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Changeset 0:834843ebe569 (2021-04-08)

Next changeset 1:2ed857799fd5 (2021-06-04)

Commit message:
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"

diff -r 000000000000 -r 834843ebe569 FROGS_data_manager/data_manager/FROGS_data_manager.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_data_manager/data_manager/FROGS_data_manager.py Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,148 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+from galaxy.util.json import from_json_string, to_json_string
+import os, sys, argparse, time, json, requests, urllib, tarfile
+
+# FROGS_data_manager.py --database=frogs_db_data --all_dbs=false --date=0 --amplicons=16S --bases=SILVA --filters=Pintail100 --only_last_versions=true \
+# --tool_data=/home/maria/galaxy/galaxy-20.09/tool-data --output /home/maria/galaxy/galaxy-20.09/database/objects/e/7/7/dataset_e7766c39-8f36-450c-adf5-3e4ee8d5c562.dat
+
+def get_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-d","--database")
+    parser.add_argument("--all_dbs")
+    parser.add_argument("--date")
+    parser.add_argument("--amplicons")
+    parser.add_argument("--bases")
+    parser.add_argument("--filters")
+    parser.add_argument("--only_last_versions")
+    parser.add_argument("--tool_data")
+    parser.add_argument("-o","--output")
+    args = parser.parse_args()
+
+    return args
+
+def _add_data_table_entry(data_manager_dict, data_table_entry,data_table):
+    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
+    data_manager_dict['data_tables'][data_table].append(data_table_entry)
+    return data_manager_dict
+
+def keep_only_last_version(db_index):
+    db_dict = dict()
+    for line in db_index:
+        db_type = "_".join(line[1:4]) if line[3] != "" else "_".join(line[1:3])
+        if db_type not in db_dict:
+            db_dict[db_type] = line
+    return list(db_dict.values())
+
+
+def frogs_sources(data_manager_dict,target_directory):
+
+    #variables
+    amplicons_list=[]
+    bases_list=[]
+    filters_list=[]
+    if  args.all_dbs=="false":
+        amplicons_list = [amplicon.lower().strip() for amplicon in args.amplicons.split(",") if amplicon != ""]
+        bases_list = [base.lower().strip() for base in args.bases.split(",") if base != ""]
+        filters_list = [filter.lower().strip() for filter in args.filters.split(",") if filter!=""]
+        bottom_date = int(args.date)
+    tool_data_path=args.tool_data
+
+    #get frogs database index
+    frogs_db_index_link="http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv"
+    with requests.Session() as s:
+        download = s.get(frogs_db_index_link)
+        decoded_content = download.content.decode('utf-8')
+        db_index = decoded_content.splitlines()
+        db_index = [line.split("\t") for line in db_index[1:]]
+        db_index = [[line[0],line[1].lower(),line[2].lower(),line[3].lower()]+line[4:] for line in db_index]
+
+    #filter databases
+    if args.all_dbs=="false":
+        if len(amplicons_list)!=0: db_index = [line for line in db_index if any([amplicon in amplicons_list for amplicon in line[1].split(',')])]   #filter by amplicons
+        if len(bases_list)!=0: db_index = [line for line in db_index if line[2] in bases_list]                                                      #filter by base
+        if len(filters_list)!=0: db_index = [line for line in db_index if line[3] in filters_list]                                                  #filter by filters
+        if bottom_date!=0: db_index = [line for line in db_index if int(line[0])>=bottom_date]                                                      #filter by date
+    if args.only_last_versions=="true":
+        db_index = keep_only_last_version(db_index)                                                          #keep only last version
+
+    #get frogs dbs
+    os.chdir(target_directory)
+    dir_name="frogs_db_"+time.strftime("%Y%m%d")
+    os.mkdir(dir_name)
+    dbs=set([])
+    for line in db_index:
+        value=line[5]
+        name=value.replace("_"," ") if not "_" in line[4] else value.replace(line[4],"").replace("_", " ") + line[4]
+        link=line[6]
+        name_dir="".join([line[6].replace(".tar.gz","").split("/")[-1]])
+        file_path=tool_data_path+"/frogs_db/"+name_dir
+        if not os.path.exists(file_path):   #if the file is not already in frogs_db directory
+
+            #download frogs db
+            dl_file =  urllib.request.URLopener()
+            dl_file.retrieve(link, "tmp.tar.gz")
+
+            #unzip frogs db
+            with tarfile.open("tmp.tar.gz") as tar:
+                tar.extractall(dir_name)
+                tar.close()
+                os.remove('tmp.tar.gz')
+
+            #get fasta file path
+            tmp = set(os.listdir(dir_name))
+            new_db = dir_name+"/"+"".join(tmp.difference(dbs))
+            files = os.listdir(new_db)
+            fasta = "".join([file for file in files if file.endswith('.fasta')])
+            path = new_db+'/'+fasta
+            dbs = os.listdir(dir_name)
+            release = value+"_"+time.strftime("%Y-%m-%d")
+            date=time.strftime("%Y%m%d")
+            path = os.path.join(target_directory,path)
+
+            data_table_entry = dict(name = name, value = value, path=path)
+            _add_data_table_entry(data_manager_dict, data_table_entry, "frogs_db")
+
+# def HVL_sources(data_manager_dict,target_directory):
+
+#     os.chdir(target_directory)
+#     for link in ["http://genoweb.toulouse.inra.fr/frogs_databanks/HVL/ITS/UNITE_s_7.1_20112016/Unite_s_7.1_20112016_ITS1.fasta","http://genoweb.toulouse.inra.fr/frogs_databanks/HVL/ITS/UNITE_s_7.1_20112016/Unite_s_7.1_20112016_ITS2.fasta"]:
+#         file_name=link.split("/")[-1].replace('.fasta',"_"+time.strftime("%Y-%m-%d")+".fasta")
+#         dl_file = urllib.URLopener()
+#         dl_file.retrieve(link,file_name)
+
+#         #get fasta file path
+#         path = os.path.join(target_directory,file_name)
+#         if link.endswith('ITS1.fasta'):
+#             name = "UNITE 7.1 ITS1 " + time.strftime("%Y-%m-%d")
+#         elif link.endswith('ITS2.fasta'):
+#             name = "UNITE 7.1 ITS2 " + time.strftime("%Y-%m-%d")
+#         value=file_name.replace('.fasta','')
+
+#         data_table_entry = dict(name = name, value = value, path=path)
+#         _add_data_table_entry(data_manager_dict, data_table_entry, "frogs_HVL_db")
+
+def main():
+
+    #get args from command line
+    global args
+    args = get_args()
+
+    # Extract json file params
+    data_manager_dict = {}
+    filename = args.output
+    params = from_json_string(open(filename).read())
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir(target_directory)
+
+    # if args.database=="frogs_db_data":
+    frogs_sources(data_manager_dict,target_directory)
+    # elif args.database=="HVL_db_data":
+    #     HVL_sources(data_manager_dict,target_directory)
+
+    #save info to json file
+    open(filename, 'wt').write(to_json_string(data_manager_dict))
+
+if __name__ == "__main__":
+    main()

diff -r 000000000000 -r 834843ebe569 FROGS_data_manager/data_manager/FROGS_data_manager.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_data_manager/data_manager/FROGS_data_manager.xml Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,65 @@
+<tool id="FROGS_data_manager" name="FROGS Data manager" version="3.2.2" tool_type="manage_data">
+    <requirements>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        $__tool_directory__/FROGS_data_manager.py
+            --database="frogs_db_data"
+
+            --all_dbs="$db_type.db"
+            #if $db_type.db=="false"
+                --date="$db_type.date"
+                --amplicons="$db_type.amplicons"
+                --bases="$db_type.bases"
+                --filters="$db_type.filters"
+            #end if
+            --only_last_versions="$only_last_versions"
+
+            --tool_data="$__tool_data_path__"
+            --output "$output"
+    ]]></command>
+    <inputs>
+        <conditional name="db_type">
+            <param name="db" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Download all databases"/>
+            <when value="true"/>
+            <when value="false">
+                <param name="date" value="0" type="text"  label="Download only most recent databases" help="Select databases uploaded later than this date. Please enter a date at the following format: YYYYMMDD, else leave 0.">
+                    <validator type="regex" message="Please enter a date at the following format: YYYYMMDD, leave 0 for no date">0|[1-2]{1}[0-9]{3}[0-1]{1}[0-9]{1}([0-2]{1}[0-9]{1}|3[0-1]{1})</validator>
+                </param>
+                <param name="amplicons" type="text" label='Select amplicon specific databases' help='Write amplicons names separated by ","; example: "COI,ITS,16S" or "23S"'/>
+                <param name="bases" type="text" label='Select database by name' help='Write base names separated by ","; example: "SILVA,PR2,MIDAS" or "BOLD"'/>
+                <param name="filters" type="text" label='Select database on filter name' help='Write filter names separated by ",";example: "Pintail100,Fungi"'/>
+            </when>
+        </conditional>
+        <param name="only_last_versions" type="boolean" checked="true" label="Download only the last version of selected database"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="data_manager_json"/>
+    </outputs>
+    <help>
+        .. image:: static/images/FROGS_logo.png
+    :height: 144
+    :width: 110
+
+        FROGS datamanager allows to download preformated databases for FROGS Affiliation OTU tool.
+
+        All databases are available at http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/.
+
+        This tools is based on the `FROGS_databases.tsv.txt <http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv.txt>`_, that we update each time a new database is formatted.
+
+ .. image:: static/images/FROGS_db.png
+    :height: 157
+    :width: 961
+
+    You may download all databases, but you may (should) filter whished database on different criteria:
+
+    - on a date, to download only last formated databases
+    - on an amplicon type
+    - on a base name
+    - eventually on a filtered name, this may be the case for example, for 16S SILVA database, for which we provide reference sequence with pintail score above a threshold
+
+    Last option allow you to download only last version of previously selected databases, indeed we provide reference database since 2016 with for example, around 1 version of SILVA per year.
+    </help>
+</tool>
\ No newline at end of file

diff -r 000000000000 -r 834843ebe569 FROGS_data_manager/data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_data_manager/data_manager_conf.xml Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/FROGS_data_manager.xml" id="frogs_data_manager">
+        <data_table name="frogs_db">
+            <output>
+                <column name="value" />
+                <column name="name" />
+                <column name="path" output_ref="output">
+                    <move type="directory" relativize_symlinks="False">
+                        <source>#echo "/".join(str($path).split('/')[:-1])#</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">frogs_db/#echo str($path).split('/')[-2]#/</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/frogs_db/#echo "/".join(str($path).split('/')[-2:])#</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>

diff -r 000000000000 -r 834843ebe569 FROGS_data_manager/tool-data/frogs_HVL_db.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_data_manager/tool-data/frogs_HVL_db.loc.sample Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,34 @@
+# Copyright (C) 2014 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/>.
+#
+#
+#This is a sample file that enables tools FROGS_affiliations_postprocess to solve
+#inclusive amplicon sequence by selecting the smallest reference among multihit
+#You will need to create or download exact amplicon sequence reference fasta file
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL_reference
+#Finally you will need to create HVL_db.loc file similar to this one in your galaxy
+#tool-data directory.The HVL_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<unique_database_name>    <name>    <file_path>
+#
+#First column will be the visible name in galaxy.
+#So, for example, if you have  UNITE 7.1 ITS1 (only!) stored
+#in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta
+#then the HVL_db.loc entry would look like this:
+#
+#
+# EXAMPLE FOR TEST :
+#Unite_extract_ITS1_test Unite_extract_ITS1_test ${__HERE__}/HVL_db_data/Unite_extract_ITS1.fasta

diff -r 000000000000 -r 834843ebe569 FROGS_data_manager/tool-data/frogs_contaminant_db.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_data_manager/tool-data/frogs_contaminant_db.loc Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,41 @@
+# Copyright (C) 2014 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/>.
+#
+#
+#This is a sample file that enables tools FROGS_filters to identify phix contaminant. You will #need to create or download Blast+ index.
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants
+#Finally you will need to create phiX_db.loc file similar to this one in your galaxy
+#tool-data directory.The phiX_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<contaminant_name> <name> <file_path>
+#
+#First column will be the visible name in galaxy.
+#So, for example, if you had phix indexed stored in
+#/galaxy_databanks/phiX/
+#then the phiX_db.loc entry would look like this:
+#
+#
+# EXAMPLE FOR TEST :
+#phiX_test phiX_test ${__HERE__}/phiX_db_data/phi.fa
+#
+#and your /galaxy_databanks/phiX/ directory
+#would contain index files:
+#
+#-rwxrwxr-x 1 gpascal FROGS 5535 16 sept.  2015 phi.fa
+#-rw-rwxr-- 1 gpascal FROGS  132 16 sept.  2015 phi.fa.nhr
+#-rw-rwxr-- 1 gpascal FROGS   88 16 sept.  2015 phi.fa.nin
+#-rw-rwxr-- 1 gpascal FROGS 1348 16 sept.  2015 phi.fa.nsq
+#

diff -r 000000000000 -r 834843ebe569 FROGS_data_manager/tool-data/frogs_db.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_data_manager/tool-data/frogs_db.loc.sample Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,53 @@
+# Copyright (C) 2014 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/>.
+#
+#
+#This is a sample file that enables tools FROGS_affiliations_OTU to use taxonomy database for
+#taxonomy affiliation. You will need to create or download Blast+ index and train your database
+#for RDP classifier these data files.
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation
+#Finally you will need to create frogs_db.loc file similar to this one in your galaxy
+#tool-data directory.The frogs_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<unique_database_name>   <file_path>
+#
+#First column will be the visible name in galaxy.
+#So, for example, if you had 16S silva 128 indexed stored in
+#/galaxy_databanks/16S/silva_128/
+#then the frogs_db.loc entry would look like this:
+#
+#silva 128 16S  /galaxy_databanks/16S/silva_128/silva_128_16S.fasta
+#
+#and your /galaxy_databanks/16S/silva_128/ directory
+#would contain index files:
+#
+#-rw-r--r-- 1 mbernard FROGS    8097966  5 déc.  16:56 bergeyTrainingTree.xml
+#-rw-r--r-- 1 mbernard FROGS 1572981589  5 déc.  16:56 genus_wordConditionalProbList.txt
+#-rw-r--r-- 1 mbernard FROGS       1654  5 déc.  16:56 LICENCE.txt
+#-rw-r--r-- 1 mbernard FROGS    1072228  5 déc.  16:56 logWordPrior.txt
+#-rw-r--r-- 1 mbernard FROGS  940834335  5 déc.  16:56 silva_128_16S.fasta
+#-rw-r--r-- 1 mbernard FROGS  152606489  5 déc.  16:56 silva_128_16S.fasta.nhr
+#-rw-r--r-- 1 mbernard FROGS    6918588  5 déc.  16:56 silva_128_16S.fasta.nin
+#-rw-r--r-- 1 mbernard FROGS  205320030  5 déc.  16:56 silva_128_16S.fasta.nsq
+#-rw-r--r-- 1 mbernard FROGS        281  5 déc.  16:56 silva_128_16S.fasta.properties
+#-rw-r--r-- 1 mbernard FROGS    3420464  5 déc.  16:56 silva_128_16S.tax
+#-rw-r--r-- 1 mbernard FROGS     964048  5 déc.  16:57 wordConditionalProbIndexArr.txt
+#
+#
+#<name>    <name>    <file_path>
+#
+# EXAMPLE FOR TEST :
+#ITS1_test ITS1_test ${__HERE__}/frogs_db_data/ITS1.rdp.fasta

diff -r 000000000000 -r 834843ebe569 FROGS_data_manager/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_data_manager/tool_data_table_conf.xml.sample Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tables>
+    
+    <table name="frogs_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/frogs_db.loc" />
+    </table>
+    <table name="frogs_HVL_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/frogs_HVL_db.loc" />
+    </table>
+    <table name="frogs_contaminant_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/frogs_contaminant_db.loc" />
+    </table>
+</tables>

diff -r 000000000000 -r 834843ebe569 FROGS_data_manager/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_data_manager/tool_dependencies.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,3 @@
+<?xml version="1.0"?>
+<tool_dependency>
+</tool_dependency>

diff -r 000000000000 -r 834843ebe569 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,401 @@\n+<p align="center">\n+ <a href="http://frogs.toulouse.inra.fr/">\n+ <img src="static/images/FROGS_logo.png" align="center" width="20%" style="display: block; margin: auto;"/>\n+ </a>\n+</p>\n+\n+Visit our web site : http://frogs.toulouse.inrae.fr/\n+\n+[![Release](https://img.shields.io/badge/release-3.2.2-blue.svg)![Date](https://img.shields.io/badge/date-April%202021-red.svg)](https://github.com/geraldinepascal/FROGS-wrappers/releases)[<img src="https://www.podcastscience.fm/wp-content/uploads/2017/12/deezer.png" width="5%" style="display: block; margin: auto;"/>](https://www.deezer.com/fr/playlist/5233843102?utm_source=deezer&utm_content=playlist-5233843102&utm_term=18632989_1545296531&utm_medium=web)\n+\n+\n+\n+# Description\n+\n+FROGS is a workflow designed to produce an OTU count matrix from high depth sequencing amplicon data.\n+\n+FROGS also provide statistical tools to explore OTU count table and taxonomical affiliations.\n+\n+FROGS-wrappers allow to add FROGS on a Galaxy instance.\n+\n+# Table of content\n+\n+* [Installing FROGS\\-wrappers](#installing-frogs-wrappers)\n+ * [Simplest way](#simplest-way)\n+ * [From sources](#from-sources)\n+ * [Prerequisites](#prerequisites)\n+ * [FROGS\\-wrappers installation](#frogs-wrappers-installation)\n+* [Use PEAR as reads merge software in preprocess](#use-pear-as-reads-merge-software-in-preprocess)\n+* [Upload and configure the databanks](#upload-and-configure-the-databanks)\n+* [Galaxy configuration](#galaxy-configuration)\n+ * [Setup Galaxy environment variables](#setup-galaxy-environment-variables)\n+ * [Install python packages inside virtual env](#install-python-packages-inside-virtual-env)\n+ * [Avoid FROGS HTML report sanitization](#avoid-FROGS-HTML-report-sanitization)\n+ * [Set memory and parallelisation settings](#set-memory-and-parallelisation-settings)\n+* [License](#license)\n+* [Copyright](#copyright)\n+* [Citation](#citation)\n+* [Contact](#contact)\n+\n+# Installing FROGS-wrappers\n+\n+## Simplest way\n+\n+FROGS is available on the Toolshed.\n+\n+It will install FROGS thanks to [conda](https://anaconda.org/bioconda/frogs), download all these XML tools and well configure them in your Galaxy.\n+\n+The 25 FROGS tools will be in random order in your tools panel. We propose to control that order by modifying the `shed_tool_conf.xml` which will render the following`integrated_tool_panel.xml ` file. \n+\n+We suppose that you installed FROGS in a specific section named `FROGS`. \n+\n+```\n+<section id="FROGS" name="FROGS" version="">\n+\n+ <label id="FROGS_OTU_toolshed_3.2.2" text="OTUs reconstruction" version="" />\n+\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_demultiplex/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clustering/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.2" /> \n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_postprocess/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_stdBiom/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_tsv/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_tsv_to_biom/3.2.2" />\n+\n+ <label id="FRO'..b'du/repos/frogs/frogs/FROGS_itsx/3.2.2\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.2\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.2\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.2\n+\n+```\n+\n+## Set memory and parallelisation settings\n+\n+If you have more than one CPU, it is recommended to increase the number of CPUs used by tools.\n+\n+All CPUs must be on the same computer/node.\n+\n+\n+ * Specifications\n+\n+ | Tool | RAM per CPU | Minimal RAM | Configuration example |\n+ | :-------------------: | :---------: | :---------: | :-------------------: |\n+ | preprocess | 8Gb | - | 12 CPUs and 96 GB |\n+ | clustering | - | 10 Gb | 16 CPUs and 60 GB |\n+ | ITSx / remove_chimera | 3Gb | 5Gb | 12 CPUs and 36 GB |\n+ | affiliation_OTU | - | 20 Gb | 30 CPUs and 300 GB |\n+\n+ * Galaxy configuration\n+\n+ You need to add `destiantion` sections (one per tool) in the `<Galaxy-Dir>/config/job_conf.xml` \n+ Example for SGE scheduler:\n+\n+\n+```\n+<destinations>\n+\t...\n+\t<destination id="FROGS_preprocess_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=5G -l h_vmem=13G -pe parallel_smp 12</param>\n+\t</destination>\n+\t<destination id="FROGS_clustering_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=10G -pe parallel_smp 16</param>\n+\t</destination>\n+\t<destination id="FROGS_remove_chimera_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12</param>\n+\t</destination>\n+\t<destination id="FROGS_itsx_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12</param>\n+\t</destination>\n+\t<destination id="FROGS_affiliation_OTU_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=7G -l h_vmem=10G -pe parallel_smp 30</param>\n+\t</destination>\n+</destinations>\n+<tools>\n+...\n+\t<tool id="FROGS_preprocess" destination="FROGS_preprocess_job"/> \n+\t<tool id="FROGS_clustering" destination="FROGS_clustering_job"/> \n+\t<tool id="FROGS_remove_chimera" destination="FROGS_remove_chimera_job"/> \n+\t<tool id="FROGS_itsx" destination="FROGS_itsx_job"/> \n+\t<tool id="FROGS_affiliation_OTU" destination="FROGS_affiliation_OTU_job"/>\n+</tools>\n+```\n+\n+# License\n+ GNU GPL v3\n+\n+# Copyright\n+ 2021 INRAE\n+\n+# Citation\n+ Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*\n+\n+# Contact\n+ frogs-support@inrae.fr\n+\n'

diff -r 000000000000 -r 834843ebe569 RELEASE_NOTE.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RELEASE_NOTE.md Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,44 @@
+# v3.2.2 [2021-04]
+
+### Tools added:
+  * DESeq2 preprocess : Compute differential abundancy analysis
+  * DESeq2 visualisation : Create table and plots to explore and illustrate the differential abundant OTUs
+  * Filters has been splitted into to new tools : FROGS OTU Filters and FROGS Affiliations Filters.
+      * FROGS OTU Filters filters OTU on presence/absence, abundances and contamination as Filters did. For contamination research, user may now use a personnal multifasta contaminant reference.
+      * FROGS Affiliation Filters delete OTU or mask affiliation that do not respect affiliation metrics criteria, or affiliated to undesirable (partial) taxon.
+  * FROGS datamanager is now available to manage affiliation reference database (frogs_db.loc for affiliation_OTU tool) thanks to @davidchristiany.
+
+### Contaminant database added
+  * add Arabidopsis thaliana chroloroplast sequence
+
+### Modifications:
+  * ITSx : add organism model option scanning, change default behavior regarding the trimming of conserved regions
+
+  * Use english typo for normalise and visualise
+
+  * rename phix_db.loc in contaminant_db.loc
+
+  * update tool dependencies version
+
+
+
+# v3.1 [2018-01-08]
+
+This release corresponds to the FROGS 3.1.0 release.
+
+* ### Tools added:
+
+  - ITSx : tool available for selecting and trimming ITS sequences based on ITSx tool
+  - Affiliation Postprocess : resolve ambiguities due to inclusiv ITS, and aggregated OTU based on
+    taxonomic affiliations
+
+* ### Modifications:
+
+  - use tool data table instead of simple loc files for filters, affiliation_OTU and affiliation_postprocess
+  - Tree do no longer support Pynast alignment thanks to a template file
+
+# v2.0.0  [2018-12-11]
+
+  First package.
+
+This release corresponds to the FROGS 2.0.0 release

diff -r 000000000000 -r 834843ebe569 affiliation_OTU.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/affiliation_OTU.xml Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,200 @@\n+<?xml version="1.0"?>\n+\n+<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="3.2.2">\n+\t<description>Taxonomic affiliation of each OTU\'s seed by RDPtools and BLAST</description>\n+ \t<requirements>\n+ <requirement type="package" version="3.2.2">frogs</requirement>\n+ <requirement type="package" version="2.10">blast</requirement>\n+ <requirement type="package" version="6.6.0">emboss</requirement>\n+ <requirement type="package" version="2.0.3">rdptools</requirement>\n+ </requirements>\n+\t<command detect_errors="exit_code">\n+\t\t#set $reference_filename = str( $ref_file.fields.path )\n+\t\taffiliation_OTU.py \n+\t\t --reference \'${reference_filename}\'\n+\t\t --input-biom $biom_abundance \n+\t\t --input-fasta $fasta_sequences\n+\t\t --output-biom $biom_affiliation \n+\t\t --summary $summary \n+\t\t --nb-cpus \\${GALAXY_SLOTS:-1}\n+\t\t --java-mem $mem \n+\t\t #if $rdp\n+\t\t \t\t--rdp\n+\t\t \t#end if\n+\t</command>\n+\t<inputs>\n+\t\t\n+\t\t<param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param>\n+\t\t\n+\t\t<param name="ref_file" type="select" label="Using reference database" help="Select reference from the list">\n+\t \t\t<options from_data_table="frogs_db"></options>\n+\t\t\t<validator type="no_options" message="A built-in database is not available" />\n+\t\t</param> \n+ \t<param name="rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allow you to perform it also with RDP classifier (default No)" />\n+ \n+ <param format="fasta" name="fasta_sequences" type="data" label="OTU seed sequence" help="OTU sequences (format: fasta)."/>\n+ <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="OTU abundances (format: BIOM)."/>\n+\t</inputs>\n+\t<outputs>\n+\t\t<data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation_abundance.biom" from_work_dir="affiliation.biom" />\n+\t\t<data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/>\n+\t</outputs>\n+ <tests>\n+ <test>\n+ <param name="ref_file" value="ITS1_test"/>\n+ <param name="fasta_sequences" value="references/04-filters.fasta"/>\n+ <param name="biom_abundance" value="references/04-filters.biom"/>\n+ <output name="biom_affiliation" file="references/06-affiliation2.biom" compare="sim_size" delta="0" />\n+ <output name="summary" file="references/06-affiliation2.html" compare="diff" lines_diff="0"/>\n+ </test>\n+ <test>\n+ <param name="ref_file" value="ITS1_test"/>\n+ <param name="fasta_sequences" value="references/04-filters.fasta"/>\n+ <param name="biom_abundance" value="references/04-filters.biom"/>\n+ <param name="rdp" value="true"/>\n+ <output name="biom_affiliation" file="references/06-affiliation.biom" compare="sim_size" delta="5" /'..b'\n+\n+All the databases we format (on demand) for RDPClassifier and NCBI Blast+ are inventoried here: http://genoweb.toulouse.inrae.fr/frogs_databanks/assignation/readme.txt\n+\n+.. class:: infomark page-header h2\n+\n+How it works\n+\n+.. csv-table:: \n+ :header: "Steps", "Description"\n+ :widths: 5, 150\n+ :class: table table-striped\n+\n+ "1", "`RDPClassifier <https://rdp.cme.msu.edu/tutorials/classifier/RDPtutorial_RDP_classifier.html>`_ may be used with database to associate to each OTU a taxonomy and a bootstrap (example: *Bacteria;(1.0);Firmicutes;(1.0);Clostridia;(1.0);Clostridiales;(1.0);Clostridiaceae 1;(1.0);Clostridium sensu stricto;(1.0);*)."\n+ "2", "`blastn+ <http://blast.ncbi.nlm.nih.gov/>`_ or `needlall <http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html>`_ is used to find alignment between each OTU and the database. Only the bests hits with the same score are reported. blastn+ is used for merged read pair, and needall is used for artificially combined sequence. For each alignment returned, several metrics are computed: identity percentage, coverage percentage, and alignment length"\n+ "3", "For each OTU with several blastn+/needlall alignment results a consensus is determined on each taxonomic level. If all the taxa at a taxonomic rank are identical the taxon name is reported otherwise *Multi-affiliation* is reported. For example, if you have an OTU with two equivalent hits, associated to *Bacteria;Proteobacteria;Gamma Proteobacteria;Enterobacteriales*, and *Bacteria;Proteobacteria;Beta Proteobacteria;Methylophilales*, the consensus will be *Bacteria;Proteobacteria;Multi-affiliation;Multi-affiliation*."\n+\n+.. class:: infomark page-header h2\n+\n+Alignment metrics details on identity percentage calculation\n+\n+**- Problem with classical %id computation method**\n+\n+* **Case 1: a sequencing of overlapping sequences i.e. 16S V3-V4 amplicon MiSeq sequencing**\n+\n+.. image:: static/images/FROGS_affiliation_overlapped_percent_id.png\n+ :height: 325\n+ :width: 807\n+\n+* **Case 2 : a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing**\n+\n+.. image:: static/images/FROGS_affiliation_combined_percent_id.png\n+ :height: 310\n+ :width: 887\n+\n+**- Finally, how percentage identity is computed ?**\n+\n+With the classical method of %id calculation, filtering on %id will systematically removed \xe2\x80\x9cFROGS combined\xe2\x80\x9d OTUs. So, we proposed to replace the classical %id by a %id computed on the sequenced bases only.\n+\n+.. image:: static/images/FROGS_affiliation_percent_id_formula.png\n+ :height: 36\n+ :width: 637\n+\n+For the precedent use cases we will obtain:\n+\n+* Case 1: 16S V3V4 overlapped sequence\n+\t% sequenced bases identity = 400 matches / 400 bp = 100%\n+\n+* Case 2: very large ITS1 \xe2\x80\x9cFROGS combined\xe2\x80\x9d shorter than the real sequence\n+\t% sequenced bases identity = (250 + 250 ) / (600 - 100) = 100%\n+\n+This calculation allows to return 100% of identity on sequenced bases for \xe2\x80\x9cFROGS combined\xe2\x80\x9d shorter or longer than reality in case of perfect sequencing, and a smaller percentage of identity in the case of small overlap repeat kept in FROGS combined sequence. \n+\n+.. class:: infomark page-header h2\n+\n+\n+Advices\n+\n+This tool can take large time. It is recommended to filter your OTU abundance and sequence files before this tool (see **FROGS OTU Filters**).\n+\n+As you can see the affiliation of each OTU is not human readable in outputed abundance file. We provide a tools to convert these BIOM file in tabulated file, see the **FROGS BIOM to TSV** tool.\n+\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs-support@inrae.fr\n+\n+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers\n+\n+Website: http://frogs.toulouse.inrae.fr/\n+\n+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_\n+\n+\t</help>\n+</tool>\n'

