conditional name="input_type"> + <param name="input_type_selected" value="archive" /> + <param name="archive_file" ftype="tgz" value="input/test_dataset.tar.gz" /> + <conditional name="archive_type"> + <param name="archive_type_selected" value="paired" /> + <param name="R1_size" value="267" /> + <param name="R2_size" value="266" /> + <param name="mismatch_rate" value="0.15" /> + <conditional name="merge_software_type"> + <param name="merge_software" value="flash" /> + <param name="expected_amplicon_size" value="420" /> + </conditional> + <param name="keep_unmerged" value="true" /> + </conditional> + </conditional> + <param name="min_amplicon_size" value="44" /> + <param name="max_amplicon_size" value="490" /> + <conditional name="sequencing_protocol"> + <param name="sequencing_protocol_selected" value="standard" /> + <param name="five_prim_primer" value="GGCGVACGGGTGAGTAA" /> + <param name="three_prim_primer" value="GTGCCAGCNGCNGCGG" /> + </conditional> + </conditional> + <output name="dereplicated_file" file="references/01-prepro-flash.fasta" compare="diff" lines_diff="0" /> + <output name="count_file" file="references/01-prepro-flash.tsv" compare="diff" lines_diff="0" /> + <output name="summary_file" file="references/01-prepro-flash.html" compare="sim_size" delta="0" /> </test> <test> <conditional name="sequencer_type"> - <param name="sequencer_selected" value="illumina"/> - <conditional name="input_type"> - <param name="input_type_selected" value="archive"/> - <param name="archive_file" ftype="tar" value="input/test_dataset.tar.gz"/> - <conditional name="archive_type"> - <param name="archive_type_selected" value="paired"/> - <param name="R1_size" value="267"/> - <param name="R2_size" value="266"/> - <param name="mm_rate" value="0.15"/> - <conditional name="merge_software_type"> - <param name="merge_software_selected" value="vsearch" /> - </conditional> - <param name="keep_unmerged" value="true"/> - </conditional> - </conditional> - <param name="min_amplicon_size" value="44"/> - <param name="max_amplicon_size" value="490"/> - <conditional name="sequencing_protocol"> - <param name="sequencing_protocol_selected" value="standard"/> - <param name="five_prim_primer" value="GGCGVACGGGTGAGTAA"/> - <param name="three_prim_primer" value="GTGCCAGCNGCNGCGG"/> - </conditional> + <param name="sequencer_selected" value="illumina" /> + <conditional name="input_type"> + <param name="input_type_selected" value="archive" /> + <param name="archive_file" ftype="tgz" value="input/test_dataset.tar.gz" /> + <conditional name="archive_type"> + <param name="archive_type_selected" value="paired" /> + <param name="R1_size" value="267" /> + <param name="R2_size" value="266" /> + <param name="mismatch_rate" value="0.15" /> + <conditional name="merge_software_type"> + <param name="merge_software" value="vsearch" /> + </conditional> + <param name="keep_unmerged" value="true" /> + </conditional> + </conditional> + <param name="min_amplicon_size" value="44" /> + <param name="max_amplicon_size" value="490" /> + <conditional name="sequencing_protocol"> + <param name="sequencing_protocol_selected" value="standard" /> + <param name="five_prim_primer" value="GGCGVACGGGTGAGTAA" /> + <param name="three_prim_primer" value="GTGCCAGCNGCNGCGG" /> + </conditional> </conditional> - <output name="dereplicated_file" file="references/01-prepro-vsearch.fasta" compare="diff" lines_diff="0" /> - <output name="count_file" file="references/01-prepro-vsearch.tsv" compare="diff" lines_diff="0" /> - <output name="summary_file" file="references/01-prepro-vsearch.html" compare="sim_size" delta="0"/> + <output name="dereplicated_file" file="references/01-prepro-vsearch.fasta" compare="diff" lines_diff="0" /> + <output name="count_file" file="references/01-prepro-vsearch.tsv" compare="diff" lines_diff="0" /> + <output name="summary_file" file="references/01-prepro-vsearch.html" compare="sim_size" delta="0" /> </test> </tests> - <help> + <help> @HELP_LOGO@ @@ -421,8 +415,8 @@ Reads pair are not merged because: - - the real amplicon length is greater than de number of base sequences (490 bp for MiSeq 2x250bp, remember of the minimum 10 bp overlap) - - the overlapped region is smaller than 10 (fixed parameter in FROGS). + - the real amplicon length is greater than de number of base sequences (490 bp for MiSeq 2x250bp, remember of the minimum 10 bp overlap) + - the overlapped region is smaller than 10 (fixed parameter in FROGS). Thus, “FROGS combined” sequences are artificial and present particular features especially on size. Imagine a MiSeq sequencing of 2x250pb with sequences that cannot overlap, the resulting “FROGS combined” sequences length will be fixed to 600 bp. @@ -480,10 +474,6 @@ @HELP_CONTACT@ - </help> - - <citations> - <expand macro="citations" /> - </citations> - + </help> + <expand macro="citations" /> </tool>