diff -r 000000000000 -r 834843ebe569 affiliation_filters.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/affiliation_filters.xml Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,301 @@\n+<?xml version="1.0"?>\n+\n+<tool id="FROGS_affiliation_filters" name="FROGS Affiliation Filters" version="3.2.2">\n+\t<description>Filters OTUs on several affiliation criteria.</description>\n+ <requirements>\n+ <requirement type="package" version="3.2.2">frogs</requirement>\n+ </requirements>\n+ <stdio> \n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\n+\t<command>\n+\n+\t\taffiliation_filters.py\n+\t\t\t--input-biom $input_biom \n+\t\t\t--input-fasta $input_fasta\n+\t\t\t--output-biom $output_biom\n+\t\t\t--impacted $output_impacted\n+\t\t\t--impacted-multihit $output_multihit\n+\t\t\t--summary $output_summary\n+\n+\t\t\t#if $conditional_mode.mode == "delete"\n+\t\t\t\t--delete\n+\t\t\t\t--output-fasta $output_fasta\n+\t\t\t#else\n+\t\t\t\t--mask\n+\t\t\t#end if\n+\n+\t\t\t--taxonomic-ranks $taxonomic_ranks\n+\n+\t\t\t#if $rdp.rdp_rank\n+\t\t\t\t--min-rdp-bootstrap $rdp.rdp_rank:$rdp.rdp_bootstrap\n+\t\t\t#end if\n+\t\t\n+\t\t\t#if $blast.min_blast_length\n+\t\t\t\t--min-blast-length $blast.min_blast_length\n+\t\t\t#end if\n+\t\t\t#if $blast.max_blast_evalue != None\n+\t\t\t\t#set $eval = \'a\' + str($blast.max_blast_evalue)\n+\t\t\t\t#if $eval != \'a\'\n+\t\t\t\t\t--max-blast-evalue $blast.max_blast_evalue\n+\t\t \t\t#end if\n+\t\t\t#end if\n+\t\t\t#if $blast.min_blast_identity\n+\t\t\t\t--min-blast-identity $blast.min_blast_identity\n+\t\t\t#end if\n+\t\t\t#if $blast.min_blast_coverage\n+\t\t\t\t--min-blast-coverage $blast.min_blast_coverage\n+\t\t\t#end if\n+\n+\t\t\t#set $sep = \' \'\n+ #if $blast.taxon_ignored\n+ \t--ignore-blast-taxa\n+ \t#for $current in $blast.taxon_ignored\n+ \t$sep\'${current.name}\'\n+ \t#end for\n+ #end if\n+\n+\t</command>\n+\t<inputs>\n+\t\t\n+\t\t<param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: fasta)." />\n+\t\t<param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)." />\n+\t\t<param name="taxonomic_ranks" type="text" label="Taxonomic ranks" help="The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space." optional="false" value="Domain Phylum Class Order Family Genus Species" size="80" />\n+\t\t\n+\t\t<conditional name="conditional_mode">\n+\t\t\t<param name="mode" type="select" label="Filtering mode" multiple="false" help="Do you want to delete OTU or hide affiliations" optional="false" display="radio">\n+\t\t\t\t<option value="hide" selected="true">Hidding mode</option>\n+\t\t\t\t<option value="delete">Deleting mode</option>\n+\t\t\t</param>\n+\t\t\t<when value="hide"/>\n+\t\t\t<when value="delete"/>\n+\t\t</conditional>\n+\n+\t\t<section name="blast" title="Filter on Blast affiliations" expanded="true" >\n+\t\t\t<param name="max_blast_evalue" type="float" min="0.0" max="1.0" optional="true" label="Maximum e-value (between 0 and 1)" size="5" help="Fill the field only if you want this treatment" /> \n+\t\t\t<param name="min_blast_identity" type="float" min="0.0" max="1.0" optional="true" label="Minimum identity % (between 0 and 1)" size="5" help="Fill the field only if you want this treatment" />\n+\t\t\t<param name="min_blast_coverage" type="float" min="0.0" max="1.0" optional="true" label="Minimum coverage % (between 0 and 1)" size="5" help="Fill the '..b'the RDP bootstrap criteria is not respected or if none of the blast affiliation respect all the criteria . **In hidding mode**, RDP affiliation is hidden (removed) if the RDP bootstrap criteria is not respected, and independantly, blast affiliations are hidden (removed) if none of the blast affiliation respect all the criteria."\n+ "4", "Write valid OTU into the filtered.biom file with potential Blast affiliation updated and impacting criteria annotations.All impacted/modified OTU with their original metadata are reported in the impacted.tsv file with its associated impacted.multihit.tsv file. Impacting status (OTU_deleted / Affiliation_masked / Blast_taxonomy_changed) and the list of impacting criteria are also reported in the impacted.tsv file."\n+\n+\n+.. class:: infomark page-header h2\n+\n+Advices\n+\n+Imagine that you want to filter out affiliations with:\n+\n+- RDP bootstrap at the Species level less than 0.8\n+- Blast %identity and %coverage less than 100\n+- Blast taxonomies with "unknown species"\n+\n+What will append in these different cases in deleting or hidding mode: \n+\n+- Cluster 1:\n+\n+.. image:: static/images/FROGS_affiliation_filter1.png\n+\n+The RDP taxonomy does not respect the RDP boostrap threshold, but all blast affiliation criteria are respected.\n+\n+In deleting mode, Cluster_1 will be removed. \n+In the summary.html, it will be considered as "Removed", and if the RDP taxonomy and/or the Blast taxonomy is/are not kept thanks to an other OTU, the RDP/Blast taxonomy(ies) will be considered as lost.\n+\n+In hidding mode, RDP taxonomy will be removed, blast taxonomy will remain unchanged and Cluster_1 will be kept.\n+In the summary.html, it will be considered as "Hidden", and if the RDP taxonomy is not kept thanks to an other OTU, the RDP taxonomy will be considered as lost.\n+\n+- Cluster 2:\n+\n+.. image:: static/images/FROGS_affiliation_filter2.png\n+\n+The RDP taxonomy respects the RDP boostrap threshold, but none of the blast affiliations respect all the blast criteria.\n+\n+In deleting mode, Cluster_1 will be removed. \n+In the summary.html, it will be considered as "Removed", and if the two blast taxonomies are not kept thanks to others OTUs, they will be considered as lost. In the same way, if there is no other OTU, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the summary.html. And idem for the RDP taxonomy.\n+\n+In hidding mode, RDP taxonomy will be remain unchanged, blast taxonomy will be removed and Cluster_2 will be kept.\n+In the summary.html, it will be considered as "Hidden", and if the two taxonomies are not kept thanks to others OTUs, they will be considered as lost. In the same way, if there is no other OTU, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the summary.html.\n+\n+- Cluster 3:\n+\n+.. image:: static/images/FROGS_affiliation_filter3.png\n+\n+The RDP taxonomy respects the RDP boostrap threshold, and one of the two blast affiliations respect all the blast criteria.\n+\n+In both deleting and hidding mode, Cluster_1 will be kept. \n+In the summary.html, it will be considered as "Modified", as the RDP taxonomy will remain unchanged and the blast taxonomy will be updated.\n+If no other OTU is affiliated to the "unknown species" of the Fusobacterium genu, this species will be considered as lost. In the same way if no other OTU is affiliated to Fusobacterium genus but with an ambiguous species, 1 Multi-affilaition at the Species level will be considered as lost in the summary.html.\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs-support@inrae.fr\n+\n+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers\n+\n+Website: http://frogs.toulouse.inrae.fr/\n+\n+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_\n+\n+\t</help>\n+</tool>\n'

diff -r 000000000000 -r 834843ebe569 affiliation_postprocess.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/affiliation_postprocess.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,152 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_affiliation_postprocess" name="FROGS Affiliation postprocess" version="3.2.2">
+ <description>Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics</description>
+ <requirements>
+     <requirement type="package" version="3.2.2">frogs</requirement>
+   </requirements>
+   <stdio>
+     <exit_code range="1:" />
+     <exit_code range=":-1" />
+   </stdio>
+ <command>
+ affiliation_postprocess.py
+ #if $is_HVL.HVL_amplicon
+            --reference $is_HVL.ref_file.fields.path
+        #end if
+ --identity $identity
+ --coverage $coverage
+                --input-biom $input_biom
+                --input-fasta $input_fasta
+                --output-biom $biom_out
+                --output-fasta $fasta_out
+                --output-compo $compo_out
+ </command>
+ <inputs>
+ 
+ <param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: fasta)." />
+ <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)." />
+ <conditional name="is_HVL">
+ <param name="HVL_amplicon" type="boolean" label="Is this an amplicon hyper variable in length?" help="Multi-affiliation tag may be resolved by selecting the shortest amplicon reference. For this you need the reference fasta file of your targetted amplicon."/>
+       <when value="true">
+         <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list">
+ <options from_data_table="frogs_HVL_db"></options>
+          <validator type="no_options" message="A built-in database is not available" />
+     
+ </param>
+       </when>
+       <when value="false"/>
+     </conditional>
+
+ <param name="identity" type="float" min="0.0" max="100.0" value="99.0" label="minimum identity for aggregation" help="OTUs will be aggregated if they share the same taxonomy with at least X% identity." />
+ <param name="coverage" type="float" min="0.0" max="100.0" value="99.0" label="minimum coverage for aggregation" help="OTUs will be aggregated if they share the same taxonomy with at least X% alignment coverage." />
+ </inputs>
+ <outputs>
+ <data format="biom1" name="biom_out" label="${tool.name}: affiliation_abundance.biom" from_work_dir="affiliation.biom" />
+ <data format="fasta" name="fasta_out" label="${tool.name}: sequences.fasta" from_work_dir="sequences.fasta" />
+ <data format="tabular" name="compo_out" label="${tool.name}: OTU_aggregation_composition.txt" from_work_dir="aggregation_composition.txt" />
+ </outputs>
+ <tests>
+     <test>
+ <param name="input_biom" value="references/06-affiliation.biom"/>
+ <param name="input_fasta" value="references/04-filters.fasta"/>
+ <conditional name="is_HVL">
+ <param name="HVL_amplicon" value="true"/>
+ <param name="ref_file" value="Unite_extract_ITS1_test"/>
+ </conditional>
+ <output name="compo_out" file="references/08-affiliation_postprocessed.compo.tsv" compare="diff" lines_diff="0" />
+ <output name="fasta_out" file="references/08-affiliation_postprocessed.fasta" compare="diff" lines_diff="0" />
+ <output name="biom_out" file="references/08-affiliation_postprocessed.biom" compare="sim_size" delta="0" />
+     </test>
+ </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+Resolves multi-hit ambiguities if exact amplicon length are available and aggregrated OTUs sharing same taxonomy based on alignment metrics thresholds
+
+
+.. class:: infomark page-header h2
+
+Inputs/outputs
+
+.. class:: h3
+
+Inputs
+
+**Abundance file**:
+
+The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_) with taxonomic affiliations metadata.
+
+**Sequence file**:
+
+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_) of each OTU seed.
+
+**Reference file** (optionnal):
+
+The exact amplicon reference sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
+
+
+.. class:: h3
+
+Outputs
+
+**Abundance file**:
+
+ The abundance file of OTUs and aggregated OTUs, with their affiliation (format `BIOM <http://biom-format.org/>`_) and with potentially less ambiguities.
+
+**Sequence file**:
+
+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_) of each aggregated OTU seed.
+
+**Composition file**:
+
+The aggregation composition file (format text) describing the composition of each resulting OTU.
+
+.. class:: infomark page-header h2
+
+How it works
+
+If a reference fasta file is provided, for each OTU with multiaffiliation, among the different possible affiliations, we only keep the affiliation of the sequence with the shorter length. The aim is to resolve ambiguities due to potential inclusive sequences such as ITS.
+
+Second step is the OTUs aggregation that share the same taxonomy inferred on alignment metrics.
+We start with the most abundant OTU. If an OTU shares at least one affiliation with another OTU with at least I% of identity and C% of alignment coverage, the OTUs are aggregated together : the different affiliations, are merged, blast concensus taxonomy is updated and abundance counts are summed. The seed of the most abundant OTU is kept.
+----
+
+**Contact**
+
+Support: please contact first your galaxy support team.
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 affiliations_stat.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/affiliations_stat.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,170 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="3.2.2">
+ <description>Process some metrics on taxonomies.</description>
+        <requirements>
+                <requirement type="package" version="3.2.2">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>
+ affiliations_stat.py
+     --input-biom $biom
+     --output-file $summary_file
+     --taxonomic-ranks $taxonomic_ranks
+     --rarefaction-ranks $rarefaction_ranks
+     #if $affiliation.affiliation_type == "FROGS_blast"
+      --multiple-tag "blast_affiliations"
+         --tax-consensus-tag "blast_taxonomy"
+         --identity-tag "perc_identity"
+         --coverage-tag "perc_query_coverage"
+ #else if $affiliation.affiliation_type == "FROGS_rdp"
+ --taxonomy-tag "rdp_taxonomy"
+ --bootstrap-tag "rdp_bootstrap"
+ #else
+ --taxonomy-tag "$affiliation.taxonomy_tag"
+ #if $affiliation.bootstrap_tag
+ --bootstrap-tag "$affiliation.bootstrap_tag"
+ #end if
+ #if $affiliation.identity_tag and $affiliation.coverage_tag
+ --identity-tag "$affiliation.identity_tag"
+ --coverage-tag "$affiliation.coverage_tag"
+ #end if
+ #end if
+ </command>
+ <inputs>
+ 
+ <param format="biom1" name="biom" type="data" label="Abundance file" help="OTUs abundances and affiliations (format: BIOM)." optional="false" />
+ 
+ <param name="taxonomic_ranks" type="text" label="Taxonomic ranks" help="The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space." optional="false" value="Domain Phylum Class Order Family Genus Species" size="80" />
+ <param name="rarefaction_ranks" type="text" label="Rarefaction ranks" help="The ranks that will be evaluated in rarefaction. Each rank is separated by one space." optional="false" value="Class Order Family Genus Species" size="80" />
+ <conditional name="affiliation">
+ <param name="affiliation_type" type="select" label="Affiliation processed" help="Select the type of affiliation processed. If your affiliation has been processed with an external tool: use 'Custom'.">
+ <option value="FROGS_blast" selected="true">FROGS blast</option>
+ <option value="FROGS_rdp">FROGS rdp</option>
+ <option value="custom">Custom</option>
+ </param>
+ <when value="FROGS_blast"></when>
+ <when value="FROGS_rdp"></when>
+ <when value="custom">
+ <param name="taxonomy_tag" type="text" label="Taxonomy tag" help="The metadata title in BIOM for the taxonomy." optional="false" value="taxonomy" size="20" />
+ <param name="bootstrap_tag" type="text" label="Bootstrap tag" help="The metadata title in BIOM for the taxonomy bootstrap." value="" size="20" />
+ <param name="identity_tag" type="text" label="Identity tag" help="The metadata tag used in BIOM file to store the alignment identity." value="" size="20" />
+ <param name="coverage_tag" type="text" label="Coverage tag" help="The metadata tag used in BIOM file to store the alignment OTUs coverage." value="" size="20" />
+ </when>
+ </conditional>
+ </inputs>
+ <outputs>
+ <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="summary.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="biom" value="references/09-normalisation.biom" />
+ <param name="rarefaction_ranks" value="Family Genus Species" />
+ <conditional name="affiliation">
+ <param name="affiliation_type" value="FROGS_blast" />
+ <param name="taxonomic_ranks" value="Domain Phylum Class Order Family Genus Species" />
+ <param name="taxonomy_tag" value="blast_taxonomy" />
+ <param name="identity_tag" value="perc_identity" />
+ <param name="coverage_tag" value="perc_query_coverage" />
+ </conditional>
+ 
+ <output name="summary_file" file="references/11-affiliationsStat.html" compare="sim_size" delta="20" />
+ <output name="summary_file" file="references/11-affiliationsStat.html" compare="diff" lines_diff="2" />
+ </test>
+ </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+FROGS Affiliations stat computes several metrics and generates a HTML file describing OTUs based on their taxonomies and eventually the quality of the affiliations.
+
+
+.. class:: infomark page-header h2
+
+Input/output
+
+.. class:: h3
+
+Input
+
+**Abundance file**:
+
+The abundance and affiliation of each OTUs (format `BIOM <http://biom-format.org/>`_). This file can be produced by FROGS Affiliation OTU.
+
+The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format.
+
+.. class:: h3
+
+Output
+
+**Summary file** (summary.html):
+
+ OTUs taxonomies and affiliations metrics (format `HTML <https://en.wikipedia.org/wiki/HTML>`_):
+
+  *-Taxonomy distribution*: display the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample
+
+  .. image:: static/images/FROGS_affiliation_stat_taxonomies.png
+    :height: 380
+    :width: 891
+
+  .. image:: static/images/FROGS_affiliation_stat_rarefaction.png
+    :height: 380
+    :width: 794
+
+  .. image:: static/images/FROGS_affiliation_stat_sunburst.png
+    :height: 380
+    :width: 440
+
+  -Bootstrap distribution: display for affiliation methods with bootstrap the bootstrap on each taxonomic rank
+
+  .. image:: static/images/FROGS_affiliation_stat_bootstrap.png
+    :height: 380
+    :width: 867
+
+  -Alignment distribution: display for affiliation methods with alignment the distribution of identity/covrage
+
+  .. image:: static/images/FROGS_affiliation_stat_alignment.png
+    :height: 380
+    :width: 859
+
+
+
+----
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 biom_to_stdBiom.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_to_stdBiom.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,105 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="3.2.2">
+ <description>Converts a FROGS BIOM in fully compatible BIOM.</description>
+        <requirements>
+            <requirement type="package" version="3.2.2">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>
+ biom_to_stdBiom.py
+                 --input-biom $input_biom
+                 --output-biom $output_biom
+                 --output-metadata $output_blast_details
+ </command>
+ <inputs>
+ 
+ <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The FROGS BIOM file to convert (format: BIOM)." optional="false" />
+ </inputs>
+ <outputs>
+ <data format="biom1" name="output_biom" label="${tool.name}: abundance.standard.biom" from_work_dir="abundance.biom"/>
+ <data format="tabular" name="output_blast_details" label="${tool.name}: all_blast_details.tsv" from_work_dir="blast_details.tsv" />
+ </outputs>
+ <tests>
+ <test>
+ <param name="input_biom" value="references/09-normalisation.biom"/>
+ <output name="output_biom" value="references/13-affiliation_std.biom" compare="sim_size" delta="0" />
+ <output name="output_blast_details" value="references/13-affiliation_multihit.tsv" compare="diff" lines_diff="0" />
+ </test>
+ </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+Converts a BIOM generated by FROGS in generic BIOM.
+
+The detailed blast affiliations can trigger problem with tools like Qiime. This tool extracts the blast details in a second file and writes a BIOM usable in every tools using BIOM.
+
+.. class:: h3
+
+Inputs
+
+**Abundance file**:
+
+The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_).
+
+.. class:: h3
+
+Outputs
+
+**Abundance file**:
+
+ The abundance without the ambiguous blast details (format `BIOM <http://biom-format.org/>`_).
+
+**Blast details file**:
+
+ The details for each alignment on clusters (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_).
+
+
+.. class:: infomark page-header h2
+
+How it works
+
+FROGS BIOM to std BIOM extracts the blast alignment details in a second file, write a BIOM usable in every tools using BIOM and defined the consensus taxonomy provided by blast as main taxonomy.
+
+
+
+----
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 biom_to_tsv.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_to_tsv.xml Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,127 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_biom_to_tsv" name="FROGS BIOM to TSV" version="3.2.2">
+ <description>Converts a BIOM file in TSV file.</description>
+        <requirements>
+            <requirement type="package" version="3.2.2">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>
+ biom_to_tsv.py
+                 --input-biom $biom_file
+               #if $sequence_file
+                 --input-fasta $sequence_file
+               #end if
+                 --output-tsv $tsv_file
+               #if $extract_multi_align
+                 --output-multi-affi $multi_affi_file
+               #end if
+ </command>
+ <inputs>
+ 
+ <param format="biom1" name="biom_file" type="data" label="Abundance file" help="The BIOM file to convert (format: BIOM)." optional="false" />
+ <param format="fasta" name="sequence_file" type="data" label="Sequences file (optional)" help="The sequences file (format: fasta). If you use this option the sequences will be add in TSV." optional="true" />
+ 
+ <param name="extract_multi_align" type="boolean" label="Extract multi-alignments" help="If you have used FROGS affiliation on your data, you can extract information about multiple alignements in a second TSV." checked="true"/>
+ </inputs>
+ <outputs>
+ <data format="tabular" name="tsv_file" label="${tool.name}: abundance.tsv" from_work_dir="abundance.tsv"/>
+ <data format="tabular" name="multi_affi_file" label="${tool.name}: multi-affiliations.tsv" from_work_dir="multi_hits.tsv" >
+ <filter>extract_multi_align</filter>
+ </data>
+ </outputs>
+ <tests>
+ <test>
+ <param name="biom_file" value="references/09-normalisation.biom"/>
+ <param name="sequence_file" value="references/09-normalisation.fasta"/>
+ <param name="extract_multi_align" value="true"/>
+ <output name="tsv_file" value="references/12-biom2tsv.tsv" compare="diff" lines_diff="0"/>
+ <output name="multi_affi_file" value="references/12-biom2tsv-affiliation_multihit.tsv" compare="diff" lines_diff="0"/>
+ </test>
+ </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+Converts a BIOM file in TSV file.
+
+.. class:: h3
+
+Inputs
+
+**Abundance file**:
+
+The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_).
+
+**Sequence file [optional]**:
+
+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
+
+.. class:: h3
+
+Outputs
+
+**Abundance file**:
+
+ The abundance of each cluster in each sample and theirs metadata (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_).
+
+ If you add the sequences file, this information is added for each cluster.
+
+**Multiple affiliation file**:
+
+ If you have used *FROGS affiliation* on your data, each OTU can have several affiliations: several alignments with same score on reference database. The multiple affiliation file contains details on these possibles affiliations (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_).
+
+
+.. class:: infomark page-header h2
+
+How it works
+
+FROGS Biom to Tsv will search if any metadata are available, and the OTU sequence if fasta file is precised. Then it will extract the OTU name, sum the sample abundance, and extract the detailed abundance for each sample. Finally it will write all these fields separated by tabulation in the TSV file.
+
+
+.. class:: infomark page-header h2
+
+Advices
+
+This output tsv file is easily readable in any spreadsheet software. Be aware that these software have a number of line limit (1 048 576 for Excel and LibreOffice calc ate least). If you have more OTU, use **FROGS Filters** to extract for example the most abundant OTU before converting your BIOM abundance table in TSV file.
+
+
+----
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clustering.xml Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,222 @@\n+<?xml version="1.0"?>\n+\n+<tool id="FROGS_clustering" name="FROGS Clustering swarm" version="3.2.2">\n+ <description>Single-linkage clustering on sequences</description>\n+ <requirements>\n+ <requirement type="package" version="3.2.2">frogs</requirement>\n+ <requirement type="package" version="3.0.0">swarm</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+ <command>\n+ clustering.py \n+ --nb-cpus \\${GALAXY_SLOTS:-1}\n+ --input-fasta $sequence_file\n+ --input-count $count_file\n+ --output-biom $abundance_biom\n+ --output-fasta $seed_file\n+ --output-compo $swarms_composition\n+ \n+ #if $FROGS_guidelines.guidelines_version == "3.2"\n+ \t--distance $FROGS_guidelines.maximal_distance\n+ $FROGS_guidelines.fastidious\n+ #end if\n+\n+ #if $FROGS_guidelines.guidelines_version == "3.1"\n+ \t--distance $FROGS_guidelines.maximal_distance\n+ \t$FROGS_guidelines.denoising\n+ #end if\n+ \n+ </command>\n+ <inputs>\n+ \n+ <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The dereplicated sequences file (format: fasta)." optional="false" />\n+ <param format="tabular" name="count_file" type="data" label="Count file" help="It contains the count by sample for each sequence (format: TSV)." optional="false" />\n+ \n+ <conditional name="FROGS_guidelines">\n+ <param name="guidelines_version" type="select" label="FROGS guidelines version" help="Denoising step prior to a d3 clustering is no more recommended since FROGS 3.2, but you can still choose it.">\n+ <option value="3.2" selected="true">New guidelines from version 3.2</option>\n+ <option value="3.1">First guidelines until 3.1</option>\n+ </param>\n+ <when value="3.2">\n+ \t<param name="maximal_distance" type="integer" label="Aggregation distance clustering" help="Maximum number of differences between sequences in each aggregation swarm step. (recommended d=1)" value="1" min="1" max="15" optional="false" />\n+ <param name="fastidious" type="boolean" checked="true" truevalue="--fastidious" falsevalue="" label="Refine OTU clustering" help="Clustering will be performed with the swarm --fastidious option, which is recommended and only usable in association with a distance of 1 (default and recommended: Yes)"/>\n+ </when>\n+ <when value="3.1">\n+ \t<param name="maximal_distance" type="integer" label="Aggregation distance clustering" help="Maximum number of differences between sequences in each aggregation swarm step." value="3" min="1" max="15" optional="false" />\n+ <param name="denoising" type="boolean" checked="true" truevalue="--denoising" falsevalue="" label="Efficient denoising ? (equals '..b'. This format is widely used in metagenomic software.\n+\n+\n+**Clusters seeds** (seed_sequences.fasta):\n+\n+ The clusters representative sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).\n+\n+ \n+**Clusters composition** (swarms_composition.tsv):\n+\n+ A text file representing the read composition of each cluster (format txt). Each line represents one cluster and is composed of read identifier separated by space.\n+\n+\n+.. class:: infomark page-header h2\n+\n+How it works\n+\n+.. csv-table:: \n+ :header: "Steps", "Without denoising", "With fastidious option (recommendations sincce FROGS 3.2)", "With denoising step (recommendations until FROGS 3.1)"\n+ :widths: 5, 150, 150, 150\n+ :class: table table-striped\n+\n+ "1", "Sorting the reads by their abundance", "Sorting the reads by their abundance", "Sorting the reads by their abundance"\n+ "2", "/", "/", "Clusters the reads (`Swarm <https://github.com/torognes/swarm>`_) with an agglomeration distance of 1"\n+ "3", "/", "/", "Sorting the pre-clusters sequences by their abundance"\n+ "4", "Clusters the reads (`Swarm <https://github.com/torognes/swarm>`_) with the distance you specified", "Clusters the reads (`Swarm <https://github.com/torognes/swarm>`_) with the distance you specified and the (`--fastidious option of swarm <https://github.com/torognes/swarm/blob/master/README.md#refine-swarm-otus>`_)", "Clusters the pre-clusters sequences (`Swarm <https://github.com/torognes/swarm>`_) with the distance you specified"\n+\n+**Swarm focus**\n+\n+Swarm use an iterative growth process and the use of sequence abundance values to delineate OTUs.\n+ \n+.. image:: static/images/FROGS_cluster_swarm.png\n+ :height: 223\n+ :width: 666 \n+\n+In each groth step the sequence of the previous step is used to find the others sequences with a number of differences inferior or equal to the "Aggregation distance".\n+\n+After agregation Swarm refines the clusters by looking at the abundancies along the connections. Theoritically the abundances must decrease when you are going away from the seed (which is often the most abundant sequence). If this abundance raises again it means that two different clusters are connected by some poorly abundant sequences, so swarm cut the connection.\n+\n+On the other hand, the fastidious option of swarm allow to aggregate small and rare cluster into bigger one if they share sequence with at most 2*d distance. In this case d is restricted to 1 so, cluster distance will be 2. (image extracted from `Swarm github <https://github.com/torognes/swarm>`_)\n+\n+.. image:: static/images/FROGS_cluster_fastidious.png\n+ :height: 319\n+ :width: 681\n+ \n+.. class:: infomark page-header h2\n+\n+\n+Advices\n+\n+The fastidious strategy is recommended since FROGS 3.2\n+\n+The fastidious option is recommended with an aggregating distance of 1. "It will reduce the number of small OTUs while maintaining a high clustering resolution, by postulating the existence of an intermediate amplicon sequences"\n+\n+The denoising strategy was recommended until FROGS 3.1\n+\n+The denoising step allows to build very fine clusters with minimal differences. In this case, the number of differences between sequences of each crowns is equal to 1. This first clustering is extremly quick. After the denoising, a second swarm is run with an aggregation distance >1 as you have configured, between seeds from this first clustering. We recommended a distance of 3.\n+ \n+To have some metrics on your clusters, you can use the tool **FROGS Clusters Stat**.\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs-support@inrae.fr\n+\n+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers\n+\n+Website: http://frogs.toulouse.inrae.fr/\n+\n+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_\n+\n+ </help>\n+</tool>\n'

diff -r 000000000000 -r 834843ebe569 clusters_stat.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clusters_stat.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,118 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_clusters_stat" name="FROGS Clusters stat" version="3.2.2">
+ <description>Process some metrics on clusters.</description>
+        <requirements>
+                <requirement type="package" version="3.2.2">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>
+ clusters_stat.py
+                  --input-biom $biom
+                  --output-file $summary_file
+ </command>
+ <inputs>
+ <param format="biom1" name="biom" type="data" label="Abundance file" help="Clusters abundance (format: BIOM)." optional="false" />
+ </inputs>
+ <outputs>
+ <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="summary.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="biom" value="references/09-normalisation.biom"/>
+ <output name="summary_file" value="references/10-clustersStat.html" compare="diff" lines_diff="0"/>
+ </test>
+ </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+FROGS Clusters stat computes several metrics and generates a HTML file describing clusters based on abundances, samples, ...
+
+
+.. class:: infomark page-header h2
+
+Input/output
+
+.. class:: h3
+
+Input
+
+**Abundance file**:
+
+The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_).
+
+The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format.
+
+.. class:: h3
+
+Output
+
+**Summary file** (summary.html):
+
+ *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables
+
+ .. image:: static/images/FROGS_cluster_stat_clusterDistrib1.png
+    :height: 1180
+    :width: 900
+
+ *Sequences distributions* : describes the sequences distribution among clusters
+
+ .. image:: static/images/FROGS_cluster_stat_seq_dist.png
+
+ *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering <http://en.wikipedia.org/wiki/Hierarchical_clustering>`_ on samples abundance profile (distance method = `braycurtis <http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis>`_, linkage method = average)
+
+ .. image:: static/images/FROGS_cluster_stat_sample_dist1.png
+    :height: 400
+    :width: 700
+
+ .. image:: static/images/FROGS_cluster_stat_sample_dist2.png
+    :height: 350
+    :width: 610
+
+.. class:: infomark page-header h2
+
+Advices
+
+This is a very usefull tool to see the evolution of your OTU. Do not hesitate to run this tool after each FROGS step beginning at the clustering step.
+
+
+----
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 conda_toolshed_frogs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/conda_toolshed_frogs Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,136 @@
+####################################################
+
+1) construction prerelease FROGS
+2) recette conda sur channel conda perso
+3) ( fork bioconda ) / ( creation branche frogs ) / ajout/update recette frogs / pull request
+4) planemo test
+5) construction prerelease FROGS-wrappers
+6) planemo shed_create --shed_target testtoolshed (update FROGS-wrappers/.shed.yml compte owner oinizan + version et URL de répo)
+ ==> planemo shed_update --shed_target testtoolshed si update
+7) planemo shed_create --shed_target toolshed (update FROGS-wrappers/.shed.yml compte owner frogs)
+
+####################################################
+
+
+
+
+ Comment faire un paquet conda (doc sur github bioconda)
+
+init:
+ fork de bioconda-recipes (github bioconda)
+ git clone https://github.com/mariabernard/bioconda-recipes.git
+ # pour mettre à jour le fork (upstream), avec le code de bioconda (origin)
+ git pull origin
+ ajout de ton recette conda
+ tester avec la chaine d'intégration circleci (cf github bioconda-recipes : https://bioconda.github.io/contrib-setup.htm)
+ou
+ conda-build ==> conda build / conda-build n'est pas fourni par défaut.==> faire un environnement conda spécifique à conda-build et faire le build dans l'env.
+ si test ok alors pullrequest via interface github à partir de la page du fork.
+ si souhait de faire test sur un channel perso alors anaconda upload (indiqué en commentaire à la fin) ==> à condition d'avoir paramétrer conda pour indiquer sur quel channel écrire.
+
+mise à jour:
+ faire un fetch de son fork
+ puis modif
+
+recette conda:
+ meta.yaml = liste des dépendances
+ build.sh = script d'install, autrement dit gestion de l'arborescence/ creation de liens symboliques
+
+
+1 check package dans conda  (ex : ITSx)
+ ajout dans meta.yaml
+
+ si paquet n'existe pas, alors il faut le créer. meta.yaml quasi vide, build.sh permet de faire le download et les compilation si necessaire.
+
+
+
+ Utiliser conda
+
+# pour lister les environnements disponibles
+
+~/miniconda3/bin/conda env list
+
+# pour installer un environnement
+ # pour ajouter un channel (ici vmarcon)
+
+~/miniconda3/bin/conda config --add channels vmarcon
+
+ # pour installer en précisant la version (@3.0.0)
+
+~/miniconda3/bin/conda create -n __frogs@3.1.0 frogs=3.1.0
+
+# pour charger un environnement (see env list)
+
+source ~/miniconda3/bin/activate <envName>@<version>
+
+# pour quitter
+
+source deactivate
+
+# pour supprimer un environnement
+
+ conda env remove -n <envName>
+
+# pour upgrade un env
+ conda env upgrade -n <envName>
+
+ Comment déposer sur le toolshed
+
+le github FROGS_wrapper doit contenir un dossier test-data qui correspond au dossier pour la section test des wrappers
+contient les fichiers loc
+
+
+1) Ajout dans les wrappers :
+ des requirements
+ des codes de sortie
+ section test
+
+
+2) Test des wrappers avec planemo
+
+ - installer planemo !!! avec Ubuntu c'est cool
+
+ # creation d'un environnement virtuel
+ virtualenv .planemo
+ # activation de l'environnement
+ . ~/.planemo/bin/activate
+ # installation avec pip (>= 7)
+ pip install planemo
+    # upgrade
+    pip install -U planemo
+
+ - Utilisation de planemo
+
+# activation de l'environnement
+. ~/planemo/bin/activate
+
+test de la structure et la dispo des dépendances sous conda:
+ planemo lint --conda_requirements <tool>.xml
+
+ failed si pas de citation alors que ce n'est qu'un warning.
+
+test de la création de l'environnement
+ planemo conda_install <tool>.xml
+ ==> cela va créer un env __<dependency_tool>@<version>
+
+test la section tests
+ planemo test <tool>.xml (note: lors du premier test il fait un install de Galaxy)
+
+# tant que la recette conda n'est pas sur bioconda, il faut ajouter le channel de test"
+ planemo test <tool>.xml --conda_channels "vmarcon,defaults,bioconda,conda-forge"
+
+ # option utile
+ --no_cleanup        Do not cleanup temp files created for and by Galaxy.
+
+publication sur toolshed
+ via l'interface
+ via planemo
+ créer un .shed.yaml
+ définition d'un catégorie (check sur le web)
+ du owner
+ description
+ planemo shed_init # à compléter
+ planemo shed_create --shed_target testtoolshed # premier dépôt : dépôt frogs (sans nom de version a été créé lors de la mise en ligne de la version 3.2.1)
+ planemo shed_update --shed_target testtoolshed # nouvelle release : pour toutes les prochaines release il suffit de faire un update
+
+Dans .planemo.yml définition des login de compte toolshed, l'idée est de partager une clé pour pouvoir pousser à plusieurs.

diff -r 000000000000 -r 834843ebe569 demultiplex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/demultiplex.xml Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,197 @@\n+<?xml version="1.0"?>\n+\n+<tool id="FROGS_demultiplex" name="FROGS Demultiplex reads" version="3.2.2">\n+\t<description>Attribute reads to samples in function of inner barcode.</description>\n+ <requirements>\n+ <requirement type="binary">perl</requirement>\n+ <requirement type="package" version="3.2.2">frogs</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\t<command>\n+\t\tdemultiplex.py\n+\t\t#if str( $fastq_input.fastq_input_selector ) == "paired":\n+\t\t --input-R1 \'${fastq_input.fastq_input1}\' \n+\t\t --input-R2 \'${fastq_input.fastq_input2}\'\n+\t\t#else:\n+\t\t --input-R1 \'${fastq_input.fastq_input1}\'\n+\t\t#end if \n+\t\t --input-barcode $barcode_file\n+\t\t --mismatches $mismatches\n+\t\t --end $end\n+\t\t --summary $summary\n+\t\t --output-demultiplexed $demultiplexed_archive\n+\t\t --output-excluded $undemultiplexed_archive\n+\t</command>\n+\t<inputs>\n+\t\t\n+\t\t<param format="tabular" name="barcode_file" type="data" label="Barcode file" help="This file describes barcodes and samples (one line by sample tabulated separated from barcode sequence(s)). See Help section" optional="false" />\n+\t\t\n+\t\t<conditional name="fastq_input">\n+\t \t<param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single-end data">\n+\t \t\t<option value="single">Single</option>\n+\t \t<option value="paired">Paired</option>\n+\t </param>\n+\t \t<when value="paired">\n+\t \t<param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" help="Specify dataset of your forward reads"/>\n+\t \t<param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" help="Specify dataset of your reverse reads"/>\n+\t </when>\n+\t <when value="single">\n+\t \t<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" help="Specify dataset of your single end reads"/>\n+\t \t</when>\n+\t \t</conditional>\n+\n+\t\t\n+\t\t<param name="mismatches" type="integer" label="Barcode mismatches" help="Number of mismatches allowed in barcode" value="0" optional="false" />\n+\t\t<param name="end" type="select" label="Barcode on which end ?" help="The barcode is placed either at the beginning of the forward end or of the reverse end or both?">\n+\t\t\t<option value="bol" selected="true">Forward</option>\n+\t\t\t<option value="eol">Reverse</option>\n+\t\t\t<option value="both">Both ends</option>\n+\t\t</param>\n+\t</inputs>\n+\t<outputs>\n+\t\t<data name="demultiplexed_archive" format="tar" label="${tool.name}: demultiplexed.tar.gz" from_work_dir="demultiplexed.tar.gz"/>\n+\t\t<data name="undemultiplexed_archive" format="tar" label="${tool.name}: undemultiplexed.tar.gz" from_work_dir="undemultiplexed.tar.gz"/>\n+\t\t<data name="summary" format="tabular" label="${tool.name}: report" from_work_dir="report.tsv"/>\n+\t</outputs>\n+ <tests>\n+ <test>\n+ <param name="barcode_file" value="input/demultiplex_barcode.txt"/>\n+\t\t\t<conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="paired"/>\n+ </conditional>\n+ <param na'..b'+\n+ "FQ_INPUT1", "Fastq input file for the first read (single-end or forward read of paired-end sequences)"\n+ "FQ_INPUT2", "Fastq input file for the second read (only for paired-end sequences)"\n+ "TXT_BARCODE", "Tabulated text file that describes barcode sequences used to multiplexe samples: SAMPLE_NAME BARCODE1 [BARCODE2]"\n+\n+**Options**\n+\n+.. csv-table::\n+ :header: "Option name", "Meaning"\n+ :widths: 20, 80\n+ :class: table table-striped\n+\n+ "-m/--mismatches MISMATCH", "Number of allowed mismatch in each barcode"\n+ "-e/--end END", "To which end must the barcode be found : forward (begin of the (first) read), reverse (end of the (second) read) or both"\n+\n+**Outputs**\n+\n+.. csv-table:: \n+ :header: "Output name", "Meaning"\n+ :widths: 20, 80\n+ :class: table table-striped\n+\n+ "TXT_SUMMARY_OUTPUT", "A tabulated text file which summarises the number of sequences (single or paired) for each sample"\n+ "TARGZ_DEMULT_ARCHIVE_OUTPUT", "A TAR.GZ archive that contains all fastq files for each sample"\n+ "TARGZ_UNDEMULT_ARCHIVE_OUTPUT", "A TAR.GZ archive that contains all fastq files for undemultiplexed reads"\n+\n+.. class:: h3\n+\n+Format\n+\n+INPUT FILE :\n+ Sequence input file(s) are expected to be in `fastq format <https://en.wikipedia.org/wiki/FASTQ_format>`_\n+\n+BARCODE_FILE :\n+ This file is expected to be tabulated\n+\t\t\n+ -first column corresponds to the sample name\n+ \n+ -second column corresponds to the sequence barcode used\n+ \n+ -third column (optional) corresponds to the reverse sequence barcode\n+ \n+.. class:: warningmark\n+\n+ Take care to indicate sequence barcode in the strand of the read, so you may need to reverse complement the reverse barcode sequence\n+\n+.. class:: warningmark\n+\n+ All barcode sequences must have the same length\n+ \n+Example of barcode file: Here the sample is multiplexed by both fragment ends.\n+\n+ .. image:: static/images/FROGS_demultiplex_barcode.png\n+ :height: 60\n+ :width: 316\n+\n+.. class:: infomark page-header h2\n+\n+How it works\n+\n+For each sequence or sequence pair, the sequence fragment at the beginning (forward multiplexing) of the (first) read or at the end (reverse multiplexing) of the (second) read will be compared to all barcodes of the barecode file.\n+\n+If this fragment is found once and only once (regarding the mismatch threshold), the fragment is trimmed and the sequence will be attributed to the corresponding sample.\n+\n+Finally fastq files (or pair of fastq files) for each sample are included in an archive and a report, describing how many sequences are attributed for each sample, is created.\n+\n+\n+.. class:: infomark page-header h2\n+\n+Advices\n+\n+Do not forget to indicate barcode sequence as they really are in the fastq sequence file, especially if you have multiplexed data via the reverse strand.\n+\n+For the mismatch threshold, we advised to let the threshold to 0. Then if you are not satisfied by the result try with 1. The number of mismatches depends on the length of the barcode, but frequently this sequences are very short so 1 mismatch is already more than the sequencing error rate.\n+\n+If you have different barcode lengths, you must demultiplex your data in several steps, beginning by the longest barcode set. Then to trim the barcodes with smaller lengths, you need to use the "unmatched" sequences file from the previous step with smaller barcodes and so on.\n+\n+If you have Roche 454 sequences in sff format, you must convert them with some programs like `sff2fastq <https://github.com/indraniel/sff2fastq>`_ or sff_to_fastq (installable in Galaxy)\n+\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs-support@inrae.fr\n+\n+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers\n+\n+Website: http://frogs.toulouse.inrae.fr/\n+\n+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_\n+\n+\t</help>\n+</tool>\n'

diff -r 000000000000 -r 834843ebe569 deseq2_preprocess.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq2_preprocess.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,139 @@
+<?xml version="1.0"?>
+
+<tool name="FROGSSTAT DESeq2 Preprocess" id="FROGSSTAT_DESeq2_Preprocess" version="3.2.2">
+  <description>import a Phyloseq object and prepare it for DESeq2 differential abundance analysis </description>
+  <requirements>
+      <requirement type="package" version="3.2.2">frogs</requirement>
+      <requirement type="package" version="3.6.3">r-base</requirement>
+      <requirement type="package" version="3.6">r-essentials</requirement>
+      <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>
+      <requirement type="package" version="1.26.0">bioconductor-deseq2</requirement>
+      <requirement type="package" version="1.6.6">r-optparse</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" />
+      <exit_code range=":-1" />
+  </stdio>
+ <command>deseq2_preprocess.py --data $data
+                                #if $multiple.seconde
+                                  --var $var1${multiple.mod}${multiple.var2}
+                                #else
+                                  --var $var1
+                                #end if
+                                --out-Rdata $dds
+ </command>
+    <inputs>
+   
+      <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGSSTAT Phyloseq Import Data with normalise option set to NO (DESeq2 is more powerful on unnormalised counts)." optional="false">
+        <validator type="empty_field" message="This parameter is required." />
+      </param>
+      
+   <param name="var1" type="text" label="Experimental variable" help="The factor suspected to have an effect on OTUs' abundances. Ex: Treatment, etc." optional="false" value="" size="20">
+        <validator type="empty_field" message="This parameter is required." />
+      </param>
+   <conditional name="multiple">
+        <param name="seconde" type="boolean" label="Do you want to correct for a confounding factor?" help="If yes, specifiy counfouding factor." optional="false" />
+     <when value="false"></when>
+     <when value="true">
+          <param name="var2" type="text" label="Variable 2" help="Confounding factor. Ex: Gender, etc." optional="false" value="" size="20"/>
+          <param name="mod" type="select" multiple="false" help="Choose an additive model (+) if the effects of Treatment and Gender are independent. Choose a model with interaction (*) if the effect of Treatment is expected to depend on Gender." label="Type of model">
+            <option value="+" selected="true">Linear (+)</option>
+            <option value="*">Interaction (*)</option>
+          </param>
+        </when>
+      </conditional>
+    </inputs>
+    <outputs>
+      <data format="rdata" name="dds" label="${tool.name}: dds.Rdata" from_work_dir="DESeq2_preprocess.Rdata"/>
+    </outputs>
+    <tests>
+      <test>
+         <param name="data" value="references/16-phylo_import.Rdata" />
+         <param name="var1" value="EnvType"/>
+         <output name="dds" file="references/23-deseq2_preprocess.Rdata" compare="sim_size" delta="0"/>
+      </test>
+    </tests>
+    <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+Launch Rscript to compute differential abundance analysis using `DESeq2 <https://bioconductor.org/packages/release/bioc/html/DESeq2.html>`_ on a `Phyloseq <https://joey711.github.io/phyloseq/>`_ object.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**phyloseq object** (format rdata):
+A phyloseq object stored in a rdata file.
+This file is the result of FROGSSTAT Phyloseq Import Data.
+
+.. class:: warningmark
+
+We need unnormalised data to analyse the abundance differencies.
+
+.. class:: h3
+
+Ouput
+
+**dds object** (format rdata):
+A DESeq2 dataset (dds) stored in rdata file.
+This result will be one of the input of the FROGSSTAT DESeq Visualisation tool.
+
+.. class:: infomark page-header h2
+
+How it works
+
+The DESeq function performs a default analysis through the steps:
+
+       1. estimation of size factors: ‘estimateSizeFactors’
+
+       2. estimation of dispersion: ‘estimateDispersions’
+
+       3. Negative Binomial GLM fitting and Wald statistics:
+          ‘nbinomWaldTest’
+
+You must precise at least on variable on which the differential abundances will be compared.
+
+You may precise a confounding factor, by adding an other variable and precise the relation between the two variables:
+
+- + for independant variables
+- * for interacting variables
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 deseq2_visualisation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq2_visualisation.xml Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,188 @@\n+<?xml version="1.0"?>\n+\n+<tool name="FROGSTAT Deseq2 Visualisation" id="FROGSSTAT_DESeq2_Visualisation" version="3.2.2">\n+ <description>to extract and visualise differentially abundant OTUs</description>\n+ <requirements>\n+ <requirement type="package" version="3.2.2">frogs</requirement>\n+ <requirement type="package" version="3.6.3">r-base</requirement>\n+ <requirement type="package" version="3.6">r-essentials</requirement>\n+ <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>\n+ <requirement type="package" version="1.26.0">bioconductor-deseq2</requirement>\n+ <requirement type="package" version="0.17">r-dt</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+ <command>deseq2_visualisation.py --phyloseqData $input_phyloseq\n+ --dds $input_DDS\n+ --var $var\n+ #if $varType.vartType_selected == "qual":\n+ --mod1 $varType.mod1 --mod2 $varType.mod2\n+ #end if\n+ --padj $padj\n+ --html $html\n+ </command>\n+ <inputs>\n+ \n+ <param format="rdata" name="input_phyloseq" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data, used in FROGSSTAT DESeq2 Preprocess tool" optional="false">\n+ <validator type="empty_field" message="This parameter is required." />\n+ </param>\n+ <param format="rdata" name="input_DDS" type="data" label="DESeq2 object (format rdata)" help="This is the result of FROGSSTAT DESeq2 Preprocess tool." optional="false">\n+ <validator type="empty_field" message="This parameter is required." />\n+ </param> \n+ \n+ <param name="var" type="text" label="Experimental variable" help="The factor suspected to have an effect on OTUs\' abundances (one of the variables used in FROGS DESeq2 Preprocess tool). Ex : Treatment" optional="false" value="" size="20">\n+ <validator type="empty_field" message="This parameter is required." />\n+ </param>\n+ <conditional name="varType">\n+ <param type="select" name="vartType_selected" label="Is your Variable quantitative or qualitative?" help="If qualitative, choose 2 conditions to compare." optional="false">\n+ <option value="qual">qualitative</option>\n+ <option value="quant">quantitative</option>\n+ </param>\n+ <when value="qual">\n+ <param type="text" name="mod1" label="Condition 1 considered as reference" help="One condition of the experimental variable (e.g. with)." optional="false" value="" size="20">\n+ <validator type="empty_field" message="This parameter is required." />\n+ </param>\n+ <param type="text" name="mod2" label="Condition 2 to be compared to the reference" help="Another condition of the experimental variable (e.g. without)." optional="false" value="" size="20">\n+ '..b' \n+ <has_text text=\'52.445510949046\' />\n+ \n+ <has_text text=\'21.6625060651457\' />\n+ \n+ <has_text text=\'2.20892675663989\' />\n+ \n+ <has_text text=\'1.0525195975273e-22\' />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+\n+.. image:: static/images/FROGS_logo.png \n+ :height: 144\n+ :width: 110\n+\n+.. class:: infomark page-header h2\n+\n+What it does\n+\n+Launch one Rmarkdown Script to visualise the DESeq2 results. \n+\n+.. class:: infomark page-header h2\n+\n+Inputs/Outputs\n+\n+.. class:: h3\n+\n+Input\n+\n+**phyloseq object** (format rdata):\n+One phyloseq object stored in a rdata file.\n+This file is the result of FROGSSTAT Phyloseq Import Data.\n+\n+**dds object** (format rdata):\n+A DESeq2 dataset (dds) stored in rdata file.\n+This file is the result of FROGSSTAT DESeq2 preprocess.\n+\n+.. class:: h3\n+\n+Ouput\n+\n+**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): visualisation of "Differential Abundance".\n+\n+The html file contains Table, Pie Chart, MA plot, Volcano plot and Heatmap plot. If the experimental variable is qualitative, only samples corresponding to the 2 compared conditions are shown in the Heatmap. Otherwise, samples are sorted in increasing order of the experimental variable. \n+\n+Table containing the differentially abundant OTUs.\n+\n+ .. image:: static/images/FROGS_DESeq2_html_table.png \n+ :height: 354\n+ :width: 1153\n+\n+Pie Chart, MA plot and Volcano plot\n+\n+ .. image:: static/images/FROGS_DESeq2_html_pieChart.png \n+ :height: 391\n+ :width: 563\n+\n+ .. image:: static/images/FROGS_DESeq2_html_MA_plot.png \n+ :height: 324\n+ :width: 525\n+\n+ .. image:: static/images/FROGS_DESeq2_html_Volcano_plot.png\n+ :height: 576\n+ :width: 720\n+\n+Heatmap plot corresponding to the differentially abundant OTUs.\n+\n+ .. image:: static/images/FROGS_DESeq2_html_heatmap_plot.png \n+ :height: 576\n+ :width: 720\n+\n+.. class:: infomark page-header h2\n+\n+How it works\n+\n+Based on the variable you precise to construct the model in FROGSSTAT DESeq2 Preprocess, this tool will construct table and graphs to visualise diff\xc3\xa9rentially abundant OTU between condition of the selected variables.\n+\n+You may first precise the variable used to construct the model during the FROGSSTAT DESeq Preprocess step. If you precised variable with a confounding factor (a second variale), you may choose between one of the variables, but remember that you will see the result of this variable corrected by the confounding factor (and reversely) not just the selected variable itself.\n+\n+If the variable is qualitative (ex: variable Treatment is define by two conditions : treatment1, treatment2, control), you must specify 2 conditions to compare (e.g. treatment1 vs treatment2 or treatment1 vs control, ...). \n+\n+**Contact**\n+\n+Contacts: frogs-support@inrae.fr\n+\n+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers\n+\n+Website: http://frogs.toulouse.inrae.fr/\n+\n+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_\n+ \n+ </help>\n+</tool>\n'

diff -r 000000000000 -r 834843ebe569 galaxy_project_logo_square.png

Binary file galaxy_project_logo_square.png has changed

diff -r 000000000000 -r 834843ebe569 itsx.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/itsx.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,184 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_itsx" name="FROGS ITSx" version="3.2.2">
+ <description>Extract the highly variable ITS1 and ITS2 subregions from ITS sequences.</description>
+    <requirements>
+        <requirement type="package" version="3.2.2">frogs</requirement>
+        <requirement type="package" version="1.1.2">itsx</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+ <command>
+ itsx.py
+                 --nb-cpus \${GALAXY_SLOTS:-1}
+                 --region $region
+                 --input-fasta $input_fasta
+                 --input-biom $input_biom
+                 --out-fasta $out_fasta
+                 --out-abundance $out_abundance_biom
+                 --out-removed $out_excluded
+                 --summary $summary_file
+                 --organism-groups $domain
+                 $trim_sequence
+
+ </command>
+ <inputs>
+ 
+ <param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: fasta)." />
+ <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)." />
+ <param name="region" type="select" label="ITS region" help="Which fungal ITS region is targeted: either ITS1 or ITS2" >
+ <option value="ITS1">ITS1</option>
+ <option value="ITS2">ITS2</option>
+ </param>
+ <param name="trim_sequence" type="boolean" checked="false" truevalue="" falsevalue="--check-its-only" label="Trim conserved sequence (SSU, 5.8S, LSU) ?" help="If Yes, only part of the sequences with ITS signature will be kept, SSU, LSU or 5.8S regions will be trimmed. (default : No)"/>
+ <param name="domain" type="select" label="Choose pertinent organisms to scan?" help="Save a lot of time by checking pertinent organism group model to scan." optional="false" multiple="true" display="checkboxes">
+ <option value="F" selected="true" >Fungi</option>
+ <option value="A">Alveolata</option>
+ <option value="B">Bryophyta</option>
+ <option value="C">Bacillariophyta</option>
+ <option value="D">Amoebozoa</option>
+ <option value="E">Euglenozoa</option>
+ <option value="G">Chlorophyta</option>
+ <option value="H">Rhodophyta</option>
+ <option value="I">Phaeophyceae</option>
+ <option value="L">Marchantiophyta</option>
+ <option value="M">Metazoa</option>
+ <option value="O">Oomycota</option>
+ <option value="P">Haptophyceae</option>
+ <option value="Q">Raphidophyceae</option>
+ <option value="R">Rhizaria</option>
+ <option value="S">Synurophyceae</option>
+ <option value="T">Tracheophyta</option>
+ <option value="U">Eustigmatophyceae</option>
+ 
+ 
+ </param>
+ </inputs>
+ <outputs>
+ <data format="fasta" name="out_excluded" label="${tool.name}: nonITS_sequence.fasta" from_work_dir="out_removed.fasta"/>
+ <data format="fasta" name="out_fasta" label="${tool.name}: ITS_sequence.fasta" from_work_dir="itsx.fasta"/>
+ <data format="biom1" name="out_abundance_biom" label="${tool.name}: itsx_abundance.biom" from_work_dir="itsx.biom"/>
+ <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="input_fasta" value="references/04-filters.fasta"/>
+ <param name="input_biom" value="references/04-filters.biom"/>
+ <param name="region" value="ITS1"/>
+ <param name="trim_sequence" value="true"/>
+ <output name="out_abundance_biom" file="references/05-itsx.biom" compare="sim_size" delta="0" />
+ <output name="out_fasta" file="references/05-itsx.fasta" compare="diff" lines_diff="0" />
+ <output name="out_excluded" file="references/05-itsx-excluded.fasta" compare="diff" lines_diff="0" />
+ <output name="summary_file" file="references/05-itsx.html" compare="diff" lines_diff="0" />
+ </test>
+ </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+Identify (and optionnaly extract) the highly variable ITS1 and ITS2 subregions from ITS sequences.
+
+.. class:: infomark page-header h2
+
+Context
+
+The ITSx software identifies and extracts only ITS regions. It excludes the highly conserved neighbouring sequences SSU, 5.8S and LSU rRNA. These sequences can lead to misleading results if they are conserved.
+If the targeted ITS region (ITS1 or ITS2) is not detected, the observation is discarded.
+
+You can choose to only check if the sequence is detected as an ITS. The sequence is not trimmed, only sequences not detected as ITS are discarded (contaminants by example).
+
+.. class:: warningmark
+
+**ITSx is a time consuming tool. Please selecte pertinent organism groups for your study.**
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Inputs
+
+**Sequence file**:
+
+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
+
+**Abundance file**:
+
+ The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_).
+
+
+.. class:: h3
+
+Outputs
+
+**Sequence file** (itsx.fasta):
+
+ The original sequence file with identified highly variable ITS, or with only ITS1 or ITS2 part if you choose to remove conserved SSU, 5.8S and LSU parts (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
+
+**Abundance file** (itsx.biom):
+
+ The abundance file with only ITS sequences (format `BIOM <http://biom-format.org/>`_).
+
+**Discarded file** (out_removed.fasta)
+
+ The sequence file with discarded sequences.
+
+**Summary file** (report.html):
+
+ This file presents the summary of process (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).
+
+
+.. class:: infomark page-header h2
+
+How it works
+
+.. csv-table::
+   :header: "Steps", "Description"
+   :widths: 10, 90
+   :class: table table-striped
+
+   "1", "Predicts positions of the ribosomal genes in the sequences (`ITSx <http://microbiology.se/software/itsx/>`_)."
+   "2", "Removes the sequences without prediction of the targeted ITS region (ITS1 or ITS2)."
+   "3", "(optional) trim conserved region."
+
+
+----
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 normalisation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/normalisation.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,122 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="3.2.2">
+        <description>Normalise OTUs abundance.</description>
+        <requirements>
+                <requirement type="package" version="3.2.2">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>
+ normalisation.py
+                        --input-biom $input_biom
+                        --input-fasta $input_fasta
+                        --num-reads $num_reads
+                        --output-biom $output_biom
+                        --output-fasta $output_fasta
+                        --summary-file $summary_file
+ </command>
+ <inputs>
+ <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." />
+ <param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." />
+ <param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
+ </inputs>
+ <outputs>
+ <data format="fasta" name="output_fasta" label="${tool.name}: normalised_sequences.fasta" from_work_dir="normalised.fasta" />
+ <data format="biom1" name="output_biom" label="${tool.name}: normalised_abundance.biom" from_work_dir="normalised.biom" />
+ <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
+ </outputs>
+    <tests>
+        <test>
+            <param name="input_fasta" value="references/08-affiliation_postprocessed.fasta"/>
+         <param name="input_biom" value="references/08-affiliation_postprocessed.biom"/>
+         <param name="num_reads" value="100"/>
+            <output name="summary_file" file="references/09-normalisation.html" compare="sim_size" delta="0" />
+            <output name="summary_file" file="references/09-normalisation.html" compare="diff" lines_diff="4" />
+            <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" />
+        </test>
+    </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+This tool keeps, in each sample, the same number of elements by random sampling.
+
+.. class:: infomark page-header h2
+
+Inputs/outputs
+
+.. class:: h3
+
+Inputs
+
+**Sequence file**:
+
+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
+
+**Abundance file**:
+
+The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_).
+
+.. class:: h3
+
+Outputs
+
+**Sequence file** (normalised_seed.fasta):
+
+ The normalised sequences file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
+
+**Abundance file** (normalised_abundance.biom):
+
+ The normalised abundance file (format `BIOM <http://biom-format.org/>`_).
+
+**Summary file** (report.html):
+
+ Information about discarded data (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).
+
+
+.. class:: infomark page-header h2
+
+Advices
+
+The number specified in "Number of reads" must be smaller than each total number of sequences by sample.
+
+
+----
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 otu_filters.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/otu_filters.xml Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,256 @@\n+<?xml version="1.0"?>\n+\n+<tool id="FROGS_OTU_filters" name="FROGS OTU Filters" version="3.2.2">\n+\t<description>Filters OTUs on several criteria.</description>\n+ <requirements>\n+ <requirement type="package" version="3.2.2">frogs</requirement>\n+ <requirement type="package" version="2.9.0">blast</requirement>\n+ </requirements>\n+ <stdio> \n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\n+\t<command>\n+\n+\t\totu_filters.py\n+\t\t\t--nb-cpus \\${GALAXY_SLOTS:-1} \n+\t\t\t--input-biom $input_biom \n+\t\t\t--input-fasta $input_fasta\n+\t\t\t--output-fasta $output_fasta\n+\t\t\t--output-biom $output_biom\n+\t\t\t--excluded $output_excluded\n+\t\t\t--summary $output_summary\n+\n+\t\t\t#if $min_sample_presence\n+\t\t\t\t--min-sample-presence $min_sample_presence\n+\t\t\t#end if\n+\n+\t\t\t#if $choice_abundance_unit.abundance_unit_type == "count"\n+\t\t\t\t#if $choice_abundance_unit.min_abundance_count\n+\t\t\t\t\t--min-abundance $choice_abundance_unit.min_abundance_count\n+\t\t\t\t#end if\n+\t\t\t#end if\n+\n+\t\t\t#if $choice_abundance_unit.abundance_unit_type == "proportion"\n+\t\t\t\t#if $choice_abundance_unit.min_abundance_proportion\n+\t\t\t\t\t--min-abundance $choice_abundance_unit.min_abundance_proportion\n+\t\t\t\t#end if\n+\t\t\t#end if\n+\n+\t\t\t#if $nb_biggest_otu\n+\t\t\t\t--nb-biggest-otu $nb_biggest_otu\n+\t\t\t#end if\n+\n+\t\t\t\n+\t\t\t#if $contaminantSource.which_contaminantSource == "history"\n+\t\t\t\t##build index on the fly\n+\t\t\t\t--contaminant \'${contaminantSource.ownContaminantFile}\'\n+\t\t\t#else if $contaminantSource.which_contaminantSource == "server"\n+\t\t\t\t##use precomputed indexes\n+\t\t\t\t--contaminant \'${contaminantSource.contaminants_db.fields.path}\'\n+\t\t\t#end if\n+\n+\t</command>\n+\t<inputs>\n+\t\t\n+\t\t<param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: fasta)." />\n+\t\t<param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)." />\n+\t\t\n+\t\t<param name="min_sample_presence" type="integer" optional="true" label="Minimum prevalence" size="5" help="Fill the field only if you want this treatment. Keep OTU if it is present in at least this number of samples.">\n+\t\t\t<validator type="in_range" min="2" message="To be effective this threshold need to be higher than 1" />\n+\t\t</param>\n+\t\t\n+\t\t<conditional name="choice_abundance_unit">\n+\t\t\t<param name="abundance_unit_type" type="select" label="Minimum OTU abundancy as proportion or count. We recommend to use a proportion of 0.00005.">\n+\t\t\t\t<option value="proportion">as proportion</option>\n+\t\t\t\t<option value="count">as count</option>\n+\t\t\t</param>\n+\t\t\t<when value="proportion">\n+\t\t\t\t<param name="min_abundance_proportion" type="float" optional="true" label="Minimum proportion of sequences abundancy to keep OTU" size="5" help=\'Fill the field only if you want this treatment. Example: 0.00005, recommended by Bokulich et al 2013, to keep OTU with at least 0.005% of all sequences).\'>\n+\t\t\t\t\t<validator type="in_range" min="0" exclude_min="true" max="1" exclude_max="true" message="Abundance proportion threshold need to be strictly greater than 0 and less than 1, otherwise you will not remove anything or remove everything." />\n+\t\t\t\t</param>\n+\t\t\t</when>\n+\t\t\t<when value="count">\n+\t\t\t\t<p'..b'" value="server"/>\n+\t\t\t\t<param name="contaminant_db" value="phiX_test" />\n+\t\t\t</conditional>\n+\t \t <output name="output_fasta" file="references/04-filters.fasta" compare="diff" lines_diff="0" />\n+\t \t <output name="output_biom" file="references/04-filters.biom" compare="sim_size" delta="0" />\n+\t\t <output name="output_excluded" file="references/04-filters.excluded" compare="diff" lines_diff="0" />\n+\t\t <output name="output_summary" file="references/04-filters.html" compare="diff" lines_diff="0" />\n+\t </test>\n+\t</tests>\n+\t<help>\n+\n+.. image:: static/images/FROGS_logo.png\n+ :height: 144\n+ :width: 110\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+What it does\n+\n+Filter the OTUs of an abundance table according to:\n+\n+-The abundance and the occurence of OTUs: presence in samples, OTU size and maximum number of OTUs.\n+ \n+-Contamination: from the list of proposition (ex : phiX, a control added in Illumina sequencing technologies) or from your history (ex : a fasta file containing a list of contaminant of your choice).\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+Inputs/outputs\n+\n+\n+.. class:: h3\n+\n+Inputs\n+\n+**Sequence file**:\n+\n+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).\n+\n+**Abundance file**:\n+\n+The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_).\n+\n+**Contaminant fasta file** (optional):\n+\n+A sequence fasta file containing the reference sequence of known contaminant\n+\n+.. class:: h3\n+\n+Outputs\n+\n+**Sequence file** (sequences.fasta):\n+\n+ The sequences after filtering (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).\n+\n+**Abundance file** (abundance.biom):\n+\n+ The abundance after filtering (format `BIOM <http://biom-format.org/>`_).\n+\n+**Excluded file** (excluded.txt):\n+\n+ The list of the OTUs deleted by filters (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_).\n+\n+**Summary file** (report.html):\n+\n+ The filters and the number of removed sequences (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+How it works\n+\n+\n+\n+\n+The OTUs kept are the ones that satisfy into the BIOM input file the thresholds specified by the user.\n+\n+The BIOM abundance table and the fasta file are written again according to the OTUs kept.\n+\n+The OTUs discarded are listed in the excluded file.\n+\n+.. csv-table:: \n+ :header: "Steps", "description"\n+ :widths: 5, 150\n+ :class: table table-striped\n+\n+ "1", "Except the filter to select the n most abundant OTUs, all the selected filters are run independently. For each filters a list of the OTUs to remove is generated. Concerning contaminant research, OTU are added to the previous list if it aligns on a contaminant reference sequence with 80% identity and 80% coverage"\n+ "2", "All the OTUs tagged to remove by at least one filter are removed."\n+ "3", "If the filter to select the N most abundant OTUs is filled it is applied."\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+Advices\n+\n+Please check that the input fasta file and the input BIOM file correspond to the same OTUs.\n+\n+Examples for the filters on abundance and occurence of the OTUs : \n+\n+-To keep the filters that are present in 5 samples, fill the corresponding field with "5".\n+\n+-To display the 20 biggest OTU, fill the corresponding field with "20".\n+\n+-To filter on abundance, we advise you to specify 0.005%. It seems to be the optimal threshold (`Bokulich *et al*, 2013 <http://www.nature.com/nmeth/journal/v10/n1/abs/nmeth.2276.html>`_ ).\n+\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs-support@inrae.fr\n+\n+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers\n+\n+Website: http://frogs.toulouse.inrae.fr/\n+\n+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_\n+\n+\t</help>\n+</tool>\n'

diff -r 000000000000 -r 834843ebe569 phyloseq_alpha_diversity.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_alpha_diversity.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,131 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<tool name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.2.2">
+ <description>with richness plot</description>
+        <requirements>
+            <requirement type="package" version="3.2.">frogs</requirement>
+            <requirement type="package" version="3.6.3">r-base</requirement>
+            <requirement type="package" version="3.6">r-essentials</requirement>
+            <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>
+
+
+        </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>phyloseq_alpha_diversity.py
+                                             --rdata $data
+                                             --varExp $varExp
+                                             --alpha-measures $measures
+                                             --alpha-out $alphaD
+                                             --html $html
+ </command>
+    <inputs>
+ 
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This file is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ 
+ <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+     <param name="measures" type="select" label="The alpha diversity indices to compute" multiple="true" display="checkboxes">
+             <option value="Observed" selected="True">Observed</option>
+             <option value="Chao1" selected="True">Chao1</option>
+             <option value="Shannon" selected="True">Shannon</option>
+             <option value="InvSimpson" selected="True">InvSimpson</option>
+             <option value="Simpson">Simpson</option>
+             <option value="ACE">ACE</option>
+             <option value="Fisher">Fisher</option>
+        </param>
+ </inputs>
+ <outputs>
+ <data format="tabular" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/>
+ <data format="html" name="html" label="${tool.name}: alpha_diversity.nb.html" from_work_dir="alpha_diversity.nb.html"/>
+ </outputs>
+    <tests>
+        <test>
+            <param name="data" value="references/16-phylo_import.Rdata" />
+            <param name="varExp" value="EnvType" />
+            <param name="measures" value="Observed,Chao1,Shannon" />
+            <output name="alphaD" file="references/18-phylo_alpha_div.tsv" compare="diff" lines_diff="0" />
+        </test>
+    </tests>
+    <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool constructs richness plots to visualise sample alpha diversity.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**Data file** (format RData):
+One phyloseq object containing OTU abundance table, their taxonomies (and optionnaly a phylogenetics tree, and the sample experiment metadata.
+This file is the result of "FROGS Phyloseq Import Data tool".
+
+.. class:: h3
+
+Output
+
+**Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): the review of richness plots and rarefaction curves.
+
+.. image:: static/images/FROGS_Phyloseq_plot_richness.png
+     :height: 400
+     :width: 525
+
+.. image:: static/images/FROGS_Phyloseq_plot_richness_box.png
+     :height: 400
+     :width: 499
+
+.. image:: static/images/FROGS_Phyloseq_rarefaction_curves.png
+     :height: 400
+     :width: 498
+
+**Alpha diversity table** (alpha_diversity.tsv):
+The data file containing table of alpha diversity indices.
+
+.. image:: static/images/FROGS_Phyloseq_alpha_diversity_table.png
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 phyloseq_beta_diversity.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_beta_diversity.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,156 @@
+<?xml version="1.0"?>
+
+<tool name="FROGSSTAT Phyloseq Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="3.2.2">
+ <description>distance matrix</description>
+        <requirements>
+            <requirement type="package" version="3.2.2">frogs</requirement>
+            <requirement type="package" version="3.6.3">r-base</requirement>
+            <requirement type="package" version="3.6">r-essentials</requirement>
+            <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>
+            <requirement type="package" version="2.3">r-gridextra</requirement>
+        </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>phyloseq_beta_diversity.py
+                                        --rdata $data
+                                        --varExp $varExp
+                                        #if $methods != "None"
+                                            #if $other_method != ""
+                                                --distance-methods $methods,$other_method
+                                            #else
+                                                --distance-methods $methods
+                                            #end if
+                                        #else
+                                            #if $other_method != ""
+                                                --distance-methods $other_method
+                                            #end if
+                                        #end if
+                                        --matrix-outdir BetaMatrix
+                                        --html $html
+ </command>
+    <inputs>
+ 
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ 
+        <param name="varExp" type="text" label="Grouping variable" help="Experimental variable used to group samples (Treatment, Host type, etc)." optional="false" value="" size="20">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="methods" type="select" label="The methods of beta diversity" help="N.B. if the tree is not available in your RData, you cannot choose Unifrac or Weighted Unifrac" multiple="true" display="checkboxes">
+            <option value="unifrac" selected="False">Unifrac</option>
+            <option value="wunifrac" selected="False">Weighted Unifrac</option>
+            <option value="bray" selected="False">Bray-Curtis</option>
+            <option value="cc" selected="False">Jaccard (as cc method in betadiver vegan funcion)</option>
+        </param>
+        <param type="text" name="other_method" label="Other method" help="The other methods of beta diversity that you want to use (comma separated value). c.f. details below." optional="false" value="" size="40"/>
+    </inputs>
+ <outputs>
+        <data format="html" name="html" label="${tool.name}: beta_diversity.nb.html" from_work_dir="beta_diversity.nb.html">
+            <discover_datasets pattern="__designation__" ext="tabular" directory="BetaMatrix" visible="true"/>
+        </data>
+ </outputs>
+    <tests>
+        <test>
+            <param name="data" value="references/16-phylo_import.Rdata" />
+            <param name="varExp" value="EnvType" />
+            <param name="methods" value="cc,unifrac" />
+            
+            <output name="html">
+                <assert_contents>
+                    <has_text text='FROGS Phyloseq: Beta Diversity Visualisation' />
+                    <has_text text='Phyloseq 1.30.0' />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool compute beta distance matrix and display them in a heatmap
+
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**data file** (format RData):
+One phyloseq object containing OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata.
+This file is the result of "FROGS Phyloseq Import Data tool".
+
+**distance methods** :
+The list of Phyloseq distanceMethodList is available here `distanceMethodList <https://www.bioconductor.org/packages/devel/bioc/manuals/phyloseq/man/phyloseq.pdf>`_ .
+You have to copy the exact name as in this list in the parameter window "Other Method".
+To use several methods, separate them by a space.
+
+.. class:: h3
+
+Output
+
+**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_):
+
+The review of beta diversity with heatmap plots:
+
+.. image:: static/images/FROGS_Phyloseq_beta_diversity.png
+     :height: 609
+     :width: 800
+
+
+**beta diversity matrix** (format tabular):
+The distance matrix of beta diversity.
+
+ .. image:: static/images/FROGS_Phyloseq_beta_diversity_matrix.png
+
+.. class:: infomark page-header h2
+
+.. class:: h3
+
+Advices/Details
+
+Jaccard distance using
+
+-the "cc" method correspond to the distance computed using presence/absence data
+
+-the "jaccard" method correspond to the distance computed using absence data and deduced from the distance of Bray-Curtis. If you want to use this method, do not check the proposed Jaccard and write jaccard in the "Other method" parameter.
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 phyloseq_clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_clustering.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,119 @@
+<?xml version="1.0"?>
+
+<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="3.2.2">
+ <description>of samples using different linkage methods</description>
+        <requirements>
+            <requirement type="package" version="3.2.2">frogs</requirement>
+            <requirement type="package" version="3.6.3">r-base</requirement>
+            <requirement type="package" version="3.6">r-essentials</requirement>
+            <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>
+        </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>phyloseq_clustering.py
+                                   --html $html
+                                   --rdata $data
+                                   --varExp $varExp
+                                   --distance-matrix $method
+ </command>
+    <inputs>
+ 
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ 
+ <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ </inputs>
+ <outputs>
+ <data format="html" name="html" label="${tool.name}: clustering.nb.html" from_work_dir="clustering.nb.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="data" value="references/16-phylo_import.Rdata"/>
+ <param name="varExp" value="EnvType"/>
+ <param name="method" value="references/unifrac.tsv"/>
+      <output name="html">
+        <assert_contents>
+          <has_text text='FROGS Phyloseq: Sample clustering using different linkage method' />
+          <has_text text='Phyloseq 1.30.0' />
+        </assert_contents>
+      </output>
+ </test>
+ </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool contructs the clustering plot for cluster analysis with different linkage methods.
+
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**data file** (format RData):
+The informations of data in one phyloseq object.
+This is the result of FROGS Phyloseq Import Data tool.
+
+**distance file** (format tabular):
+The data file containing beta diversity distance matrix.
+This file is the result of FROGS Phyloseq Beta Diversity tool.
+
+.. class:: h3
+
+Output
+
+**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_):
+
+.. container:: row
+
+ .. image:: static/images/FROGS_Phyloseq_clustering_ward.png
+   :height: 576
+   :width: 768
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 phyloseq_composition.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_composition.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,155 @@
+<?xml version="1.0"?>
+
+<tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="3.2.2">
+    <description>with bar plot and composition plot</description>
+    <requirements>
+        <requirement type="package" version="3.2.2">frogs</requirement>
+        <requirement type="package" version="3.6.3">r-base</requirement>
+        <requirement type="package" version="3.6">r-essentials</requirement>
+        <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>
+        <requirement type="package" version="4.9.3">r-plotly</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <command>phyloseq_composition.py
+                          --rdata $data
+                          --varExp $varExp
+                          --taxaRank1 $taxaRank1
+                          --taxaSet1 $taxaSet1
+                          --taxaRank2 $taxaRank2
+                          --numberOfTaxa $numberOfTaxa
+                          --html $html
+    </command>
+    <inputs>
+        
+        <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        
+        <param name="varExp" type="text" label="Grouping variable" help="Experimental variable used to group samples (Treatment, Host type, etc)." optional="false" value="" size="20">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="taxaRank1" type="text" label="Taxonomic level to filter your data" help="ex: Kingdom, Phylum, Class, Order, Family, Genus, Species" value="Kingdom"  size="20">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="taxaSet1" type="text" label="Taxa (at the above taxonomic level) to keep in the dataset" help="ex: Bacteria (when filtering at the Kingdom level), Firmicutes (when filtering at the Phylum level). Multiple taxa (separated by a space) can be specified, i.e. Firmicutes Proteobacteria" value="Bacteria" size="20">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="taxaRank2" type="text" label="Taxonomic level used for aggregation" help="ex: Family (when filtering at the Phylum level). The aggregation level must be below the filtering level." value="Phylum" size="20">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="numberOfTaxa" type="text" label="Number of most abundant taxa to keep" help="ex: 9, i.e. Tool keeps the 9 most abundant taxa and the remaining taxa are aggregated in a group 'Other'" value="9" size="20">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+    </inputs>
+    <outputs>
+        <data format="html" name="html" label="${tool.name}: composition.nb.html" from_work_dir="composition.nb.html"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="data" value="references/16-phylo_import.Rdata" />
+            <param name="varExp" value="EnvType" />
+            <param name="taxaRank1" value="Kingdom" />
+            <param name="taxaSet1" value="Bacteria" />
+            <param name="taxaRank2" value="Phylum" />
+            <param name="numberOfTaxa" value="9" />
+            <output name="html">
+                <assert_contents>
+                    
+                    <has_text_matching expression="Phylum: Actinobacteria.*Sample: BHT0.LOT07.*Abundance: 0.3806484555" />
+                    <has_text_matching expression="Phylum: Bacteroidetes.*Sample: BHT0.LOT07.*Abundance: 0.0026380734" />
+                    <has_text_matching expression="Phylum: Cyanobacteria.*Sample: BHT0.LOT07.*Abundance: 0.0000000000" />
+                    <has_text_matching expression="Phylum: Firmicutes.*Sample: BHT0.LOT07.*Abundance: 0.6024168156" />
+                    <has_text_matching expression="Phylum: Fusobacteria.*Sample: BHT0.LOT07.*Abundance: 0.0002552974" />
+                    <has_text_matching expression="Phylum: Proteobacteria.*Sample: BHT0.LOT07.*Abundance: 0.0137860608" />
+                    <has_text_matching expression="Phylum: Spirochaetes.*Sample: BHT0.LOT07.*Abundance: 0.0000000000" />
+                    <has_text_matching expression="Phylum: Tenericutes.*Sample: BHT0.LOT07.*Abundance: 0.0002552974" />
+                    <has_text_matching expression="Phylum: Other.*Sample: BHT0.LOT07.*Abundance: 0.0000000000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and custom R function, this tool constructs two plots to visualise the sample composition: one at the OTU level and another one at the specified aggregation level (*e.g.* Phylum) after keeping only a subset of taxa (*e.g.* Bacteria at the level Kingdom). It helps answer the question: "What is the composition at the Phylum level within Bacteria?". By default, the plot exhibits only the abundance of the 9 most abundant taxa (as specified). In general, the representation of more than 10 taxa is hard to read on plots.
+
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**data file** (format rdata):
+One phyloseq object containing the OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata.
+this file is the result of FROGS Phyloseq Import Data tool.
+
+.. class:: h3
+
+Output
+
+**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): data composition plots.
+
+Bar plot of OTUs is colored with aggregated taxonomic level *i.e* "Phylum" :
+
+ .. image:: static/images/FROGS_Phyloseq_bar_plot.png
+     :height: 646
+     :width: 800
+
+Composition plot: plot the most abundant sub taxonomic level among a selection of OTUs.
+
+- Selection of OTUs:
+
+    - Taxonomic level name to subset: Kingdom
+    - Taxon name: Bacteria
+
+- Aggregation of OTUs :
+
+    - Taxonomic level used to agglomerate: Phylum
+
+- Number of the most abundant taxa to keep: 9
+
+ .. image:: static/images/FROGS_Phyloseq_composition_plot.png
+     :height: 644
+     :width: 800
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+    </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 phyloseq_import_data.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_import_data.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,137 @@
+<?xml version="1.0"?>
+
+<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.2.2">
+    <description>from 3 files: biomfile, samplefile, treefile </description>
+        <requirements>
+            <requirement type="package" version="3.2.2">frogs</requirement>
+            <requirement type="package" version="3.6.3">r-base</requirement>
+            <requirement type="package" version="3.6">r-essentials</requirement>
+            <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>
+        </requirements>
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+        </stdio>
+    <command>
+                phyloseq_import_data.py   --biomfile $biomfile
+                                --samplefile $samplefile
+                                #if $treefile
+                                  --treefile $treefile
+                                #end if
+                                --ranks $ranks
+                                #if $normalisation
+                                    --normalisation
+                                #end if
+                                --html $html
+                                --rdata $data
+    </command>
+    <inputs>
+        
+        <param format="biom1" name="biomfile" type="data" label="Abundance biom file with taxonomical metadata" help="The file contains the  OTU informations (format: biom1)." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+
+        <param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+
+        <param format="nhx" name="treefile" type="data" label="Tree file (optional)" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" />
+
+        
+        <param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space."  value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/>
+        <param name="normalisation" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before statistical analysis (default : No)." optional="false" />
+    </inputs>
+    <outputs>
+        <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/>
+        <data format="html" name="html" label="${tool.name}: summary.nb.html" from_work_dir="summary.nb.html"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="biomfile" value="input/chaillou.biom"/>
+            <param name="samplefile" value="input/sample_metadata.tsv"/>
+            <param name="treefile" value="input/tree.nwk"/>
+            <output name="data" value="references/16-phylo_import.Rdata" compare="sim_size" delta="10"/>
+        </test>
+    </tests>
+    <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq <https://joey711.github.io/phyloseq/>`_ object.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**OTU biom file**:
+
+The OTU biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_).
+The example of biom file:
+
+  .. image:: static/images/FROGS_Phyloseq_biomfile.png
+     :height: 30
+     :width: 733
+
+**Newick file** (tree.nwk):
+
+Newick file (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_) is the result of FROGS Tree:
+
+  .. image:: static/images/FROGS_nwk_treefile.png
+
+**Sample file**:
+The file contains the conditions of experiment with sample ID in the first column:
+
+  .. image:: static/images/FROGS_Phyloseq_samplefile.png
+     :height: 115
+     :width: 369
+
+.. class:: h3
+
+Output
+
+**Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object.
+
+  .. image:: static/images/FROGS_Phyloseq_import_data_html.png
+
+**Data file** (format rdata): The informations of data in one phyloseq object.
+
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+    </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 phyloseq_manova.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_manova.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,116 @@
+<?xml version="1.0"?>
+
+<tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="3.2.2">
+        <description>perform Multivariate Analysis of Variance (MANOVA)</description>
+        <requirements>
+            <requirement type="package" version="3.2.2">frogs</requirement>
+            <requirement type="package" version="3.6.3">r-base</requirement>
+            <requirement type="package" version="3.6">r-essentials</requirement>
+            <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>
+        </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>phyloseq_manova.py
+                                    --rdata $data
+                                    --varExp "$varExp"
+                                    --distance-matrix $method
+                                    --html $html
+ </command>
+    <inputs>
+ 
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ 
+ <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+    </inputs>
+ <outputs>
+ <data format="html" name="html" label="${tool.name}: manova.nb.html" from_work_dir="manova.nb.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="data" value="references/16-phylo_import.Rdata"/>
+ <param name="varExp" value="EnvType"/>
+ <param name="method" value="references/unifrac.tsv"/>
+
+            <output name="html">
+                <assert_contents>
+                    <has_text_matching expression="EnvType    7    7.6565 1.09379  13.699 0.63132  1e-04 \*\*\*" />
+                    <has_text_matching expression="Residuals 56    4.4713 0.07984         0.36868           " />
+                    <has_text_matching expression="Total     63   12.1278                 1.00000           " />
+                </assert_contents>
+            </output>
+ </test>
+ </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and `vegan <https://cran.r-project.org/web/packages/vegan/index.html>`_ functions to perform Multivariate Analysis of Variance (MANOVA)
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**data file** (format RData):
+The informations of data in one phyloseq object.
+This is the result of FROGS Phyloseq Import Data tool.
+
+**distance file** (format tabular):
+The data file containing beta diversity distance matrix.
+This file is the result of FROGS Phyloseq Beta Diversity tool.
+
+.. class:: h3
+
+Output
+
+**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The review of Manova test.
+
+.. image:: static/images/FROGS_Phyloseq_manova.png
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 phyloseq_structure.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_structure.xml Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,131 @@
+<?xml version="1.0"?>
+
+<tool name="FROGSSTAT Phyloseq Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="3.2.2">
+ <description>with heatmap plot and ordination plot</description>
+    <requirements>
+        <requirement type="package" version="3.2.2">frogs</requirement>
+        <requirement type="package" version="3.6.3">r-base</requirement>
+        <requirement type="package" version="3.6">r-essentials</requirement>
+        <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>
+        <requirement type="package" version="4.9.3">r-plotly</requirement>
+    </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>phyloseq_structure.py
+                                         --html $html
+                                         --rdata $data
+                                         --varExp $varExp
+                                         --ordination-method $method
+                                         --distance-matrix $distance
+ </command>
+    <inputs>
+ 
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data Tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="distance" format="tabular" type="data" label="The beta diversity distance matrix file" help="These file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ 
+ <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ <param name="method" type="select" label="Ordination method">
+ <option value="MDS" >MDS/PCoA</option>
+ <option value="NMDS" >NMDS</option>
+            <option value="DPCoA" >DPCoA</option>
+        </param>
+ </inputs>
+ <outputs>
+ <data format="html" name="html" label="${tool.name}: structure.nb.html" from_work_dir="structure.nb.html"/>
+ </outputs>
+    <tests>
+        <test>
+            <param name="data" value="references/16-phylo_import.Rdata" />
+            <param name="varExp" value="EnvType" />
+            <param name="method" value="MDS" />
+            <param name="distance" value="references/unifrac.tsv" />
+            <output name="html">
+                <assert_contents>
+                    <has_text text='"title":{"text":"Axis.1   [22.1%]' />
+                    <has_text text='"title":{"text":"Axis.2   [12.8%]' />
+                </assert_contents>
+            </output>
+
+        </test>
+    </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool constructs heatmap plot and ordination plot with the `ordination methods <https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html#ordination-methods>`_ to visualise data structure.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**data file** (format rdata):
+The informations of data in one phyloseq object.
+This file is the result of "FROGS Phyloseq Import Data tool".
+
+**distance file** (format tabular):
+The data file containing beta diversity distance matrix.
+This file is the result of "FROGS Phyloseq Beta Diversity tool".
+
+.. class:: h3
+
+Output
+
+**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_):
+
+The review of data structure with an ordination plot and with an heatmap plot:
+
+.. image:: static/images/FROGS_Phyloseq_plot_sample_ellipse.png
+     :height: 343
+     :width: 450
+
+.. image:: static/images/FROGS_Phyloseq_plot_heatmap_red.png
+     :height: 343
+     :width: 450
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 planemo_test.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo_test.sh Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,42 @@
+#!/bin/sh
+
+mkdir -p planemo_test
+
+#######################################################################################################
+# TEST LA STRUCTURE
+for i in *.xml
+do
+ echo $i
+ planemo lint $i > planemo_test/`basename $i |sed 's/\.xml//'`.lint.log 2>&1
+done
+
+grep Failed planemo_test/*.lint.log
+
+#######################################################################################################
+# VALIDE L'EXECUTION
+for i in ` ls *.xml | grep -vE 'demultiplexe|preprocess|clustering|remove_chimera'`
+do
+ echo $i
+ planemo test --no_cleanup $i > planemo_test/`basename $i |sed 's/\.xml//'`.test.log 2>&1
+done
+
+grep FAILED planemo_test/*test.log
+
+
+grep "test(s) executed passed" planemo_test/*test.log
+
+# planemo_test/preprocess.test.log:All 2 test(s) executed passed.
+
+
+# remote: warning: File test-data/references/01-prepro-flash.fasta is 95.81 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB
+# remote: error: File test-data/references/02-clustering_fastidious.fasta is 109.85 MB; this exceeds GitHub's file size limit of 100.00 MB
+# remote: error: File test-data/references/01-prepro-vsearch.fasta is 121.32 MB; this exceeds GitHub's file size limit of 100.00 MB
+# remote: error: File test-data/references/02-clustering_denoising.fasta is 108.50 MB; this exceeds GitHub's file size limit of 100.00 MB
+# remote: error: File test-data/references/03-chimera.fasta is 109.85 MB; this exceeds GitHub's file size limit of 100.00 MB
+
+
+#######################################################################################################
+# TEST SOUS GALAXY
+
+#######################################################################################################
+# SOUMISSION AU TOOLSHED
\ No newline at end of file

diff -r 000000000000 -r 834843ebe569 planemo_test/deseq2_preprocess.test.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo_test/deseq2_preprocess.test.log Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,704 @@\n+git --git-dir /home/maria/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/maria/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/maria/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/maria/.planemo/gx_repo /tmp/tmpf6w1rwu5/galaxy-dev\n+Clonage dans \'/tmp/tmpf6w1rwu5/galaxy-dev\'...\n+error: object file ./objects/1d/3b5b4b0610a48d6950fbf2a3c49559fc28f85e is empty\n+fait.\n+Extraction des fichiers: 71% (3877/5411) \rExtraction des fichiers: 72% (3896/5411) \rExtraction des fichiers: 73% (3951/5411) \rExtraction des fichiers: 74% (4005/5411) \rExtraction des fichiers: 75% (4059/5411) \rExtraction des fichiers: 76% (4113/5411) \rExtraction des fichiers: 77% (4167/5411) \rExtraction des fichiers: 78% (4221/5411) \rExtraction des fichiers: 79% (4275/5411) \rExtraction des fichiers: 80% (4329/5411) \rExtraction des fichiers: 81% (4383/5411) \rExtraction des fichiers: 82% (4438/5411) \rExtraction des fichiers: 83% (4492/5411) \rExtraction des fichiers: 84% (4546/5411) \rExtraction des fichiers: 85% (4600/5411) \rExtraction des fichiers: 86% (4654/5411) \rExtraction des fichiers: 87% (4708/5411) \rExtraction des fichiers: 88% (4762/5411) \rExtraction des fichiers: 89% (4816/5411) \rExtraction des fichiers: 90% (4870/5411) \rExtraction des fichiers: 91% (4925/5411) \rExtraction des fichiers: 92% (4979/5411) \rExtraction des fichiers: 93% (5033/5411) \rExtraction des fichiers: 94% (5087/5411) \rExtraction des fichiers: 95% (5141/5411) \rExtraction des fichiers: 96% (5195/5411) \rExtraction des fichiers: 97% (5249/5411) \rExtraction des fichiers: 98% (5303/5411) \rExtraction des fichiers: 99% (5357/5411) \rExtraction des fichiers: 100% (5411/5411) \rExtraction des fichiers: 100% (5411/5411), fait.\n+if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/maria/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/maria/planemo/bin/virtualenv -p /home/maria/planemo/bin/python3 $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q \'skip-venv\' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/maria/.planemo/gx_venv_3\n+Set COMMON_STARTUP_ARGS to --dev-wheels\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/maria/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=8.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (21.0.1)\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple\n+Ignoring importlib-metadata: markers \'python_version < "3.8"\' don\'t match your environment\n+Ignoring importlib-resources: markers \'python_version < "3.7"\' don\'t match your environment\n+Ignoring pathlib2: markers \'python_version < "3.6"\' don\'t match your environment\n+Ignoring ruamel.yaml.clib: markers \'platform_python_implementation == "CPython" and python_version < "3.8"\' don\'t match your environment\n+Ignoring typing: markers \'python_version < "3.5"\' don\'t match your environment\n+Ignoring zipp: markers \'python_version < "3.8"\''..b'8bf93fc86139ca\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/maria/miniconda3/bin/activate\' \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/maria/miniconda3/bin/activate\' \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/maria/miniconda3/bin/activate\' \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; deseq2_preprocess.py --data /tmp/tmpf6w1rwu5/files/0/a/3/dataset_0a3efe28-a7d2-496a-b6f6-aae5fb4287e5.dat --var EnvType --out-Rdata /tmp/tmpf6w1rwu5/files/2/8/a/dataset_28ac11fe-96b4-4b27-9ec4-c2bc4ef7e731.dat]\n+ok\n+\n+----------------------------------------------------------------------\n+XML: /tmp/tmpf6w1rwu5/xunit.xml\n+----------------------------------------------------------------------\n+Ran 1 test in 1264.958s\n+\n+OK\n+2021-04-08 16:09:58,055 INFO [test_driver] Shutting down\n+2021-04-08 16:09:58,056 INFO [test_driver] Shutting down embedded galaxy web server\n+2021-04-08 16:09:58,058 INFO [test_driver] Embedded web server galaxy stopped\n+2021-04-08 16:09:58,058 INFO [test_driver] Stopping application galaxy\n+2021-04-08 16:09:58,430 INFO [galaxy.queue_worker] Sending reconfigure_watcher control task.\n+2021-04-08 16:09:58,483 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2021-04-08 16:09:58,483 INFO [galaxy.jobs.handler] job handler queue stopped\n+2021-04-08 16:09:58,483 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads\n+2021-04-08 16:09:58,483 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...\n+2021-04-08 16:09:58,484 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly\n+2021-04-08 16:09:58,484 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads\n+2021-04-08 16:09:58,484 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...\n+2021-04-08 16:09:58,484 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly\n+2021-04-08 16:09:58,484 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2021-04-08 16:09:58,485 INFO [galaxy.jobs.handler] job handler stop queue stopped\n+2021-04-08 16:09:58,485 INFO [test_driver] Application galaxy stopped.\n+Testing complete. HTML report is in "/home/maria/workspace/FROGS-wrappers_dev/tool_test_output.html".\n+All 1 test(s) executed passed.\n+FROGSSTAT_DESeq2_Preprocess (Test #1): passed\n'

diff -r 000000000000 -r 834843ebe569 preprocess.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess.xml Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,491 @@\n+<?xml version="1.0"?>\n+\n+<tool id="FROGS_preprocess" name="FROGS Pre-process" version="3.2.2">\n+\t<description>merging, denoising and dereplication.</description>\n+ <requirements>\n+ <requirement type="package" version="3.2.2">frogs</requirement>\n+ <requirement type="package" version="2.17.0">vsearch</requirement>\n+ <requirement type="package" version="1.2.11">flash</requirement>\n+ <requirement type="package" version="2.10">cutadapt</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\t<command>\n+\t\tpreprocess.py $sequencer_type.sequencer_selected\n+\t\t--output-dereplicated $dereplicated_file --output-count $count_file --summary $summary_file \n+\t\t--nb-cpus \\${GALAXY_SLOTS:-1}\n+\t\t--min-amplicon-size $sequencer_type.min_amplicon_size --max-amplicon-size $sequencer_type.max_amplicon_size \n+\t\t\n+\t\t#if $sequencer_type.sequencer_selected == "illumina"\n+\t\t #if $sequencer_type.sequencing_protocol.sequencing_protocol_selected == "standard"\n+\t\t --five-prim-primer $sequencer_type.sequencing_protocol.five_prim_primer --three-prim-primer $sequencer_type.sequencing_protocol.three_prim_primer \n+\t\t #else\n+\t\t --without-primers\n+\t\t #end if\n+\t\t#else\n+\t\t --five-prim-primer $sequencer_type.five_prim_primer --three-prim-primer $sequencer_type.three_prim_primer \n+\t\t#end if\n+\t\t\n+\t\t#if $sequencer_type.input_type.input_type_selected == "archive" \n+\t\t --input-archive $sequencer_type.input_type.archive_file\n+\t\t #if $sequencer_type.sequencer_selected == "illumina" and $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged"\n+\t\t\t --already-contiged\n+\t\t #elif $sequencer_type.sequencer_selected == "illumina"\n+\t --R1-size $sequencer_type.input_type.archive_type.R1_size --R2-size $sequencer_type.input_type.archive_type.R2_size \n+\t \t--mismatch-rate $sequencer_type.input_type.archive_type.mm_rate\n+\t \t--merge-software $sequencer_type.input_type.archive_type.merge_software_type.merge_software_selected\n+\t \t#if $sequencer_type.input_type.archive_type.merge_software_type.merge_software_selected == "flash"\n+\t\t\t\t\t--expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size\n+\t\t\t#end if\n+\t \t#if $sequencer_type.input_type.archive_type.keep_unmerged\n+\t \t\t--keep-unmerged\n+\t \t#end if\n+\t\t #end if\n+\t\t#else\n+\t\t #set $sep = \' \'\n+\t\t #if $sequencer_type.sequencer_selected == "illumina"\n+\t --samples-names \n+\t #for $current in $sequencer_type.input_type.files_by_samples_type.samples \n+\t $sep\'${current.name.strip()}\'\n+\t #end for\n+\t\t --input-R1 \n+\t\t #for $current in $sequencer_type.input_type.files_by_samples_type.samples \n+\t\t $sep${current.R1_file}\n+\t\t #end for\n+\t\t #if $sequencer_type.input_type.files_by_samples_type.files_by_samples_type_selected == "already_merged"\n+\t\t --already-contiged\n+\t\t #else\n+\t\t --input-R2\n+\t\t #for $current in $sequencer_type.input_type.files_by_samples_type.samples \n+\t\t $sep${current.R2_file}'..b'ith 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" \n+ "4", "Dereplicates sequences", "Dereplicates sequences"\n+\n+\n+.. class:: infomark page-header h2\n+\n+Advices/details on parameters\n+\n+.. class:: h3\n+\n+Keeping or not un-merged paired reads\n+\n+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.\n+\n+.. class:: h3\n+\n+What is the difference between overlapped sequences and combined sequences?\n+\n+- **Case of a sequencing of overlapping sequences: case of 16S V3-V4 amplicon MiSeq sequencing**\n+\n+.. image:: static/images/FROGS_preprocess_overlapped_sequence.png\n+ :height: 261\n+ :width: 531\n+\n+- **Case of a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing**\n+\n+.. image:: static/images/FROGS_preprocess_combined_sequence1.png\n+ :height: 279\n+ :width: 797\n+\n+.. class:: warningmark\n+\n+**\xe2\x80\x9cFROGS combined\xe2\x80\x9d warning points**\n+\n+Reads pair are not merged because:\n+\n+\t- the real amplicon length is greater than de number of base sequences (490 bp for MiSeq 2x250bp, remember of the minimum 10 bp overlap)\n+\t- the overlapped region is smaller than 10 (fixed parameter in FROGS).\n+\n+Thus, \xe2\x80\x9cFROGS combined\xe2\x80\x9d sequences are artificial and present particular features especially on size.\n+Imagine a MiSeq sequencing of 2x250pb with sequences that cannot overlap, the resulting \xe2\x80\x9cFROGS combined\xe2\x80\x9d sequences length will be fixed to 600 bp.\n+\n+.. image:: static/images/FROGS_preprocess_combined_sequence2.png\n+ :height: 357\n+ :width: 798\n+\n+.. class:: h3\n+\n+Primers parameters\n+\n+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.\n+\n+In case of Illumina standard protocol, the primers must be provided in 5\' to 3\' orientation. \n+\n+.. role:: alert-info\n+\n+Example:\n+\n+ 5\' :alert-info:`ATGCCC` GTCGTCGTAAAATGC :alert-info:`ATTTCAG` 3\'\n+ \n+ Value for parameter 5\' primer: ATGCCC\n+ \n+ Value for parameter 3\' primer: ATTTCAG\n+\n+.. class:: h3\n+\n+FLASH : Amplicons sizes parameters\n+\n+ .. class:: infomark\n+\n+ We now recommend to use PEAR if availbale (only for accademic user) or Vsearch.\n+\n+ The two following images show two examples of perfect values fors sizes parameters.\n+\n+ .. image:: static/images/FROGS_preprocess_ampliconSize_unimodal_v3.png\n+ :height: 415\n+ :width: 676\n+ \n+ .. image:: static/images/FROGS_preprocess_ampliconSize_multimodal_v3.png\n+ :height: 415\n+ :width: 676\n+\n+ Don\'t worry the "Expected amplicon size" does not need to be very accurate, and only necessary for sequences merging with FLASH.\n+\n+.. class:: h3\n+\n+If the filter \'merged\' reduce drasticaly the number of sequences:\n+\n+ 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.\n+ \n+ 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!\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs-support@inrae.fr\n+\n+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers\n+\n+Website: http://frogs.toulouse.inrae.fr/\n+\n+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_\n+\n+\t</help>\n+</tool>\n'

diff -r 000000000000 -r 834843ebe569 remove_chimera.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/remove_chimera.xml Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,178 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="3.2.2">
+ <description>Remove PCR chimera in each sample.</description>
+        <requirements>
+            <requirement type="package" version="3.2.2">frogs</requirement>
+            <requirement type="package" version="2.15.1">vsearch</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>
+ remove_chimera.py
+                 --nb-cpus \${GALAXY_SLOTS:-1}
+                 --input-fasta $sequence_file --non-chimera $non_chimera_fasta
+                 --summary $summary_file
+                 #if $abundance_type.abundance_type_selected == "biom"
+                 --input-biom $abundance_biom
+                 --out-abundance $out_abundance_biom
+                 #else
+                 --input-count $abundance_count
+                 --out-abundance $out_abundance_count
+                 #end if
+ </command>
+ <inputs>
+ 
+ <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta)." optional="false" />
+ <conditional name="abundance_type">
+ <param name="abundance_type_selected" type="select" label="Abundance type" help="Select the type of file where the abundance of each sequence by sample is stored.">
+ <option value="biom" selected="true">BIOM file</option>
+ <option value="count">TSV file</option>
+ </param>
+ <when value="biom">
+ <param format="biom1" name="abundance_biom" type="data" label="Abundance file" help="It contains the count by sample for each sequence." optional="false" />
+ </when>
+ <when value="count">
+ <param format="tabular" name="abundance_count" type="data" label="Count file" help="It contains the count by sample for each sequence (see below)." optional="false" />
+ </when>
+ </conditional>
+ </inputs>
+ <outputs>
+ <data format="fasta" name="non_chimera_fasta" label="${tool.name}: non_chimera.fasta" from_work_dir="non_chimera.fasta"/>
+ <data format="biom1" name="out_abundance_biom" label="${tool.name}: non_chimera_abundance.biom" from_work_dir="non_chimera_abundance.biom">
+ <filter>abundance_type['abundance_type_selected'] == "biom"</filter>
+ </data>
+ <data format="tabular" name="out_abundance_count" label="${tool.name}: non_chimera_abundance.tsv" from_work_dir="non_chimera_abundance.tsv">
+ <filter>abundance_type['abundance_type_selected'] == "count"</filter>
+ </data>
+ <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="sequence_file" value="references/02-clustering_fastidious.fasta"/>
+ <conditional name="abundance_type">
+ <param name="abundance_type_selected" value="biom"/>
+ <param name="abundance_biom" value="references/02-clustering_fastidious.biom" />
+ </conditional>
+ <output name="non_chimera_fasta" file="references/03-chimera.fasta" compare="diff" lines_diff="0"/>
+ <output name="summary_file" file="references/03-chimera.html" compare="diff" lines_diff="0"/>
+ <output name="out_abundance_biom" file="references/03-chimera.biom" compare="sim_size" delta="0"/>
+ </test>
+ </tests>
+ <help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+Remove chimeric sequences by sample.
+
+
+.. class:: infomark page-header h2
+
+Context
+
+Chimeras are sequences formed from two or more biological sequences joined together.
+
+The majority of these anomalous sequences are formed from an incomplete extension during a PCR cycle. During subsequent cycles, a partially extended strand can bind to a template derived from a different but similar sequence.
+
+This phenomena is particularly common in amplicon sequencing where closely related sequences are amplified.
+
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Inputs
+
+**Sequence file**:
+
+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
+
+**Abundance file**:
+
+ The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_).
+
+OR
+
+ The abundance of each sequence in each sample (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). This type of file is produced by *FROGS pre-process*.
+
+ Example:
+
+.. csv-table::
+   :header: "#id", "splA","splB"
+   :widths: 10,10,10
+   :class: table table-striped
+
+    "seq1", "1289", "2901"
+    "seq2", "3415", "0"
+
+.. class:: h3
+
+Outputs
+
+**Sequence file** (non_chimera.fasta):
+
+ The sequence file with only non-chimera (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
+
+**Abundance file** (non_chimera.biom or non_chimera.tsv):
+
+ The abundance file with only non-chimera (format the same of the abundance input).
+
+**Summary file** (report.html):
+
+ This file presents the number of removed elements (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).
+
+
+.. class:: infomark page-header h2
+
+How it works
+
+.. csv-table::
+   :header: "Steps", "Description"
+   :widths: 10, 90
+   :class: table table-striped
+
+   "1", "Split input data by sample (classicaly the PCR is realised by sample)."
+   "2", "Find chimera in each sample (`vsearch <https://github.com/torognes/vsearch>`_)."
+   "3", "Remove the sequences identify as chimera in all samples where they are present."
+
+
+----
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 shedSave.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/shedSave.yml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,13 @@
+categories:
+- Metagenomics
+description: Suite for metabarcoding analysis
+long_description: |
+  This is FROGS version 3.2.2 Galaxy Wrappers
+  FROGS: Find Rapidly OTUs through Galaxy Solution
+  FROGS is a workflow designed to produce an OTU count matrix from high depth sequencing amplicon data.
+  Adviced :
+  reorder integrated_tool_panel.xml as indicated here : https://github.com/geraldinepascal/FROGS-wrappers#simplest-way
+name: frogs
+owner: oinizan #TestToolshed
+homepage_url: https://github.com/geraldinepascal/FROGS-wrappers
+remote_repository_url: https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2

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diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_HVL_db.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_HVL_db.loc Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,34 @@
+# Copyright (C) 2014 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/>.
+#
+#
+#This is a sample file that enables tools FROGS_affiliations_postprocess to solve
+#inclusive amplicon sequence by selecting the smallest reference among multihit
+#You will need to create or download exact amplicon sequence reference fasta file
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL_reference
+#Finally you will need to create HVL_db.loc file similar to this one in your galaxy
+#tool-data directory.The HVL_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<unique_database_name>    <name>    <file_path>
+#
+#First column will be the visible name in galaxy.
+#So, for example, if you have  UNITE 7.1 ITS1 (only!) stored
+#in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta
+#then the HVL_db.loc entry would look like this:
+#
+#
+# EXAMPLE FOR TEST :
+Unite_extract_ITS1_test Unite_extract_ITS1_test ${__HERE__}/frogs_HVL_db_data/Unite_extract_ITS1.fasta

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_HVL_db_data/Unite_extract_ITS1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_HVL_db_data/Unite_extract_ITS1.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,497 @@\n+>AB594796_SH278638.07FU_refs\n+GATCATTACAGAGTTATCTAACTCCCAAACCCATGTGAACTTACCATTTGTTGCCTCGGC\n+AGAGGCTACCCGGTACCTACCCTGGAGCAGCTACCCTGTAGCTACCCTGGAACGGCCTAC\n+CCTGTAGCGCATCCTGCCGGTGGACCTTTAAACTCTTGTTATTTTAAAGTAATCTGAGCG\n+TCTTATTTTAATAAGTCA\n+>AB747657_SH134902.07FU_refs\n+CTGAGTATTTGTCTTTTAAAGACATCTCTCTATCCATACACTCTTTTTTTTAAAAAGACA\n+TGATTTATACAGTTAGTCTGAATGATTTTTTAAAATCTTCA\n+>AF033454_SH086742.07FU_refs_singleton\n+AAGGATCATTACCGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATCGTACC\n+TCGTTGCTTCGGCGGGCCCGCCGCAAGGCCGCCGGGGGGCTTCTGCCCCCGGGCCCGTGC\n+CCGCCGAAGACACCATTGAACGCTGTCTGAAGATTGCAGTCTGAGCAATTAGCTAAATAA\n+GTTA\n+>AF033476_SH407699.07FU_refs\n+AAGGATCATTACCGAGTGAGGGCCCTTTGGGTCCAACCTCCCACCCGTGTTTATTTTACC\n+TTGTTGCTTCGGCGGGCCCGCCTTTACTGGCCGCCGGGGGGCTTCACGCCCCCGGGCCCG\n+CGCCCGCCGAAGACACCCTCGAACTCTGTCTGAAGATTGAAGTCTGAGTGAAAATATAAA\n+TTATTTA\n+>AF033486_SH207156.07FU_refs\n+AAGGATCATTACTGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTGTACC\n+TTGTTGCTTCGGCGGGCCCGCCCTAGTGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCG\n+CCCGCCGAAGACACCCTCGAACTCTGTCTGAAGATTGTAGTCTGAGTGGAATTATAAATT\n+ATTTA\n+>AF054858_SH194959.07FU_refs\n+CCGAGTTTACAACTCCCAAACCCCATGTGAACCTACCACTACGTTGCTTCGGCGGGATGC\n+CCCGGGCGCGGGCCGCAAGGCCTCAGCCCCGGAACCAGGCGCCCGCCGGAGGCCCAAACC\n+AAACTCTTGTTTTTATAGAATCTTCTGAGTGGCCTTTTAGGCAACAAATGAATCA\n+>AF118139_SH214931.07FU_refs\n+GAACCAGCGGAGGGATCATTAACGAGTTTCGTACTCCAAACCCTTTGTGAACATACCTGT\n+TTTCGTTGCTTCGGCAGGTGAAGGCGGAGGGCCTCCGGGCCTGAAGCCGCCGCCGGGCGG\n+ACCCCTCGCGGGGCGCTGCCGGGTGGGCCTGCCGGAGGGCACAGACTCTGTATTACAACG\n+TACCTCTCTGAGTTATATTTTACAAACAAGTAA\n+>AF456924_SH097201.07FU_refs\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATC\n+TCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAAC\n+TCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCG\n+TAGGCGTTTCGAAAATGAATCA\n+>AJ786644_SH470265.07FU_refs_singleton\n+CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCT\n+TTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGG\n+TGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAA\n+AACCTAATTATTA\n+>AY373856_SH207595.07FU_refs\n+CTGAGTGAGGGTCCCTCGGGGCCCAACCTCCCACCCGTGTATACCGTACCTTGTTGCTTC\n+GGCGAGCCCGCCCCCTTTTTCTTTTAGGGGGCACAGCGCTCGCCGGAGACACCAACGTGA\n+ACACTGTCTGAAGTTTTGTCGTCTGAGTCGATTGTATCGCAATCAGTTA\n+>AY443470_SH407688.07FU_refs\n+CGAGCGAGAATTCTCTGAATTCAACCTCCCACCCGTGTTTATTGTACCTTGTTGCTTCGG\n+CGGGCCCGCCTCACGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCGCCCGCCGAAGACA\n+CCTTGAACTCTGTATGAAAATTGCAGTCTGAGTCTAAATATAAATTATTTA\n+>AY615141_SH195460.07FU_refs\n+GGAAGGATCATTACCGAGTTGACTCGAGCTCCGGCTCGACTCTCCCACCCTATGTGTACC\n+TACCTCTGTTGCTTTGGCGGGCCGCGGTCCTCCGCACCGGCCCCCTTTGGGGGCTGGCCA\n+GCGCCCGCCAGAGGACCACAAAACTCCAGTCAGTAAACGTTGCAGTCTGAAAACCAAGTT\n+AATAAACTA\n+>AY616689_SH196294.07FU_refs\n+GAGGAATACCCAAAACCTCCCAACCCCTGTGAACTTACCACTGTTTCCTCGGCGTGCGCA\n+CCTGGTTGCCCGCGGGGGATCCGAGCCTACCCTGTAGCTACCCTGTAGCTACCCTGTAGA\n+CCCGGGTCCTCAGCACACGGCGCCGCTCAAGGTCCCGCCGAAGTACCCTGAACTCTGTTT\n+AACGTGGAATTCTGAATGCTTCAACTAAATAAGTTA\n+>AY737760_SH296378.07FU_refs\n+CTGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACT\n+GTTGCCTCGGCGGGATCTCTGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCG\n+GAGGAAAAAACAACCAAAACTCTTTTTGTATACCCCCTCGCGGGTTTTTTACTTCTGAGA\n+ACTTCTCGGCGCCCCTTTGCGGGCGTTTCGAAAATGAATCA\n+>AY953383_SH113362.07FU_refs\n+TACTGAGTTTTTGTACTCTATAAACCATGTGTGAACGTACCTATCTTGTAGTGAGATGAA\n+TGCTGTTTTGGTGGTAGGGCCCTTCTGAAGAGAGGGCACCGCTGCCAGCAGTATAGTCTC\n+ACCACTATAAAACTCTTTTATTATTTTCTAGATTTTTCATTGCTGAGTGGCATAACTATA\n+AAAAAGTTA\n+>DQ267916_SH386829.07FU_refs\n+CCGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTATACCTTGTTGCTTCG\n+GCGGGCCCGCCGTATGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCGCCCGCCGAAGAC\n+ATCTCGAACTCTGTCTGAAGATTGTAGTCTGAGTCAAAATATAAATTATTTA\n+>DQ317630_SH187202.07FU_refs\n+TGGGTTTTCCACTCTGTGGTAACCCTCACTACAATACACCAACATCCATATACACCTGTG\n+CACCGTTGGCTAGATGTGGCTCATTCGTGAGTCTTCGTCTGCTGACAACAATTTATAAAC\n+TCTGAGTTATAATGAATGTTAATTGTATCTTGCCATTTGGCAGAAACTAAATA\n+>DQ898183_SH216206.07FU_refs\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCAT\n+GTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTT\n+TGGGGAAGGGCCAGTTATTAAACCTTTATACCAATT'..b'SH188638.07FU_refs\n+TTGAAATAAACCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCAT\n+CTTTATATCTCCACCTGTGCACTTTTTGTAGACCTTTCAGGTCTATGTTTTCTCATTTTA\n+CCCCAATGTATGTCGATAGAATGTTGTGCCTTTATAATGTATA\n+>KP170652_SH495686.07FU_refs_singleton\n+CACTCAGTAGTTTACTACTGTTAAAGAGGCTGTTAGTCTGTATAGCTTTACCGCTGACGA\n+GCAGCTTGCCTCTTTTCTCTACCCTTGTCTTTTGCGTACCCATGTTTCCTCGGCAGGCCT\n+GCCTGCCGATAGGACCCTTCTACAACCTTTATTATTTCAATCAGCGTCTGAAAAACTTAA\n+TAATTA\n+>KP744516_SH528288.07FU_refs\n+CCGAGTGAGGGTCTTCAAAGGCTCAACCTCCCAAACCCCTTGTATATCACCGAGAGTTTT\n+ATTGTTGCTTCGGTGGGTCCACAGTGCCCACCGAAGACCCACCAAAAATCCTAGTAAGAG\n+TGTCGTCTGAGTAATTAAAAAATAATCA\n+>KT716464_SH554678.07FU_refs_singleton\n+CATTACAGAGTTGCAAAACTCCCAAACCCATTGCGTACATACCATGTCGTTGCTTCGGCG\n+GGCTGCCGTCCTCCCCCAGGGGAGGCGGACCCGGCCCCTCGGGGAGCCCGCCGGAGGTAT\n+AAACTCTTATCTTTATAGAAAAGCCTTCTGAGTATCTTGAAAAATCAAGTAA\n+>UDB000320_SH220111.07FU_refs\n+TCGTACAACATGTGTGAGGCGTGCGAGGGCTGTCGCTGACTTCAAAGTCGTGCACGCCGG\n+AGCGCGTCCTCTCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCC\n+TTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAA\n+AGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATA\n+>UDB001086_SH222381.07FU_refs\n+CTGCGGAAGGATCATTATTGAAATAAATCTGATGAGTTGCTGCTGGTTCTCTTAGGGAGC\n+ATGTGCACACTTGTCATCTTTATATTCTCCACCTTGTGCACCTTTTGTAGACCTGGATAT\n+CTCTCTGAGTGCTTTTAGCACTCAGGTTTGGAGGATTGACTTTTCTGTCTTTCCTTACCT\n+TTCCCGGCCTATGTTTCTTCAAATACCCAATGTGTATGTCATTAGAATGTAATAAATGGG\n+CTTTTGTGCCTTATAAATCTATA\n+>UDB001581_SH219736.07FU_refs\n+TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCAT\n+CTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCG\n+GTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATAC\n+ACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATA\n+>UDB002317_SH221025.07FU_refs\n+CTGAACGAAATGGGTGGCAAGGCTGTCGCTGGCTCAAATGAGCATGTGCACGTCTTTTGC\n+TGCTTACTTCATTCTCTTTTCCACCTGTGCACTCTTTGTAAACACTTGGGATGTGAGAGA\n+GGGTTGGCATTTATTGTTGAACCTCTCTTGATATTGAAAAAGTCTGGGTGTTTATGTATT\n+TTTTGACATACACGGTCGAATGTCTATAGAATGAAATTAATAGGCTCTTGTCAGCCTTTA\n+AATGATAAAATA\n+>UDB003291_SH182302.07FU_refs\n+GGACTGCGGAGGACATTAATGAAATCGACGTTTCGGGAAAGGTTGTTGCTGGCCCCACGG\n+CATGTGCACGCCTTTACCGGATGTATTCGTCCTTTCTTTACACCTGTGCACGATCTGTAG\n+CTAGGGATGATCACGGAGCCTGTCGGTTCCGAATGCCCTGGCTATGAACGTTTTTATACC\n+CTCTTATAAAGTTTTTTTTGAATGTTTGTCCTGCGTGTAACAGCGCGAATGAAATA\n+>UDB006042_SH184945.07FU_refs\n+CCGAGTTTACACAACTCCCAAACCCACTGTGAACCTTACCGAATCGTTGCTTCGGCGGGA\n+ACGCCCCGGGCCCCGTCGCCCGGACCCAGGCGCCCGCCGGAGGCCCGAAAAAACTCTCGT\n+GTTTCTCCCAGCGGAATCAAGTCTGAGTGGCCCACAGCGGCAAGAAAATGAATCA\n+>UDB009021_SH177627.07FU_refs\n+CATTATTGAAATCCAAGGTGCAGAGGGGGACCGGAGAAATCCATTCCTCTGAAGCCCTTT\n+TACCTCTTTCACACCTGTGTGCACCCACATTCGCAAAGTCCTTCGGGACCTGCGCTTTCT\n+ATCTCGAACTCGCATGTCTACAGAATGTCGCTAGCGTTTGAAATGAAATA\n+>UDB011541_SH194446.07FU_refs\n+GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCT\n+TTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCT\n+GTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAA\n+ATAAATAAATA\n+>UDB011569_SH190415.07FU_refs\n+GTGACTGCGGAGGATCATTATTGAAATAAAGCTTGGTTAGGTTGTTGCTGGCTCTTCGGG\n+GCATGTGCACACCTGACACCAACTTTTCTTACCACCTGTGCACTTTTTGTAGACTTTGGA\n+ATACCTCTCGAGGAAACTCGGTTTTGAGGACTGCTGTGCGCAAGCCGGCTTTCCTTACAT\n+TTTCCGGTCTATGTTTTTCTATATACCCTATAGTATGTCACAGAATGTCATTTTAATGGG\n+CTTAATTGCCTTTAAACCTATA\n+>UDB015350_SH176685.07FU_refs\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCT\n+GGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCC\n+TGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCC\n+GGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACAT\n+GTTTGGAAAAAATATAAATGAAATATA\n+>UDB016091_SH210668.07FU_refs\n+ATGAAATCAAAACTTTCATTGAAAGGTTGTTGCTGATATATATATATATATGTGCACACC\n+TGGATTTGAAAGTCTTCATCCTTTACCTCCCTTGTGCACGATCTGTAGCTTTGGGATGAT\n+TACAGAGTTTACTCTTTTTATTAGAGGATTCTGAATGCCCTTTGCTATGAACGTTTTTAC\n+ACACACAAATGTTTATTAGAATGTATGCTCGAGCGTGTAACAACGTGAATTGAAATA\n+>UDB016470_SH189377.07FU_refs\n+CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTT\n+TACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTT\n+CCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAA\n+CGCAATAAAATA\n'

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_contaminant_db.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_contaminant_db.loc Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,42 @@
+# Copyright (C) 2014 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/>.
+#
+#
+#This is a sample file that enables tools FROGS_filters to identify phix contaminant. You will #need to create or download Blast+ index.
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants
+#Finally you will need to create phiX_db.loc file similar to this one in your galaxy
+#tool-data directory.The phiX_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<contaminant_name> <name> <file_path>
+#
+#First column will be the visible name in galaxy.
+#So, for example, if you had phix indexed stored in
+#/galaxy_databanks/phiX/
+#then the phiX_db.loc entry would look like this:
+#
+#
+# EXAMPLE FOR TEST :
+phiX_test phiX_test ${__HERE__}/frogs_contaminant_db_data/phi.fa
+#
+#and your /galaxy_databanks/phiX/ directory
+#would contain index files:
+#
+#-rwxrwxr-x 1 gpascal FROGS 5535 16 sept.  2015 phi.fa
+#-rw-rwxr-- 1 gpascal FROGS  132 16 sept.  2015 phi.fa.nhr
+#-rw-rwxr-- 1 gpascal FROGS   88 16 sept.  2015 phi.fa.nin
+#-rw-rwxr-- 1 gpascal FROGS 1348 16 sept.  2015 phi.fa.nsq
+#
+

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_contaminant_db_data/phi.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_contaminant_db_data/phi.fa Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,79 @@
+>gi|9626372|ref|NC_001422.1| Coliphage phiX174, no SNPs True Reference
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTAGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+GATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCTCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_contaminant_db_data/phi.fa.nhr

Binary file test-data/databases/frogs_contaminant_db_data/phi.fa.nhr has changed

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_contaminant_db_data/phi.fa.nin

Binary file test-data/databases/frogs_contaminant_db_data/phi.fa.nin has changed

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_contaminant_db_data/phi.fa.nsq

Binary file test-data/databases/frogs_contaminant_db_data/phi.fa.nsq has changed

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_db.loc Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,54 @@
+# Copyright (C) 2014 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/>.
+#
+#
+#This is a sample file that enables tools FROGS_affiliations_OTU to use taxonomy database for
+#taxonomy affiliation. You will need to create or download Blast+ index and train your database
+#for RDP classifier these data files.
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation
+#Finally you will need to create frogs_db.loc file similar to this one in your galaxy
+#tool-data directory.The frogs_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<unique_database_name>   <file_path>
+#
+#First column will be the visible name in galaxy.
+#So, for example, if you had 16S silva 128 indexed stored in
+#/galaxy_databanks/16S/silva_128/
+#then the frogs_db.loc entry would look like this:
+#
+#silva 128 16S  /galaxy_databanks/16S/silva_128/silva_128_16S.fasta
+#
+#and your /galaxy_databanks/16S/silva_128/ directory
+#would contain index files:
+#
+#-rw-r--r-- 1 mbernard FROGS    8097966  5 déc.  16:56 bergeyTrainingTree.xml
+#-rw-r--r-- 1 mbernard FROGS 1572981589  5 déc.  16:56 genus_wordConditionalProbList.txt
+#-rw-r--r-- 1 mbernard FROGS       1654  5 déc.  16:56 LICENCE.txt
+#-rw-r--r-- 1 mbernard FROGS    1072228  5 déc.  16:56 logWordPrior.txt
+#-rw-r--r-- 1 mbernard FROGS  940834335  5 déc.  16:56 silva_128_16S.fasta
+#-rw-r--r-- 1 mbernard FROGS  152606489  5 déc.  16:56 silva_128_16S.fasta.nhr
+#-rw-r--r-- 1 mbernard FROGS    6918588  5 déc.  16:56 silva_128_16S.fasta.nin
+#-rw-r--r-- 1 mbernard FROGS  205320030  5 déc.  16:56 silva_128_16S.fasta.nsq
+#-rw-r--r-- 1 mbernard FROGS        281  5 déc.  16:56 silva_128_16S.fasta.properties
+#-rw-r--r-- 1 mbernard FROGS    3420464  5 déc.  16:56 silva_128_16S.tax
+#-rw-r--r-- 1 mbernard FROGS     964048  5 déc.  16:57 wordConditionalProbIndexArr.txt
+#
+#
+#<name>    <name>    <file_path>
+#
+# EXAMPLE FOR TEST :
+ITS1_test ITS1_test ${__HERE__}/frogs_db_data/ITS1.rdp.fasta
+

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/ITS1.rdp.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_db_data/ITS1.rdp.fasta Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,204 @@\n+>JX089579_SH215375.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Dothideomycetes [id: 3];o__Pleosporales [id: 4];f__Pleosporaceae [id: 5];g__Bipolaris [id: 6];s__Bipolaris_microstegii [id: 7]\n+CACAACAAAATATGAAGGCCTGGCTTCGCGGCCGGCTGAAATATTTTTTCACCCATGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCACCAGGACCAAACCATAAACCTTTTTTTTATGCAGTTACCATCAGCGTCAGTAAAAACAATGTAATTAATTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCAAAGGGCATGCCTGTTCGAGCGTCATTTGTACCTTCAAGCTTTGCTTGGTGTTGGGTGTTTTTGTCTCCCTCTTTCTGGGAGACTCGCCTTAAAACGATTGGCAGCCGGCCTACTGGTTTCGGAGCGCAGCACATAATTTGCGCTTTGTATCAGGAGAAAAGGACGGTAATCCATCAAGACTCTACATTTTTCACT\n+>DQ898183_SH216206.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Pezizomycetes [id: 8];o__Pezizales [id: 9];f__Tuberaceae [id: 10];g__Tuber [id: 11];s__Tuber_latisporum [id: 12]\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTCAGGGCATGCCTGTTCGAGCGTCACTAACAACCATCTCACAGAGAATGTGGTATTGGCCTGAGTGGGTTGCACTTGCAGTGCAAATCTCACTTGGCTGAAATGGATTGGCCAGACAAGGAGACAATGGCAACAGACTCTCAGAGTGTTTTTGAAATGCTAAACTAGTCTGTGGCAGGTTGAACTCTGAGCTAAAAGGACTGATATTTAGTGTAAACAAGAAAT\n+>JQ716403_SH219241.07FU_refs Root;k__Fungi [id: 1];p__Basidiomycota [id: 13];c__Agaricomycetes [id: 14];o__Hymenochaetales [id: 15];f__Hymenochaetaceae [id: 16];g__Pseudochaete [id: 17];s__Pseudochaete_subrigidula [id: 18]\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCCTTTGGTATTCCGAAGGGCATGCCTGTTTGAGTGTCATGTTAATCTCAATACCCTTGTTTTTCTTAATTGAAGACTTGGAGATTGGACTTGGAGGTTTATTGCTGGCCCCCTTTGTGGTCGGCTCCTCTTAAATATATTAGTTGGACTTTGGTTCGCGTGAAGATGTAATAATTTATTCATCATTAGCGCTTGCCTAACGGGTCTGCTTCTAATTGTCTTCGGACAAGGATTAACTTCCTTCTTGACTCT\n+>AY373856_SH207595.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 19];o__Eurotiales [id: 20];f__Trichocomaceae [id: 21];g__Aspergillus [id: 22];s__Aspergillus_ochraceus [id: 23]\n+CTGAGTGAGGGTCCCTCGGGGCCCAACCTCCCACCCGTGTATACCGTACCTTGTTGCTTCGGCGAGCCCGCCCCCTTTTTCTTTTAGGGGGCACAGCGCTCGCCGGAGACACCAACGTGAACACTGTCTGAAGTTTTGTCGTCTGAGTCGATTGTATCGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAATTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCACCCCCTGGTATTCCGGGGGGTATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCACGGCTTGTGTGTTGGGTCGTCGTCCCCCCCCAGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTTGTAGGCCCGGCCGGCTGCTGGCCGACGCTGAAAAGCAACCAACTATTTTTCCAG\n+>JF747094_SH197643.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 19];o__Chaetothyriales [id: 24];f__Herpotrichiellaceae [id: 25];g__Exophiala [id: 26];s__Exophiala_equina [id: 27]\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTCCAGTGAGTCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAAGGGCATGCCTGTTCGAGCGTCATTATCACCCCTCAAGCCCCTGGCTTGGTGTTGGACGGTTTGGTGGAGGCCCCCTCGGGGGCTCCTGCCCCTCCCAAAGACAATGACGGCGGCCTCGTTGGACCCCCGGTACACTGAGTTCTTCACGGGACACGTATCGGATACATGGGTTTACGGGACACGGTCTGCCTCCCCTCAGGGAGAATCTTTCTAAGGTTGACC\n+>KC774589_SH195184.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Sordariomycetes [id: 28];o__Xylariales [id: 29];f__Xylariaceae [id: 30];g__Lopadostoma [id: 31];s__Lop'..b'TTGCTTCGGCGAGCCTGCCTTTTGGCTGCCGGGGGACATCTGTCCCCGGGTCCGCGCTCGCCGAAGACACCTTAGAACTCTGTCTGAAGATTGTAGTCTGAGATTAAATATAAATTATTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCACGGCTTGTGTGTTGGGCTCCGTCCTCCTTCCGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCAAGCGTATGGGGCTTTGTCACCCGCTTTGTAGGACTGGCCGGCGCCTGCCGATCAACCAAACTTTTTTCCAG\n+>DQ267916_SH386829.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 19];o__Eurotiales [id: 20];f__Trichocomaceae [id: 21];g__Penicillium [id: 151];s__Penicillium_ribium [id: 237]\n+CCGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTATACCTTGTTGCTTCGGCGGGCCCGCCGTATGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCGCCCGCCGAAGACATCTCGAACTCTGTCTGAAGATTGTAGTCTGAGTCAAAATATAAATTATTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCACGGCTTGTGTGTTGGGCTCCGTCCTCCGATCCCGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTGTAGGCCCGGCCGGCGCTTGCCGATCAACCAAATTTTTATCCA\n+>AY443470_SH407688.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 19];o__Eurotiales [id: 20];f__Trichocomaceae [id: 21];g__Penicillium [id: 151];s__Penicillium_jensenii [id: 238]\n+CGAGCGAGAATTCTCTGAATTCAACCTCCCACCCGTGTTTATTGTACCTTGTTGCTTCGGCGGGCCCGCCTCACGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCGCCCGCCGAAGACACCTTGAACTCTGTATGAAAATTGCAGTCTGAGTCTAAATATAAATTATTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCCCGGCTTGTGTGTTGGGTCTCGTCCCCCTTCCCGGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTGTAGGCCCGGCCGGCGCTTGCCGATCAACCAAAACTTTTTTCCAG\n+>AF033476_SH407699.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 19];o__Eurotiales [id: 20];f__Trichocomaceae [id: 21];g__Penicillium [id: 151];s__Penicillium_aurantiogriseum [id: 239]\n+AAGGATCATTACCGAGTGAGGGCCCTTTGGGTCCAACCTCCCACCCGTGTTTATTTTACCTTGTTGCTTCGGCGGGCCCGCCTTTACTGGCCGCCGGGGGGCTTCACGCCCCCGGGCCCGCGCCCGCCGAAGACACCCTCGAACTCTGTCTGAAGATTGAAGTCTGAGTGAAAATATAAATTATTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCCCGGCTTGTGTGTTGGGCCCCGTCCTCCGATTCCGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCCGTAGGCCCGGCCGGCGCTTGCCGATCAACCCAAATTTTTATCCAG\n+>KM189666_SH407780.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 19];o__Eurotiales [id: 20];f__Trichocomaceae [id: 21];g__Penicillium [id: 151];s__Penicillium_brunneoconidiatum [id: 240]\n+AAGGATCATTACTGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTGTACCTTGTTGCTTCGGTGAGCCCGCCTCACGGCCGCCGGGGGGCTTCTGCCCCCGGGCCCGCGCCCACCGAAGACACCATTGAACTCTGTCTGAAGATTGCAGTCTGAGCATAAACTAAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAACTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCACGGCTTGTGTGTTGGGCTCCGTCCCCCCCGGGACGGGCCCGAAAGGCAGCGGCGGCACCGAGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTGTAGGCCCGGCCGGCGCCAGCCGACAACCCATCATCCTTTTCAG\n+>KJ638312_SH419903.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Dothideomycetes [id: 3];o__Botryosphaeriales [id: 96];f__Botryosphaeriaceae [id: 97];g__Lasiodiplodia [id: 136];s__Lasiodiplodia_mediterranea [id: 241]\n+GATCATTACCGAGTTCTCGGGCTTCGGCTCGACTCTCCCACCCTTTGTGAACGTACCTCTGTTGCTTTGGCGGCTCCGGCCGCCAAAGGACCTCCAAACTCCAGTCAGTAAACGCAGACGTCTGATAAACAAGTTAATAAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTACAACCCTCAAGCTCTGCTTGGAATTGGGCACCGTCCTCGCTGCGGACGCGCCTCAAAGACCTCGGCGGTGGCTGTTCAGCCCTCAAGCGTAGTAGAATACACCTCGCTTTGGAGCGGTTGGCGTCGCCCGCCGGACGAACCTTCTGAACTTTTCTCAAGGTTGACCTCGGAT\n'

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/ITS1.rdp.fasta.nhr

Binary file test-data/databases/frogs_db_data/ITS1.rdp.fasta.nhr has changed

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/ITS1.rdp.fasta.nin

Binary file test-data/databases/frogs_db_data/ITS1.rdp.fasta.nin has changed

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/ITS1.rdp.fasta.nsq

Binary file test-data/databases/frogs_db_data/ITS1.rdp.fasta.nsq has changed

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/ITS1.rdp.fasta.properties
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_db_data/ITS1.rdp.fasta.properties Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,11 @@
+# Sample ResourceBundle properties file
+bergeyTree=bergeyTrainingTree.xml
+
+probabilityList=genus_wordConditionalProbList.txt
+
+probabilityIndex=wordConditionalProbIndexArr.txt
+
+wordPrior=logWordPrior.txt
+
+classifierVersion=RDP Naive Bayesian rRNA Classifier Version 2.5, May 2012
+

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/ITS1.rdp.tax
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_db_data/ITS1.rdp.tax Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,242 @@\n+0*Root*-1*0*rootrank\n+1*k__Fungi [id: 1]*0*1*k\n+2*p__Ascomycota [id: 2]*1*2*p\n+28*c__Sordariomycetes [id: 28]*2*3*c\n+29*o__Xylariales [id: 29]*28*4*o\n+226*f__Amphisphaeriaceae [id: 226]*29*5*f\n+227*g__Pestalotiopsis [id: 227]*226*6*g\n+228*s__Pestalotiopsis_diversiseta [id: 228]*227*7*s\n+229*g__Adisciso [id: 229]*226*6*g\n+230*s__Adisciso_tricellulare [id: 230]*229*7*s\n+30*f__Xylariaceae [id: 30]*29*5*f\n+31*g__Lopadostoma [id: 31]*30*6*g\n+32*s__Lopadostoma_insulare [id: 32]*31*7*s\n+79*s__Lopadostoma_dryophilum [id: 79]*31*7*s\n+174*g__Hypoxylon [id: 174]*30*6*g\n+175*s__Hypoxylon_fragiforme [id: 175]*174*7*s\n+46*o__Hypocreales [id: 46]*28*4*o\n+47*f__Hypocreaceae [id: 47]*46*5*f\n+167*g__Hypomyces [id: 167]*47*6*g\n+168*s__Hypomyces_australasiaticus [id: 168]*167*7*s\n+142*g__Sepedonium [id: 142]*47*6*g\n+143*s__Sepedonium_laevigatum [id: 143]*142*7*s\n+48*g__Trichoderma [id: 48]*47*6*g\n+232*s__Trichoderma_cremeum [id: 232]*48*7*s\n+203*s__Trichoderma_aggressivum [id: 203]*48*7*s\n+49*s__Trichoderma_mienum [id: 49]*48*7*s\n+144*s__Trichoderma_rhododendri [id: 144]*48*7*s\n+234*s__Trichoderma_rodmanii [id: 234]*48*7*s\n+213*f__Cordycipitaceae [id: 213]*46*5*f\n+214*g__Beauveria [id: 214]*213*6*g\n+215*s__Beauveria_australis [id: 215]*214*7*s\n+86*o__Diaporthales [id: 86]*28*4*o\n+87*f__Diaporthaceae [id: 87]*86*5*f\n+88*g__Diaporthe [id: 88]*87*6*g\n+197*s__Diaporthe_lusitanicae [id: 197]*88*7*s\n+89*s__Diaporthe_longispora [id: 89]*88*7*s\n+169*f__Togniniaceae [id: 169]*86*5*f\n+170*g__Phaeoacremonium [id: 170]*169*6*g\n+171*s__Phaeoacremonium_rubrigenum [id: 171]*170*7*s\n+222*o__Calosphaeriales [id: 222]*28*4*o\n+223*f__Calosphaeriaceae [id: 223]*222*5*f\n+224*g__Jattaea [id: 224]*223*6*g\n+225*s__Jattaea_taediosa [id: 225]*224*7*s\n+208*o__Microascales [id: 208]*28*4*o\n+209*f__Ceratocystidaceae [id: 209]*208*5*f\n+210*g__Ceratocystis [id: 210]*209*6*g\n+211*s__Ceratocystis_manginecans [id: 211]*210*7*s\n+19*c__Eurotiomycetes [id: 19]*2*3*c\n+20*o__Eurotiales [id: 20]*19*4*o\n+138*f__Elaphomycetaceae [id: 138]*20*5*f\n+139*g__Elaphomyces [id: 139]*138*6*g\n+140*s__Elaphomyces_compleximurus [id: 140]*139*7*s\n+21*f__Trichocomaceae [id: 21]*20*5*f\n+151*g__Penicillium [id: 151]*21*6*g\n+236*s__Penicillium_kongii [id: 236]*151*7*s\n+239*s__Penicillium_aurantiogriseum [id: 239]*151*7*s\n+240*s__Penicillium_brunneoconidiatum [id: 240]*151*7*s\n+231*s__Penicillium_paneum [id: 231]*151*7*s\n+152*s__Penicillium_levitum [id: 152]*151*7*s\n+199*s__Penicillium_alutaceum [id: 199]*151*7*s\n+189*s__Penicillium_crystallinum [id: 189]*151*7*s\n+237*s__Penicillium_ribium [id: 237]*151*7*s\n+238*s__Penicillium_jensenii [id: 238]*151*7*s\n+146*g__Rasamsonia [id: 146]*21*6*g\n+180*s__Rasamsonia_emersonii [id: 180]*146*7*s\n+147*s__Rasamsonia_piperina [id: 147]*146*7*s\n+90*g__Talaromyces [id: 90]*21*6*g\n+91*s__Talaromyces_pittii [id: 91]*90*7*s\n+22*g__Aspergillus [id: 22]*21*6*g\n+200*s__Aspergillus_ivoriensis [id: 200]*22*7*s\n+23*s__Aspergillus_ochraceus [id: 23]*22*7*s\n+145*s__Aspergillus_caninus [id: 145]*22*7*s\n+207*s__Aspergillus_microcysticus [id: 207]*22*7*s\n+62*o__Verrucariales [id: 62]*19*4*o\n+63*f__Verrucariaceae [id: 63]*62*5*f\n+64*g__Verrucaria [id: 64]*63*6*g\n+65*s__Verrucaria_hydrophila [id: 65]*64*7*s\n+141*s__Verrucaria_lapidicola [id: 141]*64*7*s\n+178*g__Dermatocarpon [id: 178]*63*6*g\n+179*s__Dermatocarpon_dolomiticum [id: 179]*178*7*s\n+24*o__Chaetothyriales [id: 24]*19*4*o\n+25*f__Herpotrichiellaceae [id: 25]*24*5*f\n+26*g__Exophiala [id: 26]*25*6*g\n+27*s__Exophiala_equina [id: 27]*26*7*s\n+3*c__Dothideomycetes [id: 3]*2*3*c\n+96*o__Botryosphaeriales [id: 96]*3*4*o\n+97*f__Botryosphaeriaceae [id: 97]*96*5*f\n+98*g__Neofusicoccum [id: 98]*97*6*g\n+99*s__Neofusicoccum_eucalypticola [id: 99]*98*7*s\n+136*g__Lasiodiplodia [id: 136]*97*6*g\n+137*s__Lasiodiplodia_crassispora [id: 137]*136*7*s\n+241*s__Lasiodiplodia_mediterranea [id: 241]*136*7*s\n+4*o__Pleosporales [id: 4]*3*4*o\n+148*f__Phaeosphaeriaceae [id: 148]*4*5*f\n+149*g__Neosphaerellopsis [id: 149]*148*6*g\n+150*s__Neos'..b'*4*o\n+35*f__Uropyxidaceae [id: 35]*34*5*f\n+36*g__Dasyspora [id: 36]*35*6*g\n+37*s__Dasyspora_mesoamericana [id: 37]*36*7*s\n+14*c__Agaricomycetes [id: 14]*13*3*c\n+42*o__Agaricales [id: 42]*14*4*o\n+116*f__Amanitaceae [id: 116]*42*5*f\n+117*g__Amanita [id: 117]*116*6*g\n+187*s__Amanita_friabilis [id: 187]*117*7*s\n+118*s__Amanita_franchetii [id: 118]*117*7*s\n+80*f__Entolomataceae [id: 80]*42*5*f\n+81*g__Entoloma [id: 81]*80*6*g\n+82*s__Entoloma_sp [id: 82]*81*7*s\n+68*f__Tricholomataceae [id: 68]*42*5*f\n+69*g__Tricholoma [id: 69]*68*6*g\n+70*s__Tricholoma_portentosum [id: 70]*69*7*s\n+172*g__Gamundia [id: 172]*68*6*g\n+173*s__Gamundia_leucophylla [id: 173]*172*7*s\n+119*f__Inocybaceae [id: 119]*42*5*f\n+120*g__Inocybe [id: 120]*119*6*g\n+121*s__Inocybe_sindonia [id: 121]*120*7*s\n+113*f__Strophariaceae [id: 113]*42*5*f\n+181*g__Pholiota [id: 181]*113*6*g\n+182*s__Pholiota_highlandensis [id: 182]*181*7*s\n+114*g__Hypholoma [id: 114]*113*6*g\n+115*s__Hypholoma_capnoides [id: 115]*114*7*s\n+50*f__Omphalotaceae [id: 50]*42*5*f\n+51*g__Gymnopus [id: 51]*50*6*g\n+52*s__Gymnopus_hybridus [id: 52]*51*7*s\n+104*f__Marasmiaceae [id: 104]*42*5*f\n+105*g__Megacollybia [id: 105]*104*6*g\n+106*s__Megacollybia_subfurfuracea [id: 106]*105*7*s\n+53*f__Psathyrellaceae [id: 53]*42*5*f\n+107*g__Psathyrella [id: 107]*53*6*g\n+108*s__Psathyrella_sublatispora [id: 108]*107*7*s\n+166*s__Psathyrella_multipedata [id: 166]*107*7*s\n+54*g__Coprinopsis [id: 54]*53*6*g\n+55*s__Coprinopsis_candidolanata [id: 55]*54*7*s\n+177*s__Coprinopsis_pachyderma [id: 177]*54*7*s\n+43*f__Cortinariaceae [id: 43]*42*5*f\n+66*g__Phaeocollybia [id: 66]*43*6*g\n+67*s__Phaeocollybia_kauffmanii [id: 67]*66*7*s\n+44*g__Cortinarius [id: 44]*43*6*g\n+122*s__Cortinarius_caesiocolor [id: 122]*44*7*s\n+202*s__Cortinarius_disjungendus [id: 202]*44*7*s\n+176*s__Cortinarius_gentianeus [id: 176]*44*7*s\n+92*s__Cortinarius_calojanthinus [id: 92]*44*7*s\n+193*s__Cortinarius_parkeri [id: 193]*44*7*s\n+164*s__Cortinarius_aavae [id: 164]*44*7*s\n+192*s__Cortinarius_limonius [id: 192]*44*7*s\n+212*s__Cortinarius_sinapivelus [id: 212]*44*7*s\n+221*s__Cortinarius_amnicola [id: 221]*44*7*s\n+45*s__Cortinarius_subexitiosus [id: 45]*44*7*s\n+233*s__Cortinarius_aurantiobasis [id: 233]*44*7*s\n+186*s__Cortinarius_savegrensis [id: 186]*44*7*s\n+194*f__Agaricaceae [id: 194]*42*5*f\n+195*g__Lepiota [id: 195]*194*6*g\n+196*s__Lepiota_geogenia [id: 196]*195*7*s\n+15*o__Hymenochaetales [id: 15]*14*4*o\n+16*f__Hymenochaetaceae [id: 16]*15*5*f\n+56*g__Hymenochaete [id: 56]*16*6*g\n+57*s__Hymenochaete_longispora [id: 57]*56*7*s\n+17*g__Pseudochaete [id: 17]*16*6*g\n+18*s__Pseudochaete_subrigidula [id: 18]*17*7*s\n+38*o__Thelephorales [id: 38]*14*4*o\n+39*f__Bankeraceae [id: 39]*38*5*f\n+40*g__Sarcodon [id: 40]*39*6*g\n+41*s__Sarcodon_quercophilus [id: 41]*40*7*s\n+71*g__Hydnellum [id: 71]*39*6*g\n+85*s__Hydnellum_suaveolens [id: 85]*71*7*s\n+72*s__Hydnellum_peckii [id: 72]*71*7*s\n+93*f__Thelephoraceae [id: 93]*38*5*f\n+94*g__Thelephora [id: 94]*93*6*g\n+95*s__Thelephora_atra [id: 95]*94*7*s\n+58*o__Boletales [id: 58]*14*4*o\n+133*f__Suillaceae [id: 133]*58*5*f\n+134*g__Truncocolumella [id: 134]*133*6*g\n+135*s__Truncocolumella_rubra [id: 135]*134*7*s\n+76*f__Sclerodermataceae [id: 76]*58*5*f\n+77*g__Pisolithus [id: 77]*76*6*g\n+78*s__Pisolithus_capsulifer [id: 78]*77*7*s\n+59*f__Boletaceae [id: 59]*58*5*f\n+60*g__Xerocomus [id: 60]*59*6*g\n+61*s__Xerocomus_porophyllus [id: 61]*60*7*s\n+183*f__Paxillaceae [id: 183]*58*5*f\n+184*g__Alpova [id: 184]*183*6*g\n+188*s__Alpova_corsicus [id: 188]*184*7*s\n+185*s__Alpova_alpestris [id: 185]*184*7*s\n+100*o__Russulales [id: 100]*14*4*o\n+101*f__Russulaceae [id: 101]*100*5*f\n+102*g__Lactarius [id: 102]*101*6*g\n+198*s__Lactarius_sp [id: 198]*102*7*s\n+191*s__Lactarius_lanceolatus [id: 191]*102*7*s\n+103*s__Lactarius_semisanguifluus [id: 103]*102*7*s\n+235*s__Lactarius_cyathuliformis [id: 235]*102*7*s\n+109*o__Polyporales [id: 109]*14*4*o\n+110*f__Meruliaceae [id: 110]*109*5*f\n+111*g__Junghuhnia [id: 111]*110*6*g\n+112*s__Junghuhnia_nitida [id: 112]*111*7*s\n'

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/bergeyTrainingTree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_db_data/bergeyTrainingTree.xml Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,243 @@\n+<trainsetNo>1</trainsetNo><version>null</version><modversion>null</modversion><file>bergeyTrainingTree</file>\n+<TreeNode name="Root" taxid="0" rank="rootrank" parentTaxid="-1" leaveCount="102" genusIndex="-1"></TreeNode>\n+<TreeNode name="k__Fungi [id: 1]" taxid="1" rank="k" parentTaxid="0" leaveCount="102" genusIndex="-1"></TreeNode>\n+<TreeNode name="p__Ascomycota [id: 2]" taxid="2" rank="p" parentTaxid="1" leaveCount="56" genusIndex="-1"></TreeNode>\n+<TreeNode name="c__Saccharomycetes [id: 216]" taxid="216" rank="c" parentTaxid="2" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="o__Saccharomycetales [id: 217]" taxid="217" rank="o" parentTaxid="216" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="f__Lipomycetaceae [id: 218]" taxid="218" rank="f" parentTaxid="217" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="g__Lipomyces [id: 219]" taxid="219" rank="g" parentTaxid="218" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Lipomyces_orientalis [id: 220]" taxid="220" rank="s" parentTaxid="219" leaveCount="1" genusIndex="0"></TreeNode>\n+<TreeNode name="c__Eurotiomycetes [id: 19]" taxid="19" rank="c" parentTaxid="2" leaveCount="21" genusIndex="-1"></TreeNode>\n+<TreeNode name="o__Eurotiales [id: 20]" taxid="20" rank="o" parentTaxid="19" leaveCount="17" genusIndex="-1"></TreeNode>\n+<TreeNode name="f__Trichocomaceae [id: 21]" taxid="21" rank="f" parentTaxid="20" leaveCount="16" genusIndex="-1"></TreeNode>\n+<TreeNode name="g__Aspergillus [id: 22]" taxid="22" rank="g" parentTaxid="21" leaveCount="4" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Aspergillus_microcysticus [id: 207]" taxid="207" rank="s" parentTaxid="22" leaveCount="1" genusIndex="1"></TreeNode>\n+<TreeNode name="s__Aspergillus_caninus [id: 145]" taxid="145" rank="s" parentTaxid="22" leaveCount="1" genusIndex="2"></TreeNode>\n+<TreeNode name="s__Aspergillus_ivoriensis [id: 200]" taxid="200" rank="s" parentTaxid="22" leaveCount="1" genusIndex="3"></TreeNode>\n+<TreeNode name="s__Aspergillus_ochraceus [id: 23]" taxid="23" rank="s" parentTaxid="22" leaveCount="1" genusIndex="4"></TreeNode>\n+<TreeNode name="g__Talaromyces [id: 90]" taxid="90" rank="g" parentTaxid="21" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Talaromyces_pittii [id: 91]" taxid="91" rank="s" parentTaxid="90" leaveCount="1" genusIndex="5"></TreeNode>\n+<TreeNode name="g__Rasamsonia [id: 146]" taxid="146" rank="g" parentTaxid="21" leaveCount="2" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Rasamsonia_emersonii [id: 180]" taxid="180" rank="s" parentTaxid="146" leaveCount="1" genusIndex="6"></TreeNode>\n+<TreeNode name="s__Rasamsonia_piperina [id: 147]" taxid="147" rank="s" parentTaxid="146" leaveCount="1" genusIndex="7"></TreeNode>\n+<TreeNode name="g__Penicillium [id: 151]" taxid="151" rank="g" parentTaxid="21" leaveCount="9" genusIndex="-1"></TreeNode>\n+<TreeNode 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taxid="231" rank="s" parentTaxid="151" leaveCount="1" genusIndex="15"></TreeNode>\n+<TreeN'..b'ntTaxid="117" leaveCount="1" genusIndex="90"></TreeNode>\n+<TreeNode name="s__Amanita_friabilis [id: 187]" taxid="187" rank="s" parentTaxid="117" leaveCount="1" genusIndex="91"></TreeNode>\n+<TreeNode name="f__Tricholomataceae [id: 68]" taxid="68" rank="f" parentTaxid="42" leaveCount="2" genusIndex="-1"></TreeNode>\n+<TreeNode name="g__Gamundia [id: 172]" taxid="172" rank="g" parentTaxid="68" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Gamundia_leucophylla [id: 173]" taxid="173" rank="s" parentTaxid="172" leaveCount="1" genusIndex="92"></TreeNode>\n+<TreeNode name="g__Tricholoma [id: 69]" taxid="69" rank="g" parentTaxid="68" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Tricholoma_portentosum [id: 70]" taxid="70" rank="s" parentTaxid="69" leaveCount="1" genusIndex="93"></TreeNode>\n+<TreeNode name="o__Polyporales [id: 109]" taxid="109" rank="o" parentTaxid="14" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="f__Meruliaceae [id: 110]" taxid="110" rank="f" parentTaxid="109" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="g__Junghuhnia [id: 111]" taxid="111" rank="g" parentTaxid="110" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Junghuhnia_nitida [id: 112]" taxid="112" rank="s" parentTaxid="111" leaveCount="1" genusIndex="94"></TreeNode>\n+<TreeNode name="o__Thelephorales [id: 38]" taxid="38" rank="o" parentTaxid="14" leaveCount="4" genusIndex="-1"></TreeNode>\n+<TreeNode name="f__Thelephoraceae [id: 93]" taxid="93" rank="f" parentTaxid="38" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="g__Thelephora [id: 94]" taxid="94" rank="g" parentTaxid="93" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Thelephora_atra [id: 95]" taxid="95" rank="s" parentTaxid="94" leaveCount="1" genusIndex="95"></TreeNode>\n+<TreeNode name="f__Bankeraceae [id: 39]" taxid="39" rank="f" parentTaxid="38" leaveCount="3" genusIndex="-1"></TreeNode>\n+<TreeNode name="g__Hydnellum [id: 71]" taxid="71" rank="g" parentTaxid="39" leaveCount="2" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Hydnellum_peckii [id: 72]" taxid="72" rank="s" parentTaxid="71" leaveCount="1" genusIndex="96"></TreeNode>\n+<TreeNode name="s__Hydnellum_suaveolens [id: 85]" taxid="85" rank="s" parentTaxid="71" leaveCount="1" genusIndex="97"></TreeNode>\n+<TreeNode name="g__Sarcodon [id: 40]" taxid="40" rank="g" parentTaxid="39" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Sarcodon_quercophilus [id: 41]" taxid="41" rank="s" parentTaxid="40" leaveCount="1" genusIndex="98"></TreeNode>\n+<TreeNode name="o__Hymenochaetales [id: 15]" taxid="15" rank="o" parentTaxid="14" leaveCount="2" genusIndex="-1"></TreeNode>\n+<TreeNode name="f__Hymenochaetaceae [id: 16]" taxid="16" rank="f" parentTaxid="15" leaveCount="2" genusIndex="-1"></TreeNode>\n+<TreeNode name="g__Pseudochaete [id: 17]" taxid="17" rank="g" parentTaxid="16" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Pseudochaete_subrigidula [id: 18]" taxid="18" rank="s" parentTaxid="17" leaveCount="1" genusIndex="99"></TreeNode>\n+<TreeNode name="g__Hymenochaete [id: 56]" taxid="56" rank="g" parentTaxid="16" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Hymenochaete_longispora [id: 57]" taxid="57" rank="s" parentTaxid="56" leaveCount="1" genusIndex="100"></TreeNode>\n+<TreeNode name="c__Exobasidiomycetes [id: 156]" taxid="156" rank="c" parentTaxid="13" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="o__Microstromatales [id: 157]" taxid="157" rank="o" parentTaxid="156" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="f__Microstromataceae [id: 158]" taxid="158" rank="f" parentTaxid="157" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="g__Microstroma [id: 159]" taxid="159" rank="g" parentTaxid="158" leaveCount="1" genusIndex="-1"></TreeNode>\n+<TreeNode name="s__Microstroma_phylloplanum [id: 160]" taxid="160" rank="s" parentTaxid="159" leaveCount="1" genusIndex="101"></TreeNode>\n'

diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/genus_wordConditionalProbList.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_db_data/genus_wordConditionalProbList.txt Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,55231 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diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/logWordPrior.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_db_data/logWordPrior.txt Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,65537 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diff -r 000000000000 -r 834843ebe569 test-data/databases/frogs_db_data/wordConditionalProbIndexArr.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/databases/frogs_db_data/wordConditionalProbIndexArr.txt Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,65538 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diff -r 000000000000 -r 834843ebe569 test-data/input/chaillou.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/chaillou.biom Thu Apr 08 14:30:48 2021 +0000

[

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"c__Bacilli", "o__Lactobacillales", "f__Leuconostocaceae", "g__Weissella", "s__NA"]}}, {"id": "otu_01833", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Actinomycetales", "f__Actinomycetaceae", "g__Actinomyces", "s__NA"]}}, {"id": "otu_00156", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Micrococcales", "f__Brevibacteriaceae", "g__Brevibacterium", "s__Marinum"]}}, {"id": "otu_01719", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Neisseriales", "f__Neisseriaceae", "g__Neisseria", "s__Perflava"]}}, {"id": "otu_00015", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Aerococcaceae", "g__Facklamia", "s__Tabacinasalis"]}}, {"id": "otu_00769", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lactobacillus", "s__Sakei"]}}, {"id": "otu_00768", 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"o__Lactobacillales", "f__Aerococcaceae", "g__Abiotrophia", "s__Defectiva"]}}, {"id": "otu_00569", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Serratia", "s__Proteamaculans"]}}, {"id": "otu_00568", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Serratia", "s__Fonticola"]}}, {"id": "otu_00602", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Aestuarii"]}}, {"id": "otu_00386", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Comamonas", "s__Aquatica"]}}, {"id": "otu_00604", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Sibiricum"]}}, {"id"'..b'], [505, 27, 3], [505, 28, 8], [505, 29, 187], [505, 30, 3], [505, 31, 3], [505, 32, 3], [505, 33, 7], [505, 34, 2], [505, 35, 9], [505, 38, 5], [505, 40, 7], [505, 41, 36], [505, 42, 41], [505, 43, 37], [505, 44, 12], [505, 45, 7], [505, 46, 15], [505, 47, 13], [505, 48, 95], [505, 49, 6], [505, 51, 7], [505, 52, 7], [505, 53, 7], [505, 54, 36], [505, 55, 11], [505, 58, 3], [505, 59, 3], [505, 61, 2], [506, 0, 2], [506, 1, 1], [506, 2, 5], [506, 3, 11], [506, 4, 8], [506, 5, 18], [506, 6, 73], [506, 7, 11], [506, 9, 15], [506, 10, 10], [506, 12, 29], [506, 19, 5], [506, 32, 5], [506, 41, 11], [506, 42, 3], [506, 43, 12], [506, 44, 3], [506, 47, 3], [506, 48, 125], [506, 49, 11], [506, 50, 2], [506, 51, 4], [506, 52, 4], [506, 54, 42], [506, 55, 7], [506, 56, 3], [506, 59, 8], [506, 61, 3], [506, 62, 4], [506, 63, 4], [507, 3, 3], [507, 5, 3], [507, 7, 4], [507, 32, 3], [507, 34, 2], [507, 35, 9], [507, 36, 6], [507, 37, 1], [507, 39, 2], [507, 40, 7], [507, 41, 33], [507, 43, 20], [507, 45, 4], [507, 46, 3], [507, 47, 3], [507, 48, 2], [507, 49, 4], [507, 51, 2], [507, 52, 8], [507, 53, 8], [507, 55, 3], [507, 57, 29], [507, 58, 101], [507, 59, 41], [507, 60, 3], [507, 61, 2], [507, 62, 7], [507, 63, 20]], "generated_by": null, "matrix_type": "sparse", "shape": [508, 64], "format_url": "http://biom-format.org", "date": "2016-02-19T14:01:52", "type": "OTU table", "id": null, "columns": [{"id": "DLT0.LOT08", "metadata": null}, {"id": "DLT0.LOT05", "metadata": null}, {"id": "DLT0.LOT03", "metadata": null}, {"id": "DLT0.LOT07", "metadata": null}, {"id": "DLT0.LOT06", "metadata": null}, {"id": "DLT0.LOT01", "metadata": null}, {"id": "DLT0.LOT04", "metadata": null}, {"id": "DLT0.LOT10", "metadata": null}, {"id": "MVT0.LOT05", "metadata": null}, {"id": "MVT0.LOT01", "metadata": null}, {"id": "MVT0.LOT06", "metadata": null}, {"id": "MVT0.LOT07", "metadata": null}, {"id": "MVT0.LOT03", "metadata": null}, {"id": "MVT0.LOT09", "metadata": null}, {"id": "MVT0.LOT08", "metadata": null}, {"id": "MVT0.LOT10", "metadata": null}, {"id": "BHT0.LOT01", "metadata": null}, {"id": "BHT0.LOT07", "metadata": null}, {"id": "BHT0.LOT06", "metadata": null}, {"id": "BHT0.LOT03", "metadata": null}, {"id": "BHT0.LOT10", "metadata": null}, {"id": "BHT0.LOT05", "metadata": null}, {"id": "BHT0.LOT04", "metadata": null}, {"id": "BHT0.LOT08", "metadata": null}, {"id": "VHT0.LOT02", "metadata": null}, {"id": "VHT0.LOT10", "metadata": null}, {"id": "VHT0.LOT03", "metadata": null}, {"id": "VHT0.LOT01", "metadata": null}, {"id": "VHT0.LOT08", "metadata": null}, {"id": "VHT0.LOT06", "metadata": null}, {"id": "VHT0.LOT07", "metadata": null}, {"id": "VHT0.LOT04", "metadata": null}, {"id": "SFT0.LOT08", "metadata": null}, {"id": "SFT0.LOT07", "metadata": null}, {"id": "SFT0.LOT06", "metadata": null}, {"id": "SFT0.LOT03", "metadata": null}, {"id": "SFT0.LOT02", "metadata": null}, {"id": "SFT0.LOT05", "metadata": null}, {"id": "SFT0.LOT04", "metadata": null}, {"id": "SFT0.LOT01", "metadata": null}, {"id": "FST0.LOT07", "metadata": null}, {"id": "FST0.LOT08", "metadata": null}, {"id": "FST0.LOT05", "metadata": null}, {"id": "FST0.LOT06", "metadata": null}, {"id": "FST0.LOT01", "metadata": null}, {"id": "FST0.LOT03", "metadata": null}, {"id": "FST0.LOT10", "metadata": null}, {"id": "FST0.LOT02", "metadata": null}, {"id": "FCT0.LOT06", "metadata": null}, {"id": "FCT0.LOT10", "metadata": null}, {"id": "FCT0.LOT05", "metadata": null}, {"id": "FCT0.LOT03", "metadata": null}, {"id": "FCT0.LOT08", "metadata": null}, {"id": "FCT0.LOT02", "metadata": null}, {"id": "FCT0.LOT07", "metadata": null}, {"id": "FCT0.LOT01", "metadata": null}, {"id": "CDT0.LOT10", "metadata": null}, {"id": "CDT0.LOT08", "metadata": null}, {"id": "CDT0.LOT05", "metadata": null}, {"id": "CDT0.LOT04", "metadata": null}, {"id": "CDT0.LOT06", "metadata": null}, {"id": "CDT0.LOT09", "metadata": null}, {"id": "CDT0.LOT07", "metadata": null}, {"id": "CDT0.LOT02", "metadata": null}]}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/input/demultiplex_barcode.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/demultiplex_barcode.txt Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,9 @@
+MgArd0001_A ACAGCGT ACGTACA
+MgArd0002 ACAGCGT ACGTCAG
+MgArd0003 ACAGCGT ACTAGCA
+MgArd0004 ACAGCGT ACTCGTC
+MgArd0009 ACAGTAG ACGTACA
+MgArd0010 ACAGTAG ACGTCAG
+MgArd0011 ACAGTAG ACTAGCA
+MgArd0012 ACAGTAG ACTCGTC
+MgArd0001_B ACAGCGC ACGTACT

diff -r 000000000000 -r 834843ebe569 test-data/input/demultiplex_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/demultiplex_summary.txt Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,12 @@
+#sample count
+ambiguous 1
+MgArd0009 1
+MgArd0011 1
+MgArd0004 1
+MgArd0002 1
+MgArd0010 1
+MgArd0001_B 0
+MgArd0001_A 1
+unmatched 1
+MgArd0003 1
+MgArd0012 1

diff -r 000000000000 -r 834843ebe569 test-data/input/demultiplex_test2_R1.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/demultiplex_test2_R1.fq Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,40 @@
+@MgArd0001_A
+ACAGCGTCAGGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGGTATTAGCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACGTACA
++
+CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIJJIJHHHHFF@DEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD
+@MgArd0002
+ACAGCGTGCAGGAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCTGAAAAAAAATAAAAATAACTGCAACGAATTGACGTCAG
++
+#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHE:9@CC?ACBCCCC:@A8>CC?#########################
+@MgArd0003
+ACAGCGTGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGGTATTAGCATCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACTAGCA
++
+CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIJJIJHHHHFEDEEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD
+@MgArd0004
+ACAGCGTGGAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTTGAAAAAAAATAAAAATAACTGCAACGAATTGACTCGTC
++
+#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHE:9@CC?ABBCCCC:@A8>CC?#########################
+@MgArd0009
+ACAGTAGGCAGGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGTAGCATCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACGTACA
++
+CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIHFF@DFFFEEDEEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD
+@MgArd0010
+ACAGTAGGTGCAGGAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATTGCCGTCTGAAAAAAAATAAAAATAACTGCAACGAATTGACGTCAG
++
+#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHECDCDBB=BBCCCC:@A8>CC?#########################
+@MgArd0011
+ACAGTAGAGGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGGTTAGCATCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACTAGCA
++
+CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIHFF@DFFFEEDEEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD
+@MgArd0012
+ACAGTAGTGCAGGAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTGCCGTCTGAAAAAAAATAAAAATAACTGCAACGAATTGACTCGTC
++
+#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHECDCDBB=BBCCCC:@A8>CC?#########################
+@unmatched
+AAAAAAAAAAAAAAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTGCCGTCTGAAAAAAAATAAAAATAACTGCAACGAATTGACTCGTC
++
+#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHECDCDBB=BBCCCC:@A8>CC?#########################
+@ambiguous
+ACAGCGACAGGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGGTATTAGCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACGTACC
++
+CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIJJIJHHHHFF@DEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD

diff -r 000000000000 -r 834843ebe569 test-data/input/demultiplex_test2_R1.fq.gz

Binary file test-data/input/demultiplex_test2_R1.fq.gz has changed

diff -r 000000000000 -r 834843ebe569 test-data/input/demultiplex_test2_R2.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/demultiplex_test2_R2.fq Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,40 @@
+@MgArd0001
+AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATAGGTGGAGAAAGAAATAAACGTACA
++
+JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB
+@MgArd0002
+AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATATCAGGCTAACGTCAG
++
+JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?###########################
+@MgArd0003
+AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATGGTGGAAAGAAATAATGAACTAGCA
++
+JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB
+@MgArd0004
+AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATATGCAGGCTACTCGTC
++
+JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?###########################
+@MgArd0009
+AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATGGTGGAGAAGAAATAATGACGTACA
++
+JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB
+@MgArd0010
+AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATTGCAGGCTAACGTCAG
++
+JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?###########################
+@MgArd0011
+AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATGGATGGAGAAAGAAATAAACTAGCA
++
+JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB
+@MgArd0012
+AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATATCAGGCTAACTCGTC
++
+JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?###########################
+@unmatched
+AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATATAAAAAAAAAAAAAA
++
+JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?###########################
+@ambiguous
+AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATAGGTGGAGAAAGAAATAAACGTACA
++
+JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB

diff -r 000000000000 -r 834843ebe569 test-data/input/demultiplex_test2_R2.fq.gz

Binary file test-data/input/demultiplex_test2_R2.fq.gz has changed

diff -r 000000000000 -r 834843ebe569 test-data/input/sample_metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/sample_metadata.tsv Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,65 @@
+ EnvType Description FoodType
+BHT0.LOT01 BoeufHache LOT1 Meat
+BHT0.LOT03 BoeufHache LOT3 Meat
+BHT0.LOT04 BoeufHache LOT4 Meat
+BHT0.LOT05 BoeufHache LOT5 Meat
+BHT0.LOT06 BoeufHache LOT6 Meat
+BHT0.LOT07 BoeufHache LOT7 Meat
+BHT0.LOT08 BoeufHache LOT8 Meat
+BHT0.LOT10 BoeufHache LOT10 Meat
+VHT0.LOT01 VeauHache LOT1 Meat
+VHT0.LOT02 VeauHache LOT2 Meat
+VHT0.LOT03 VeauHache LOT3 Meat
+VHT0.LOT04 VeauHache LOT4 Meat
+VHT0.LOT06 VeauHache LOT6 Meat
+VHT0.LOT07 VeauHache LOT7 Meat
+VHT0.LOT08 VeauHache LOT8 Meat
+VHT0.LOT10 VeauHache LOT10 Meat
+DLT0.LOT01 DesLardons LOT1 Meat
+DLT0.LOT03 DesLardons LOT3 Meat
+DLT0.LOT04 DesLardons LOT4 Meat
+DLT0.LOT05 DesLardons LOT5 Meat
+DLT0.LOT06 DesLardons LOT6 Meat
+DLT0.LOT07 DesLardons LOT7 Meat
+DLT0.LOT08 DesLardons LOT8 Meat
+DLT0.LOT10 DesLardons LOT10 Meat
+MVT0.LOT01 MerguezVolaille LOT1 Meat
+MVT0.LOT03 MerguezVolaille LOT3 Meat
+MVT0.LOT05 MerguezVolaille LOT5 Meat
+MVT0.LOT06 MerguezVolaille LOT6 Meat
+MVT0.LOT07 MerguezVolaille LOT7 Meat
+MVT0.LOT08 MerguezVolaille LOT8 Meat
+MVT0.LOT09 MerguezVolaille LOT9 Meat
+MVT0.LOT10 MerguezVolaille LOT10 Meat
+SFT0.LOT01 SaumonFume LOT1 Seafood
+SFT0.LOT02 SaumonFume LOT2 Seafood
+SFT0.LOT03 SaumonFume LOT3 Seafood
+SFT0.LOT04 SaumonFume LOT4 Seafood
+SFT0.LOT05 SaumonFume LOT5 Seafood
+SFT0.LOT06 SaumonFume LOT6 Seafood
+SFT0.LOT07 SaumonFume LOT7 Seafood
+SFT0.LOT08 SaumonFume LOT8 Seafood
+FST0.LOT01 FiletSaumon LOT1 Seafood
+FST0.LOT02 FiletSaumon LOT2 Seafood
+FST0.LOT03 FiletSaumon LOT3 Seafood
+FST0.LOT05 FiletSaumon LOT5 Seafood
+FST0.LOT06 FiletSaumon LOT6 Seafood
+FST0.LOT07 FiletSaumon LOT7 Seafood
+FST0.LOT08 FiletSaumon LOT8 Seafood
+FST0.LOT10 FiletSaumon LOT10 Seafood
+FCT0.LOT01 FiletCabillaud LOT1 Seafood
+FCT0.LOT02 FiletCabillaud LOT2 Seafood
+FCT0.LOT03 FiletCabillaud LOT3 Seafood
+FCT0.LOT05 FiletCabillaud LOT5 Seafood
+FCT0.LOT06 FiletCabillaud LOT6 Seafood
+FCT0.LOT07 FiletCabillaud LOT7 Seafood
+FCT0.LOT08 FiletCabillaud LOT8 Seafood
+FCT0.LOT10 FiletCabillaud LOT10 Seafood
+CDT0.LOT02 Crevette LOT2 Seafood
+CDT0.LOT04 Crevette LOT4 Seafood
+CDT0.LOT05 Crevette LOT5 Seafood
+CDT0.LOT06 Crevette LOT6 Seafood
+CDT0.LOT07 Crevette LOT7 Seafood
+CDT0.LOT08 Crevette LOT8 Seafood
+CDT0.LOT09 Crevette LOT9 Seafood
+CDT0.LOT10 Crevette LOT10 Seafood

diff -r 000000000000 -r 834843ebe569 test-data/input/test_dataset.tar.gz

Binary file test-data/input/test_dataset.tar.gz has changed

diff -r 000000000000 -r 834843ebe569 test-data/input/tree.nwk
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/tree.nwk Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,1 @@\n+(((((((((((((otu_00520:0.016,otu_00555:0.01122):0.01094,((otu_00568:0.00301,otu_00566:0.01354):0.00617,otu_00569:0.00821):0.00998):0.00828,otu_00545:0.03879):0.02824,((otu_00527:0.02225,otu_00521:0.00934):0.0236,otu_00526:0.03119):0.01691):0.01749,(((otu_01626:0.00438,otu_01827:0.01766):0.04919,otu_01630:0.04558):0.00228,(((otu_01798:0.02312,((otu_01825:0.00592,otu_01826:0.01341):0.01757,otu_01824:0.01755):0.02979):0.01078,((otu_01097:0.05816,(otu_01100:0.0007,otu_01095:0.01485):0.00946):0.01094,otu_01091:0.00751):0.00993):0.01257,(otu_01093:0.0495,((otu_01094:0.02211,otu_01101:0.00604):0.00289,otu_01098:0.01391):0.01489):0.00311):0.01657):0.01694):0.00822,((((otu_01781:0.07375,((otu_00029:0.00599,otu_00034:0.00551):0.00331,otu_00032:0.01147):0.0211):0.00681,((((otu_01802:0.03646,otu_01451:0.01259):0.00281,otu_01447:0.01744):0.0043,(otu_01448:0.01331,otu_01461:0.00669):0.00642):0.00223,otu_01450:0.02671):0.01927):0.01694,otu_01803:0.04852):0.00908,otu_01160:0.05446):0.00152):0.02122,((((((otu_01732:0.02898,otu_00011:0.00843):0.0138,((otu_00013:0.02504,otu_00010:0.00761):0.01053,(otu_00001:0.01789,otu_00006:0.00934):0.00647):0.00236):0.00476,otu_00012:0.01634):0.00304,(otu_00005:0.0171,otu_00004:0.00949):0.00613):0.04845,(otu_01665:0.02051,((otu_01221:0.01382,(otu_01209:0.01161,(otu_01213:0.0086,otu_01680:0.0051):0.00296):0.00345):0.00594,(otu_01210:0.00898,otu_01208:0.00854):0.00705):0.00664):0.05875):0.0111,((((((((otu_01175:0.00037,otu_01205:0.00037):0.00733,otu_01177:0.00103):0.00514,otu_01203:0.00494):0.00164,(otu_01187:0.00468,otu_01204:0.00522):0.00417):0.00632,otu_01192:0.02757):0.00105,(otu_01168:0.01668,otu_01184:0.00562):0.00546):0.00363,(otu_01182:0.00687,otu_01169:0.00675):0.00702):0.0111,otu_01789:0.04424):0.04737):0.01791):0.01798,((otu_01717:0.02449,otu_01697:0.02454):0.02559,otu_01902:0.07794):0.02317):0.00756,((((otu_01408:0.02838,(otu_01386:0.02478,otu_01430:0.02239):0.01459):0.01765,otu_01420:0.03907):0.01646,(((otu_01432:0.01327,((otu_01393:0.01047,otu_01407:0.00549):0.01395,otu_01444:0.01092):0.00442):0.00164,otu_01439:0.01802):0.02663,otu_01409:0.02785):0.02817):0.0296,(((otu_00165:0.07163,((((otu_01719:0.01466,otu_01025:0.01651):0.03479,otu_01015:0.03658):0.00458,otu_01750:0.05152):0.01686,otu_01794:0.06009):0.02098):0.00622,otu_00720:0.06484):0.0045,((((((((otu_00402:0.00677,otu_00366:0.01229):0.00706,(otu_00358:0.01454,otu_00386:0.0108):0.01615):0.0171,(((otu_01734:0.0184,(otu_01671:0.0098,(otu_00398:0.00772,otu_00417:0.01189):0.00202):0.00736):0.00794,otu_00385:0.02166):0.00474,(otu_00380:0.02071,otu_00411:0.02728):0.00662):0.00582):0.01579,((otu_00391:0.04565,((otu_00396:0.0108,otu_00357:0.00287):0.0155,(otu_00418:0.03771,(otu_00403:0.0075,otu_00365:0.00427):0.01185):0.00083):0.00882):0.00486,(otu_00404:0.01127,otu_00359:0.00495):0.02628):0.01828):0.01222,otu_00360:0.04744):0.0143,((((otu_01667:0.03424,otu_00371:0.0288):0.00647,otu_00177:0.03391):0.0167,otu_00168:0.04721):0.00717,otu_00182:0.0574):0.00513):0.00481,(((((otu_01039:0.00625,otu_01040:0.00585):0.00609,otu_01034:0.01127):0.02388,(otu_01045:0.01551,otu_01041:0.01259):0.00807):0.00571,otu_01043:0.02839):0.01365,otu_01698:0.05536):0.02346):0.00506,otu_01744:0.0709):0.00627):0.01882):0.01491):0.00935,(otu_01357:0.06291,otu_01374:0.06027):0.03181):0.01807,(((((otu_01788:0.04604,(((otu_01687:0.02108,((((otu_01085:0.01064,otu_01084:0.00965):0.00842,otu_01086:0.01446):0.00865,(((otu_01075:0.01167,otu_01083:0.00179):0.00682,otu_01080:0.01188):0.00555,((otu_01082:0.01007,otu_01087:0.00981):0.00492,otu_01088:0.01164):0.00437):0.00167):0.0051,otu_01658:0.03594):0.0015):0.00329,(otu_01079:0.02363,(otu_01769:0.03961,otu_01659:0.02094):0.02058):0.00893):0.01673,otu_01723:0.04871):0.00971):0.00845,((((otu_01336:0.02832,otu_01342:0.0145):0.01241,otu_01330:0.0148):0.0136,otu_01226:0.0437):0.00446,((otu_01264:0.02109,otu_01275:0.00717):0.01533,otu_01231:0.03338):0.01204):0.01443):0.01145,((otu_01293:0.02613,otu_01257:0.01996):0.02292,(otu_0'..b'1741:0.14325,(otu_00056:0.0345,otu_01799:0.05546):0.14431):0.02928,otu_01888:0.1447):0.02133):0.00496):0.00971,(((otu_01816:0.08071,(((otu_00260:0.01147,otu_00273:0.01248):0.00939,otu_01683:0.02112):0.0311,(otu_01730:0.05755,otu_01648:0.15684):0.01826):0.00873):0.02373,(((otu_01689:0.13456,(otu_00263:0.09152,((((otu_01874:0.06378,otu_01670:0.0428):0.0068,otu_01740:0.04616):0.0366,otu_01841:0.07705):0.00698,otu_01792:0.0821):0.00919):0.01145):0.00383,otu_01699:0.1084):0.01293,((otu_01891:0.06482,(otu_01854:0.03213,otu_00276:0.0232):0.01531):0.01612,(otu_00311:0.04092,otu_00296:0.03054):0.01426):0.04308):0.00747):0.01253,((((((otu_01774:0.0527,otu_01856:0.14151):0.06415,otu_01784:0.07789):0.00658,otu_01704:0.10528):0.00571,(otu_01643:0.07551,otu_01661:0.08483):0.01819):0.01277,otu_01647:0.10236):0.01938,((otu_01691:0.04462,(otu_01873:0.04079,otu_01847:0.01842):0.03763):0.02029,((((otu_00266:0.02169,otu_01690:0.01611):0.01489,otu_00254:0.04496):0.01293,((otu_01694:0.02653,otu_00259:0.03515):0.012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diff -r 000000000000 -r 834843ebe569 test-data/references/01-prepro-flash.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro-flash.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,140562 @@\n+>01_3118;size=12 reference=AB747657_SH134902.07FU_refs position=1..151 \n+CTGAGTATTTGTCTTTTAAAGACATCTCTCTATCCATACACTCTTTTTTTTAAAAAGACATGATTTATACAGTTAGTCTGAATGATTTTTTAAAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_7682;size=17 reference=KJ922376_SH187578.07FU_refs position=1..170 errors=108%G \n+TACCCTTGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCTCCAGGACCACACCATAAACCTTTTTTATGCAGTTGCAATCAGCGTCAGTACAACAAATGTAAATCATTTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_72347;size=10 reference=JN192372_SH093189.07FU_refs position=1..193 errors=129%C \n+GCGGCCGGCTGAATATTTTTTTTCACCCATGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCACCAGGACCAAACCATAAACCTTTTTCTTATGCAGTTTCCATCAGCGTCAGTAAAAACAATGTAATTATTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_52289;size=9 reference=JX272968_SH208843.07FU_refs position=1..194 \n+CCGAGTGAGGGTCCCCTCCGGGGGGCCCAACCTCCCACCCGTGTCTACTGTACCATGTTGCTTCGGCGGGCGCGCCCGTGCCCGCCGGAGACCCCTTGAACGCTGTTGTGAATGAGGTTGTCTGAGTGAGATTGCAAACTGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>01_8007;size=9 reference=KJ638312_SH419903.07FU_refs position=1..194 \n+GATCATTACCGAGTTCTCGGGCTTCGGCTCGACTCTCCCACCCTTTGTGAACGTACCTCTGTTGCTTTGGCGGCTCCGGCCGCCAAAGGACCTCCAAACTCCAGTCAGTAAACGCAGACGTCTGATAAACAAGTTAATAAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_1497;size=12 reference=GU237816_SH186616.07FU_refs position=1..198 \n+ATCATTACCTAGAGTTGTGGGCTCTGCCTACCATCTCTTACCCATGTCTTTTGAGTACCTTCGTTTCCTCGGCGGGTCCGCCCGCCGATCGGACAACACTTAAACCCTTTGTAATTGAAATCAGCGTCTGAAAAAACTTTAATAGTTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_17752;size=6 reference=KP744516_SH528288.07FU_refs position=1..198 \n+CCGAGTGAGGGTCTTCAAAGGCTCAACCTCCCAAACCCCTTGTATATCACCGAGAGTTTTATTGTTGCTTCGGTGGGTCCACAGTGCCCACCGAAGACCCACCAAAAATCCTAGTAAGAGTGTCGTCTGAGTAATTAAAAAATAATCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGC\n+>01_21530;size=5 reference=DQ103550_SH211946.07FU_refs position=1..202 \n+GGAAGGATCATTACCGAGTTCTCGAGCTTCGGCTCGACTCTCCCACCCTTTGTGAACACACCTCTGTTGCCTCGGCGGCCGCTCCGGCCGCCGAAGGACCTTCAAACTCCAGTCAGTAAACGCAGACGTCTGATAAACAAGTCAATGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_83487;size=12 reference=HE861827_SH187575.07FU_refs position=1..202 \n+TACAATATGAAGGCTTCGGCTGGATTATTTATTTCACCCTTGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCACCAGGACCACACCATAAACCTTTTTTGTTAATGCAGTCAGCGTCAGTACAACAAATGTAAATCATTTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_10273;size=9 reference=JQ746601_SH188617.07FU_refs position=1..210 errors=109%C \n+TTGAAATAAACCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACTTTTGTAGACTTTCCAAGTCTATGTTGCTTCATTTACCCCAATGTATGTTAATAGAATGTTGTCTTTTATAATATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_19311;size=12 reference=HQ880789_SH123218.07FU_refs position=1..211 errors=22%G \n+CCGAGTTTTCAACTCCCTAACCCTTTTGTGAACCTACCTATTGTTGCTTCGGCGGACTCGCCCCAGCCGGACGCGGACTGGACCAGCGGCCGCCGGGGACCCTCAAACTCTTGTATTATCAGCATCTTCTGAATACGCCGCAAGGCAAAACAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGC\n+>01_12586;size=12 reference=KP165574_SH188638.07FU_refs position=1..213 errors=93%G \n+TTGAAATAAACCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACTTTTTGTAGACCTTTCAGGTCTATGTTTTCTCATTTTACCCCAATGTATGTCGATAGAATGTTGTGCCTTTATAATGTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_96708;size=5 reference=KP013190_SH094425.07FU_refs position=1..213 \n+TTGAAATAAATCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACTTTTTGTAGACCCTTCAAGGTCTATGTCGCTTAATTTACCCCAAACAAATAATAGAATGTTGTGCCTTTGAAAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_235;size=10 reference=EF652441_SH091530.07FU_refs_singleton position=1..215 \n+AAGGATCATTACCGAGTGTAGGGTGCCTCCGGGCGCCCAACCTCCCACCCGTGACTACCTAACCCTGTTGCTTCGGCGGGGCGCCCCCCCGGGGGGCCGCCGCCGGGGACTACTGAACCTCCTGTCTGAGCCTGATGCAGTCTGAGCTTTGATATTAAATAGTCAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>01_53715;size=15 reference=JX436920_SH182391.07FU_refs position=1..216 \n+CGTGCACGCCCGAG'..b'TCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_36531_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=178%T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=95+A \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTTAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATTGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>03_11710_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=157+G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=42%A \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCGATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCTACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>03_1160_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=126%G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=75+C \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTGCTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_7615_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=101+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=15%G \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAATAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCCATGAAGAACGCAGC\n+>02_91186_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=52+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=82%C \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCGTTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/01-prepro-flash.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro-flash.html Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,828 @@\n+<!DOCTYPE html>\n+\n+<html>\n+ <head>\n+ <title>FROGS Pre-process</title>\n+ <meta charset="UTF-8">\n+ <meta name="version" content="3.2.2">\n+ \n+ \n+ \n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"></link>\n+ <style type="text/css">\n+ #js-alert {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ #content {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ .clear {\n+ clear: both;\n+ height: 0px;\n+ width: 100%;\n+ float: none !important;\n+ }\n+ ul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 0px;\n+\t\t\t\tmargin-bottom: 15px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 20px;\n+\t\t\t\twidth: 20px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue background */\n+\t\t\t.container input:checked ~ .checkmark {\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\topacity:1;\n+\t\t\t}\n+\n+\t\t\t/* Create the checkmark/indicator (hidden when not checked) */\n+\t\t\t.checkmark:after {\n+\t\t\t\tcontent: "";\n+\t\t\t\tposition: absolute;\n+\t\t\t\tdisplay: none;\n+\t\t\t}\n+\n+\t\t\t/* Show the checkmark when checked */\n+\t\t\t.container input:checked ~ .checkmark:after {\n+\t\t\t\tdisplay: block;\n+\t\t\t}\n+\n+\t\t\t/* Style the checkmark/indicator */\n+\t\t\t.container .checkmark:after {\n+\t\t\t\tleft: 7px;\n+\t\t\t\ttop: 3px;\n+\t\t\t\twidth: 6px;\n+\t\t\t\theight: 10px;\n+\t\t\t\tborder: solid white;\n+\t\t\t\tborder-width:'..b'oad("artificial combined", false, "filterBySample-table-artificialCombined", false); \n+ }else{\n+ $("#filterBySample-table-artificialCombined").prev("h2").remove();\n+ $("#filterBySample-table-artificialCombined").remove();\n+ }\n+ /*$("select").addClass("selectpicker");\n+ $(".dataTables_length select").selectpicker({\n+\t\t\t\t\tstyle: \'btn-info\',\n+\t\t\t\t\tsize: 2,\n+\t\t\t\t\twidth : \'60px\'\n+\t\t\t\t});\n+\t\t\t\t$(\'.selectpicker\').selectpicker(\'refresh\');\n+\t\t\t\t//$(\'select\').selectpicker(\'refresh\');\n+\t\t\t\t*/\n+ });\n+ </script>\n+ </head>\n+ <body>\n+ \n+ <p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+ </p>\n+ \n+ \n+ <div id="content" class="hidden">\n+\t\t\t<h2 class="pb-2-first mt-4 mb-2 border-bottom" style="margin-top: 1rem">Preprocess summary</h2>\n+ <div id="filter-summary"></div>\n+ \n+ <div id="filter-log">\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Details on merged sequences</h2>\n+ <table id="filterBySample-table-combined" class="table table-striped">\n+ <thead>\n+\t\t\t\t\t\t\n+ </thead>\n+ <tbody></tbody>\n+ <tfoot>\n+ <tr>\n+ <th>\n+ <span class="table-action">With selection:</span> \n+ <button id="display-spl-lengths" class="btn table-action fusion-right" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="before-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display amplicon lengths</span> </button>\n+ <button id="display-after-spl-lengths" class="btn table-action" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="after-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display preprocessed amplicon lengths</span></button>\n+ </th>\n+ </tr>\n+ </tfoot>\n+ </table>\n+ <h2 class="pb-2 mt-4 mb-2 border-bottom">Details on artificial combined sequences</h2>\n+ <table id="filterBySample-table-artificialCombined" class="table table-striped">\n+ <thead>\n+ </thead>\n+ <tbody></tbody>\n+ </table>\n+ </div>\n+ </div>\n+ \n+ \n+ \n+ \n+ <div class="modal" id="lengths-modal" tabindex="-1" role="dialog" aria-hidden="true">\n+ <div class="modal-dialog modal-lg">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <h4 class="modal-title">Amplicons lengths</h4>\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ \n+ \n+ </div>\n+ <div class="modal-body">\n+ <div id="lengths-chart"></div>\n+ </div>\n+ <div class="modal-footer">\n+ <button class="btn table-action fusion-right" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n+ </div>\n+ </div>\n+ </div>\n+ </div>\n+ </body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/01-prepro-flash.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro-flash.log Thu Apr 08 14:30:48 2021 +0000

b"@@ -0,0 +1,331 @@\n+## Application\n+Software: preprocess.py (version: 3.2.2)\n+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/preprocess.py illumina --min-amplicon-size 44 --max-amplicon-size 490 --five-prim-primer GGCGVACGGGTGAGTAA --three-prim-primer GTGCCAGCNGCNGCGG --R1-size 267 --R2-size 266 --expected-amplicon-size 420 --merge-software flash --nb-cpus 1 --mismatch-rate 0.15 --keep-unmerged --input-archive /home/maria/miniconda3/envs/frogs@3.2.2/bin/test/data/test_dataset2.tar.gz --output-dereplicated res_3.2.2//01-prepro-flash.fasta --output-count res_3.2.2//01-prepro-flash.tsv --summary res_3.2.2//01-prepro-flash.html --log-file res_3.2.2//01-prepro-flash.log\n+\n+## Application\n+Software: preprocess.py (version: 3.2.2)\n+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/preprocess.py illumina --min-amplicon-size 44 --max-amplicon-size 490 --five-prim-primer GGCGVACGGGTGAGTAA --three-prim-primer GTGCCAGCNGCNGCGG --R1-size 267 --R2-size 266 --expected-amplicon-size 420 --merge-software flash --nb-cpus 2 --mismatch-rate 0.15 --keep-unmerged --input-archive data/test_dataset2.tar.gz --output-dereplicated res_3.2.2/01-prepro-flash.fasta --output-count res_3.2.2/01-prepro-flash.tsv --summary res_3.2.2/01-prepro-flash.html --log-file res_3.2.2/01-prepro-flash.log\n+\n+\n+##Sample\n+R1 : res_3.2.2/1617285415.591807_15700_01_subsample_R1.fastq.gz\n+R2 : res_3.2.2/1617285415.591807_15700_01_subsample_R2.fastq.gz\n+Sample name : 01_subsample\n+nb seq before process : 50000\n+##Commands\n+########################################################################################################\n+# Join overlapping paired reads. (flash version : v1.2.11)\n+Command:\n+\tflash --threads 1 --allow-outies --min-overlap 43 --max-overlap 133 --max-mismatch-density 0.15 --compress res_3.2.2/1617285415.591807_15700_01_subsample_R1.fastq.gz res_3.2.2/1617285415.591807_15700_01_subsample_R2.fastq.gz --output-directory res_3.2.2 --output-prefix 1617285416.0384917_15702_01_subsample_flash 2> res_3.2.2/1617285416.0384917_15702_01_subsample_flash.stderr\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:56:56\n+\tend: 01 Apr 2021 15:57:01\n+\n+Results:\n+\tnb seq paired-end assembled: 29070\n+########################################################################################################\n+# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10)\n+Command:\n+\tcutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.2/1617285416.0384917_15702_01_subsample_flash.extendedFrags.fastq.gz > res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_5prim_log.txt 2> res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_5prim_err.txt\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:02\n+\tend: 01 Apr 2021 15:57:05\n+\n+Results:\n+\tnb seq with 5' primer : 29070\n+########################################################################################################\n+# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10)\n+Command:\n+\tcutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt.fastq.gz res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_3prim_log.txt 2> res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_3prim_err.txt\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:05\n+\tend: 01 Apr 2021 15:57:09\n+\n+Results:\n+\tnb seq with 3' primer : 29070\n+########################################################################################################\n+# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0)\n+Command:\n+\tfilterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt.fast"..b' and 3\' primer and removes primer sequence. (cutadapt version : 2.10)\n+Command:\n+\tcutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.2/1617285447.6133468_15702_03_subsample_flash.notCombined_1.fastq.gz res_3.2.2/1617285447.6133468_15702_03_subsample_flash.notCombined_2.fastq.gz > res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_err.txt\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:38\n+\tend: 01 Apr 2021 15:57:41\n+\n+Results:\n+\tnb seq with 5\' primer : 20851\n+\tnb seq with 3\' primer : 20851\n+########################################################################################################\n+# Concatenate paired reads. (combine_and_split.py version : 1.0.0)\n+Command:\n+\tcombine_and_split.py --reads1 res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.2/1617285447.6133468_15702_03_subsample_artificial_combined.fastq.gz\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:41\n+\tend: 01 Apr 2021 15:57:48\n+\n+########################################################################################################\n+# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0)\n+Command:\n+\tfilterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.2/1617285447.6133468_15702_03_subsample_artificial_combined.fastq.gz --output-file res_3.2.2/1617285447.6133468_15702_03_subsample_art_N_filter.fasta --log-file res_3.2.2/1617285447.6133468_15702_03_subsample_art_N_filter_log.txt\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:48\n+\tend: 01 Apr 2021 15:57:48\n+\n+Results:\n+\tnb seq with expected length : 20851\n+\tnb seq without N : 20851\n+########################################################################################################\n+# Replace join tag. (combine_and_split.py version : 1.0.0)\n+Command:\n+\tcombine_and_split.py --reads1 res_3.2.2/1617285447.6133468_15702_03_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.2/1617285447.6133468_15702_03_subsample_art_XtoN.fasta\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:48\n+\tend: 01 Apr 2021 15:57:49\n+\n+########################################################################################################\n+# Dereplicates sample sequences. (derepSamples.py version : 1.6.1)\n+Command:\n+\tderepSamples.py --sequences-files res_3.2.2/1617285447.6133468_15702_03_subsample_N_and_length_filter.fasta res_3.2.2/1617285447.6133468_15702_03_subsample_art_XtoN.fasta --dereplicated-file res_3.2.2/1617285415.591807_15700_03_subsample_filtered.fasta --count-file res_3.2.2/1617285447.6133468_15702_03_subsample_derep_count.tsv\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:49\n+\tend: 01 Apr 2021 15:57:51\n+\n+\n+\n+##Sample\n+All\n+##Commands\n+########################################################################################################\n+# Dereplicates together sequences from several samples. (derepSamples.py version : 1.6.1)\n+Command:\n+\tderepSamples.py --nb-cpus 2 --size-separator \';size=\' --samples-ref res_3.2.2/1617285415.591807_15700_derep_inputs.tsv --dereplicated-file res_3.2.2/01-prepro-flash.fasta --count-file res_3.2.2/01-prepro-flash.tsv\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:51\n+\tend: 01 Apr 2021 15:57:55\n+\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/01-prepro-flash.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro-flash.tsv Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,70282 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diff -r 000000000000 -r 834843ebe569 test-data/references/01-prepro-vsearch.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro-vsearch.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,167778 @@\n+>03_41215;size=1 reference=EF420145_SH015623.07FU_refs_singleton position=1..238 errors=181%T \n+ACCTGCGGAAGGATCATTATTGAAGTAAACCTGATGGGCTGTCGCTGGCTCTCTAGGGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGGCCTTCCCAGGTCTATGTTGCTTCATTTGCCCCCCGATGTATGTCGATAGAATGTAATGTGCCTATAAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_97159;size=3 reference=AY953383_SH113362.07FU_refs position=1..239 errors=161%A \n+TACTGAGTTTTTGTACTCTATAAACCATGTGTGAACGTACCTATCTTGTAGTGAGATGAATGCTGTTTTGGTGGTAGGGCCCTTCTGAAGAGAGGGCACCGCTGCCAGCAGTATAGTCTCACCACTATAAAACTCTTTTATTATTTTCTAGATTTTTCATTGCTGAGTGGCATAACTATAAAAAAGTTAAAACTTTCAACAACGGATCTCTTGGCTCTAGCATCGATGAAGAACGCAGC\n+>01_67609;size=10 reference=UDB011541_SH194446.07FU_refs position=1..241 errors=109%G \n+GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\n+>01_4641;size=45 reference=FJ860822_SH177722.07FU_refs position=1..242 errors=22%A \n+CATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_3904;size=37 reference=UDB016470_SH189377.07FU_refs position=1..242 errors=108%A \n+CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_210;size=83 reference=AJ786644_SH470265.07FU_refs_singleton position=1..243 errors=78%G \n+CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_1953;size=59 reference=EF669607_SH109271.07FU_refs_singleton position=1..243 \n+CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>01_88865;size=244 reference=GQ159830_SH222371.07FU_refs position=1..244 \n+TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>03_4913;size=1 reference=GQ159830_SH222371.07FU_refs position=1..244 errors=151%A \n+TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATTCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_86;size=542 reference=GQ169315_SH195598.07FU_refs position=1..245 errors=79%A \n+TGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>01_93240;size=1 reference=GQ169315_SH195598.07FU_refs position=1..245 errors=174%A \n+TGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTTAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>03_65019;size=1 reference=GQ169315_SH195598.07FU_refs position=1..245 errors=106%A \n+TGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCTTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>03_789'..b'TCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_36531_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=178%T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=95+A \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTTAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATTGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>03_11710_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=157+G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=42%A \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCGATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCTACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>03_1160_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=126%G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=75+C \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTGCTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_7615_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=101+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=15%G \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAATAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCCATGAAGAACGCAGC\n+>02_91186_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=52+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=82%C \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCGTTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/01-prepro-vsearch.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro-vsearch.html Thu Apr 08 14:30:48 2021 +0000

diff -r 000000000000 -r 834843ebe569 test-data/references/01-prepro-vsearch.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro-vsearch.log Thu Apr 08 14:30:48 2021 +0000

b"@@ -0,0 +1,327 @@\n+## Application\n+Software: preprocess.py (version: 3.2.2)\n+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/preprocess.py illumina --min-amplicon-size 44 --max-amplicon-size 490 --five-prim-primer GGCGVACGGGTGAGTAA --three-prim-primer GTGCCAGCNGCNGCGG --R1-size 267 --R2-size 266 --merge-software vsearch --nb-cpus 2 --mismatch-rate 0.15 --keep-unmerged --input-archive data/test_dataset2.tar.gz --output-dereplicated res_3.2.2/01-prepro-vsearch.fasta --output-count res_3.2.2/01-prepro-vsearch.tsv --summary res_3.2.2/01-prepro-vsearch.html --log-file res_3.2.2/01-prepro-vsearch.log\n+\n+\n+##Sample\n+R1 : res_3.2.2/1617285475.3604712_15868_01_subsample_R1.fastq.gz\n+R2 : res_3.2.2/1617285475.3604712_15868_01_subsample_R2.fastq.gz\n+Sample name : 01_subsample\n+nb seq before process : 50000\n+##Commands\n+########################################################################################################\n+# join overlapping paired reads (vsearch version : v2.17.0_linux_x86_64)\n+Command:\n+\tvsearch --threads 1 --fastq_mergepairs res_3.2.2/1617285475.3604712_15868_01_subsample_R1.fastq.gz --reverse res_3.2.2/1617285475.3604712_15868_01_subsample_R2.fastq.gz --fastqout res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.assembled.fastq --fastqout_notmerged_fwd res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.unassembled_R1.fastq --fastqout_notmerged_rev res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.unassembled_R2.fastq --fastq_allowmergestagger --fastq_ascii 33 --fastq_maxdiffpct 15.0 --fastq_minovlen 43 2> res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.log\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:56\n+\tend: 01 Apr 2021 15:57:58\n+\n+Results:\n+\tnb seq paired-end assembled: 24402\n+########################################################################################################\n+# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10)\n+Command:\n+\tcutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.assembled.fastq > res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_5prim_log.txt 2> res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_5prim_err.txt\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:57:58\n+\tend: 01 Apr 2021 15:58:00\n+\n+Results:\n+\tnb seq with 5' primer : 24402\n+########################################################################################################\n+# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10)\n+Command:\n+\tcutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt.fastq.gz res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_3prim_log.txt 2> res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_3prim_err.txt\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:58:00\n+\tend: 01 Apr 2021 15:58:03\n+\n+Results:\n+\tnb seq with 3' primer : 24402\n+########################################################################################################\n+# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0)\n+Command:\n+\tfilterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt.fastq.gz --output-file res_3.2.2/1617285475.569636_15869_01_subsample_N_and_length_filter.fasta --log-file res_3.2.2/1617285475.569636_15869_01_subsample_N_and_length_filter_log.txt\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:58:03\n+\tend: 01 Apr 2021 15:58:04\n+\n+Results:\n+\tnb seq with expected length : 24402\n+\tnb seq without N : 24402\n+########################################################################################################\n+# Removes read pa"..b'\' primer and removes primer sequence. (cutadapt version : 2.10)\n+Command:\n+\tcutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.2/1617285503.8445683_15869_03_subsample_vsearch.unassembled_R1.fastq res_3.2.2/1617285503.8445683_15869_03_subsample_vsearch.unassembled_R2.fastq > res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_err.txt\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:58:31\n+\tend: 01 Apr 2021 15:58:35\n+\n+Results:\n+\tnb seq with 5\' primer : 25457\n+\tnb seq with 3\' primer : 25457\n+########################################################################################################\n+# Concatenate paired reads. (combine_and_split.py version : 1.0.0)\n+Command:\n+\tcombine_and_split.py --reads1 res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.2/1617285503.8445683_15869_03_subsample_artificial_combined.fastq.gz\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:58:35\n+\tend: 01 Apr 2021 15:58:44\n+\n+########################################################################################################\n+# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0)\n+Command:\n+\tfilterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.2/1617285503.8445683_15869_03_subsample_artificial_combined.fastq.gz --output-file res_3.2.2/1617285503.8445683_15869_03_subsample_art_N_filter.fasta --log-file res_3.2.2/1617285503.8445683_15869_03_subsample_art_N_filter_log.txt\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:58:44\n+\tend: 01 Apr 2021 15:58:44\n+\n+Results:\n+\tnb seq with expected length : 25457\n+\tnb seq without N : 25457\n+########################################################################################################\n+# Replace join tag. (combine_and_split.py version : 1.0.0)\n+Command:\n+\tcombine_and_split.py --reads1 res_3.2.2/1617285503.8445683_15869_03_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.2/1617285503.8445683_15869_03_subsample_art_XtoN.fasta\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:58:45\n+\tend: 01 Apr 2021 15:58:46\n+\n+########################################################################################################\n+# Dereplicates sample sequences. (derepSamples.py version : 1.6.1)\n+Command:\n+\tderepSamples.py --sequences-files res_3.2.2/1617285503.8445683_15869_03_subsample_N_and_length_filter.fasta res_3.2.2/1617285503.8445683_15869_03_subsample_art_XtoN.fasta --dereplicated-file res_3.2.2/1617285475.3604712_15868_03_subsample_filtered.fasta --count-file res_3.2.2/1617285503.8445683_15869_03_subsample_derep_count.tsv\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:58:46\n+\tend: 01 Apr 2021 15:58:48\n+\n+\n+\n+##Sample\n+All\n+##Commands\n+########################################################################################################\n+# Dereplicates together sequences from several samples. (derepSamples.py version : 1.6.1)\n+Command:\n+\tderepSamples.py --nb-cpus 2 --size-separator \';size=\' --samples-ref res_3.2.2/1617285475.3604712_15868_derep_inputs.tsv --dereplicated-file res_3.2.2/01-prepro-vsearch.fasta --count-file res_3.2.2/01-prepro-vsearch.tsv\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:58:48\n+\tend: 01 Apr 2021 15:58:52\n+\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/01-prepro-vsearch.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro-vsearch.tsv Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,83890 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diff -r 000000000000 -r 834843ebe569 test-data/references/02-clustering_denoising.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering_denoising.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T16:00:42", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_74803"}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_22"}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_103"}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_94"}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_108"}}, {"id": "Cluster_8", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_10", "metadata": {"comment": [], "seed_id": "01_97858"}}, {"id": "Cluster_11", "metadata": {"comment": [], "seed_id": "01_60934"}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_13", "metadata": {"comment": [], "seed_id": "01_85419"}}, {"id": "Cluster_14", "metadata": {"comment": [], "seed_id": "01_81"}}, {"id": "Cluster_15", "metadata": {"comment": [], "seed_id": "01_66997"}}, {"id": "Cluster_16", "metadata": {"comment": [], "seed_id": "01_54"}}, {"id": "Cluster_17", "metadata": {"comment": [], "seed_id": "01_92546"}}, {"id": "Cluster_18", "metadata": {"comment": [], "seed_id": "01_59"}}, {"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_96725"}}, {"id": "Cluster_20", "metadata": {"comment": [], "seed_id": "01_71661"}}, {"id": "Cluster_21", "metadata": {"comment": [], "seed_id": "01_25"}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_201"}}, {"id": "Cluster_23", "metadata": {"comment": [], "seed_id": "01_76"}}, {"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_38"}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_10"}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_97506"}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_190"}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_30", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_31", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_90"}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_155"}}, {"id": "Cluster_34", "metadata": {"comment": [], "seed_id": "01_54706"}}, {"id": "Cluster_35", "metadata": {"comment": [], "seed_id": "01_259"}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_51488"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_40"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_151"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_76743"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_90304"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_54589"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_101"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_67"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_66"}}, {"id": "Cluster_48_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_50", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": 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"sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/02-clustering_denoising.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering_denoising.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,148254 @@\n+>Cluster_1 reference=KM668101_SH491630.07FU_refs_singleton position=1..250\n+AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\n+>Cluster_2 reference=JX118731_SH218995.07FU_refs position=1..250 errors=164%A\n+GGCTCTTCGGGGCATGTGCTCGCCTGTCACCTTTATCTTTCCACCTGTGCACACACTGTAGTCCTGGATACCTCTCGCCGCAAGGCGGATGCAGAGACTGCTGCTCAGCCTCCGAAAGGGGGAGGACGGCTATCTTTGAATTTCCAGGTCTACGATTATCACATACCCCAATTGAATGTTACAGAATGTTATCAAAGGGCCTTGTGCCTATAAACCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3 reference=HG007976_SH219743.07FU_refs position=1..250 errors=127%C,210%A\n+AAGGATCATTATTGAATGAACTTGGCGTGGTTGTTGCTGGTCCTCTCGGGGGCATGTGCACACCCGTCATCTTTATCTTTCCACCTGTGCACGTTTTGTAGGTCCAAAAAATTTTTCCGAGGCAACTCGTTTTAGGGGACTGGCGTTCGTTACTGTCGCCTTTCCCTGGATTTTAGGCCTATGTTTTCACATACACCATAACAATGTAATAGAATGTTATTAATGGGCTTTATTGCCTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_4 reference=UDB002317_SH221025.07FU_refs position=1..250 errors=99%A\n+CTGAACGAAATGGGTGGCAAGGCTGTCGCTGGCTCAAATGAGCATGTGCACGTCTTTTGCTGCTTACTTCATTCTCTTTTCCACCTGTGCACTCTTTGTAAACACTTGGGATGTGAGAGAGGGTTGGCATTTATTGTTGAACCTCTCTTGATATTGAAAAAGTCTGGGTGTTTATGTATTTTTTGACATACACGGTCGAATGTCTATAGAATGAAATTAATAGGCTCTTGTCAGCCTTTAAATGATAAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_5 reference=GU234142_SH201120.07FU_refs position=1..250\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_6 reference=UDB015350_SH176685.07FU_refs position=1..250 errors=205%A\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_7 reference=KF732310_SH222414.07FU_refs position=1..250 errors=173%G\n+TTGAAATAAACCTGATGAGTTGCTGCTGGCTCTCTTGGGAGCATGTGCACACTTGTCGTCTTTATATCTCCACCTGTGCACCTTTTGTAGACTTTGGATATCTTTCTGAGTGCTTGTCACTCAGGTTCTTGAGGATTGACTTTACGTCTCTCTTTACATTTCCAAGTCTATGTTTCTTCATATACTCAATGTATGTCTTAGAGTGTAATTAATGGGCCATTGTGCCTATAAACTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_8 reference=JQ320113_SH190746.07FU_refs position=1..250 errors=210%G\n+TCGAAATAAAAACTTGGTTTGGGTTGTTGCTGGCTTCTAGAAGCATGTGCACACTTACTCCATTTTTTCAACCACCTGTGCACTTTGTGTAGACCTGAAACACTTTTTCAAGGTAGTTAAACTAACTACTCTTGGTTTGAGAATCGTCGCTACATGGCTTTTCTCGCGTCTCAGGTTTATGTTCTTTTATATGTACCCTACGAGAATGTATATGAATGTCTACAATTGGCCTCGTGCCTTTTAAAAATTAAAACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_10 reference=JQ621972_SH177703.07FU_refs position=1..250\n+TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_9 reference=JQ279537_SH175098.07FU_refs position=1..250\n+CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11 reference=JX536175_SH183774.07FU_refs position=1..250 errors=71%T\n+AACTTCTTTGGAGATAGTACTGTTGCTGGCCTTGTAATGAGGTATGTGCACGTTCTATTGCCAATTTATTCATCCACCTGTGCACTTTTTGTAGGAGTTCTTTGGGGTTATTTTGTACTTGGTGCAATTTGGCTTTGAAAGGCTTCTATGTCTTATAAACCATTAGTATGTCTCTGAATGTTTTTTATTGGGACTTGATTGGCCCTTTAAACTTGT'..b'CAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_52229_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=122+T;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=47%A\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCTAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAATTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_8899_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=105%G;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=100+G\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTGTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCACATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_65152_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=92%T;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=107+T\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGATCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATAATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_10490_FROGS_combined R1_desc:reference=UDB001581_SH219736.07FU_refs position=1..250 errors=237%G;R2_desc=R2_desc=reference=UDB001581_SH219736.07FU_refs position=1..250 errors=165+A\n+TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATGCAACTTTCAGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_6064_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=197+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=181%C\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCGGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/02-clustering_denoising.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering_denoising.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,69 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/clustering.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/clustering.py --distance 3 --denoising --input-fasta res_3.2.2/01-prepro-vsearch.fasta --input-count res_3.2.2/01-prepro-vsearch.tsv --output-biom res_3.2.2/02-clustering_denoising.biom --output-fasta res_3.2.2/02-clustering_denoising.fasta --output-compo res_3.2.2/02-clustering_denoising_compo.tsv --log-file res_3.2.2/02-clustering_denoising.log --nb-cpus 2
+
+########################################################################################################
+# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0)
+Command:
+ sortAbundancies.py --size-separator ';size=' --input-file res_3.2.2/01-prepro-vsearch.fasta --output-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted.fasta
+
+Execution:
+ start: 01 Apr 2021 15:59:16
+ end:   01 Apr 2021 15:59:19
+
+repalce 100 N tags by 50A-50C in: res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted.fasta out : res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted_NtoA.fasta
+########################################################################################################
+# Clustering sequences. (swarm version : 3.0.0)
+Command:
+ swarm --differences 1 --threads 2 --log res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_log.txt --output-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_composition.txt res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted_NtoA.fasta
+
+Execution:
+ start: 01 Apr 2021 15:59:20
+ end:   01 Apr 2021 15:59:22
+
+########################################################################################################
+# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1)
+Command:
+ extractSwarmsFasta.py --input-fasta res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted_NtoA.fasta --input-swarms res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_composition.txt --output-fasta res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_seeds.fasta
+
+Execution:
+ start: 01 Apr 2021 15:59:22
+ end:   01 Apr 2021 15:59:24
+
+########################################################################################################
+# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0)
+Command:
+ sortAbundancies.py --size-separator '_' --input-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_resizedSeeds.fasta --output-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_sortedSeeds.fasta
+
+Execution:
+ start: 01 Apr 2021 15:59:26
+ end:   01 Apr 2021 15:59:28
+
+########################################################################################################
+# Clustering sequences. (swarm version : 3.0.0)
+Command:
+ swarm --differences 3 --threads 2 --log res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_swarm_log.txt --output-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_swarmD3_composition.txt res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_sortedSeeds.fasta
+
+Execution:
+ start: 01 Apr 2021 15:59:28
+ end:   01 Apr 2021 16:00:42
+
+########################################################################################################
+# Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0)
+Command:
+ swarm2biom.py --clusters-file res_3.2.2/02-clustering_denoising_compo.tsv --count-file res_3.2.2/01-prepro-vsearch.tsv --output-file res_3.2.2/02-clustering_denoising.biom
+
+Execution:
+ start: 01 Apr 2021 16:00:42
+ end:   01 Apr 2021 16:00:44
+
+########################################################################################################
+# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1)
+Command:
+ extractSwarmsFasta.py --input-fasta res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_sortedSeeds.fasta --input-swarms res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_swarmD3_composition.txt --output-fasta res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_final_seeds.fasta
+
+Execution:
+ start: 01 Apr 2021 16:00:45
+ end:   01 Apr 2021 16:00:46
+
+replace 50A-50C  tags by N. in: res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_final_seeds.fasta out : res_3.2.2/02-clustering_denoising.fasta

diff -r 000000000000 -r 834843ebe569 test-data/references/02-clustering_denoising_compo.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering_denoising_compo.tsv Thu Apr 08 14:30:48 2021 +0000

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03_45909'..b'44243_FROGS_combined_1\n+01_44244_FROGS_combined_1\n+01_44248_FROGS_combined_1\n+01_44256_FROGS_combined_1\n+01_13184_FROGS_combined_1\n+01_44264_FROGS_combined_1\n+01_44268_FROGS_combined_1\n+01_44269_FROGS_combined_1\n+01_4426_FROGS_combined_1\n+01_44271_FROGS_combined_1\n+01_44273_FROGS_combined_1\n+01_44274_FROGS_combined_1\n+01_44275_FROGS_combined_1\n+01_44276_FROGS_combined_1\n+01_44278_FROGS_combined_1\n+01_13187_FROGS_combined_1\n+01_44279_FROGS_combined_1\n+01_4427_FROGS_combined_1\n+01_44288_FROGS_combined_1\n+01_4429_FROGS_combined_1\n+01_44306_FROGS_combined_1\n+01_44307_FROGS_combined_1\n+01_44310_FROGS_combined_1\n+01_44319_FROGS_combined_1\n+01_44321_FROGS_combined_1\n+01_44334_FROGS_combined_1\n+01_1318_FROGS_combined_1\n+01_44335_FROGS_combined_1\n+01_4433_FROGS_combined_1\n+01_44342_FROGS_combined_1\n+01_44353_FROGS_combined_1\n+01_44358_FROGS_combined_1\n+01_4435_FROGS_combined_1\n+01_44360_FROGS_combined_1\n+01_44364_FROGS_combined_1\n+01_44368_FROGS_combined_1\n+01_44369_FROGS_combined_1\n+01_13199_FROGS_combined_1\n+01_1012_FROGS_combined_1\n+01_44371_FROGS_combined_1\n+01_44375_FROGS_combined_1\n+01_44376_FROGS_combined_1\n+01_44382_FROGS_combined_1\n+01_44383_FROGS_combined_1\n+01_44391_FROGS_combined_1\n+01_44398_FROGS_combined_1\n+01_4439_FROGS_combined_1\n+01_44401_FROGS_combined_1\n+01_44402_FROGS_combined_1\n+01_1320_FROGS_combined_1\n+01_44403_FROGS_combined_1\n+01_4440_FROGS_combined_1\n+01_44410_FROGS_combined_1\n+01_44411_FROGS_combined_1\n+01_44412_FROGS_combined_1\n+01_44417_FROGS_combined_1\n+01_4441_FROGS_combined_1\n+01_44428_FROGS_combined_1\n+01_44435_FROGS_combined_1\n+01_13210_FROGS_combined_1\n+01_44445_FROGS_combined_1\n+01_44446_FROGS_combined_1\n+01_44449_FROGS_combined_1\n+01_44461_FROGS_combined_1\n+01_44470_FROGS_combined_1\n+01_44474_FROGS_combined_1\n+01_4447_FROGS_combined_1\n+01_44487_FROGS_combined_1\n+01_44488_FROGS_combined_1\n+01_44490_FROGS_combined_1\n+01_13212_FROGS_combined_1\n+01_44508_FROGS_combined_1\n+01_44512_FROGS_combined_1\n+01_44514_FROGS_combined_1\n+01_44520_FROGS_combined_1\n+01_44523_FROGS_combined_1\n+01_44526_FROGS_combined_1\n+01_44533_FROGS_combined_1\n+01_44538_FROGS_combined_1\n+01_44542_FROGS_combined_1\n+01_44549_FROGS_combined_1\n+01_13213_FROGS_combined_1\n+01_44550_FROGS_combined_1\n+01_44551_FROGS_combined_1\n+01_44552_FROGS_combined_1\n+01_44553_FROGS_combined_1\n+01_44556_FROGS_combined_1\n+01_44558_FROGS_combined_1\n+01_44574_FROGS_combined_1\n+01_44593_FROGS_combined_1\n+01_44596_FROGS_combined_1\n+01_44597_FROGS_combined_1\n+01_13215_FROGS_combined_1\n+01_445_FROGS_combined_1\n+01_44601_FROGS_combined_1\n+01_4460_FROGS_combined_1\n+01_44618_FROGS_combined_1\n+01_4461_FROGS_combined_1\n+01_44623_FROGS_combined_1\n+01_44626_FROGS_combined_1\n+01_4463_FROGS_combined_1\n+01_44648_FROGS_combined_1\n+01_44649_FROGS_combined_1\n+01_13217_FROGS_combined_1\n+01_4464_FROGS_combined_1\n+01_44651_FROGS_combined_1\n+01_44652_FROGS_combined_1\n+01_44657_FROGS_combined_1\n+01_44658_FROGS_combined_1\n+01_44664_FROGS_combined_1\n+01_44666_FROGS_combined_1\n+01_4466_FROGS_combined_1\n+01_44674_FROGS_combined_1\n+01_44676_FROGS_combined_1\n+01_1321_FROGS_combined_1\n+01_44682_FROGS_combined_1\n+01_44691_FROGS_combined_1\n+01_44694_FROGS_combined_1\n+01_44702_FROGS_combined_1\n+01_44704_FROGS_combined_1\n+01_44708_FROGS_combined_1\n+01_44719_FROGS_combined_1\n+01_44720_FROGS_combined_1\n+01_44722_FROGS_combined_1\n+01_44726_FROGS_combined_1\n+01_13221_FROGS_combined_1\n+01_44730_FROGS_combined_1\n+01_44739_FROGS_combined_1\n+01_44741_FROGS_combined_1\n+01_44742_FROGS_combined_1\n+01_44743_FROGS_combined_1\n+01_44746_FROGS_combined_1\n+01_44747_FROGS_combined_1\n+01_44748_FROGS_combined_1\n+01_44750_FROGS_combined_1\n+01_44752_FROGS_combined_1\n+01_13224_FROGS_combined_1\n+01_44753_FROGS_combined_1\n+01_44755_FROGS_combined_1\n+01_44757_FROGS_combined_1\n+01_44759_FROGS_combined_1\n+01_44762_FROGS_combined_1\n+01_44764_FROGS_combined_1\n+01_44768_FROGS_combined_1\n+01_44774_FROGS_combined_1\n+01_44779_FROGS_combined_1\n+01_44786_FROGS_combined_1\n+01_13232_FROGS_combined_1\n+01_10132_FROGS_combined_1\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/02-clustering_fastidious.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering_fastidious.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54"}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546"}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59"}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81"}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25"}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803"}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_38"}}, {"id": "Cluster_8", "metadata": {"comment": [], "seed_id": "01_90"}}, {"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_97858"}}, {"id": "Cluster_10", "metadata": {"comment": [], "seed_id": "01_259"}}, {"id": "Cluster_11", "metadata": {"comment": [], "seed_id": "01_90304"}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_22"}}, {"id": "Cluster_13", "metadata": {"comment": [], "seed_id": "01_94"}}, {"id": "Cluster_14", "metadata": {"comment": [], "seed_id": "01_76"}}, {"id": "Cluster_15", "metadata": {"comment": [], "seed_id": "01_60934"}}, {"id": "Cluster_16", "metadata": {"comment": [], "seed_id": "01_85419"}}, {"id": "Cluster_17", "metadata": {"comment": [], "seed_id": "01_54589"}}, {"id": "Cluster_18", "metadata": {"comment": [], "seed_id": "01_40"}}, {"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_66"}}, {"id": "Cluster_20", "metadata": {"comment": [], "seed_id": "01_51488"}}, {"id": "Cluster_21", "metadata": {"comment": [], "seed_id": "01_54706"}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_155"}}, {"id": "Cluster_23", "metadata": {"comment": [], "seed_id": "01_101"}}, {"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_10"}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_97506"}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_151"}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_108"}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_71661"}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id": "01_201"}}, {"id": "Cluster_30", "metadata": {"comment": [], "seed_id": "01_66997"}}, {"id": "Cluster_31", "metadata": {"comment": [], "seed_id": "01_190"}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_96725"}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_103"}}, {"id": "Cluster_34", "metadata": {"comment": [], "seed_id": "01_67"}}, {"id": "Cluster_35", "metadata": {"comment": [], "seed_id": "01_76743"}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_48", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": {"comment": [], "seed_id"'..b', 2, 1], [74661, 2, 1], [74662, 2, 1], [74663, 2, 1], [74664, 2, 1], [74665, 2, 1], [74666, 2, 1], [74667, 2, 1], [74668, 2, 1], [74669, 2, 1], [74670, 2, 1], [74671, 2, 1], [74672, 2, 1], [74673, 2, 1], [74674, 2, 1], [74675, 2, 1], [74676, 2, 1], [74677, 2, 1], [74678, 2, 1], [74679, 2, 1], [74680, 2, 1], [74681, 2, 1], [74682, 2, 1], [74683, 2, 1], [74684, 2, 1], [74685, 2, 1], [74686, 2, 1], [74687, 2, 1], [74688, 2, 1], [74689, 2, 1], [74690, 2, 1], [74691, 2, 1], [74692, 2, 1], [74693, 2, 1], [74694, 2, 1], [74695, 2, 1], [74696, 2, 1], [74697, 2, 1], [74698, 2, 1], [74699, 2, 1], [74700, 2, 1], [74701, 2, 1], [74702, 2, 1], [74703, 2, 1], [74704, 2, 1], [74705, 2, 1], [74706, 2, 1], [74707, 2, 1], [74708, 2, 1], [74709, 2, 1], [74710, 2, 1], [74711, 2, 1], [74712, 2, 1], [74713, 2, 1], [74714, 2, 1], [74715, 2, 1], [74716, 2, 1], [74717, 2, 1], [74718, 2, 1], [74719, 2, 1], [74720, 2, 1], [74721, 2, 1], [74722, 2, 1], [74723, 2, 1], [74724, 2, 1], [74725, 2, 1], [74726, 2, 1], [74727, 2, 1], [74728, 2, 1], [74729, 2, 1], [74730, 2, 1], [74731, 2, 1], [74732, 2, 1], [74733, 2, 1], [74734, 2, 1], [74735, 2, 1], [74736, 2, 1], [74737, 2, 1], [74738, 2, 1], [74739, 2, 1], [74740, 2, 1], [74741, 2, 1], [74742, 2, 1], [74743, 2, 1], [74744, 2, 1], [74745, 2, 1], [74746, 2, 1], [74747, 2, 1], [74748, 2, 1], [74749, 2, 1], [74750, 2, 1], [74751, 2, 1], [74752, 2, 1], [74753, 2, 1], [74754, 2, 1], [74755, 2, 1], [74756, 2, 1], [74757, 2, 1], [74758, 2, 1], [74759, 2, 1], [74760, 2, 1], [74761, 2, 1], [74762, 2, 1], [74763, 2, 1], [74764, 2, 1], [74765, 2, 1], [74766, 2, 1], [74767, 2, 1], [74768, 2, 1], [74769, 2, 1], [74770, 2, 1], [74771, 2, 1], [74772, 2, 1], [74773, 2, 1], [74774, 2, 1], [74775, 2, 1], [74776, 2, 1], [74777, 2, 1], [74778, 2, 1], [74779, 2, 1], [74780, 2, 1], [74781, 2, 1], [74782, 2, 1], [74783, 2, 1], [74784, 2, 1], [74785, 2, 1], [74786, 2, 1], [74787, 2, 1], [74788, 2, 1], [74789, 2, 1], [74790, 2, 1], [74791, 2, 1], [74792, 2, 1], [74793, 2, 1], [74794, 2, 1], [74795, 2, 1], [74796, 2, 1], [74797, 2, 1], [74798, 2, 1], [74799, 2, 1], [74800, 2, 1], [74801, 2, 1], [74802, 2, 1], [74803, 2, 1], [74804, 2, 1], [74805, 2, 1], [74806, 2, 1], [74807, 2, 1], [74808, 2, 1], [74809, 2, 1], [74810, 2, 1], [74811, 2, 1], [74812, 2, 1], [74813, 2, 1], [74814, 2, 1], [74815, 2, 1], [74816, 2, 1], [74817, 2, 1], [74818, 2, 1], [74819, 2, 1], [74820, 2, 1], [74821, 2, 1], [74822, 2, 1], [74823, 2, 1], [74824, 2, 1], [74825, 2, 1], [74826, 2, 1], [74827, 2, 1], [74828, 2, 1], [74829, 2, 1], [74830, 2, 1], [74831, 2, 1], [74832, 2, 1], [74833, 2, 1], [74834, 2, 1], [74835, 2, 1], [74836, 2, 1], [74837, 2, 1], [74838, 2, 1], [74839, 2, 1], [74840, 2, 1], [74841, 2, 1], [74842, 2, 1], [74843, 2, 1], [74844, 2, 1], [74845, 2, 1], [74846, 2, 1], [74847, 2, 1], [74848, 2, 1], [74849, 2, 1], [74850, 2, 1], [74851, 2, 1], [74852, 2, 1], [74853, 2, 1], [74854, 2, 1], [74855, 2, 1], [74856, 2, 1], [74857, 2, 1], [74858, 2, 1], [74859, 2, 1], [74860, 2, 1], [74861, 2, 1], [74862, 2, 1], [74863, 2, 1], [74864, 2, 1], [74865, 2, 1], [74866, 2, 1], [74867, 2, 1], [74868, 2, 1], [74869, 2, 1], [74870, 2, 1], [74871, 2, 1], [74872, 2, 1], [74873, 2, 1], [74874, 2, 1], [74875, 2, 1], [74876, 2, 1], [74877, 2, 1], [74878, 2, 1], [74879, 2, 1], [74880, 2, 1], [74881, 2, 1], [74882, 2, 1], [74883, 2, 1], [74884, 2, 1], [74885, 2, 1], [74886, 2, 1], [74887, 2, 1], [74888, 2, 1], [74889, 2, 1], [74890, 2, 1], [74891, 2, 1], [74892, 2, 1], [74893, 2, 1], [74894, 2, 1], [74895, 2, 1], [74896, 2, 1], [74897, 2, 1], [74898, 2, 1], [74899, 2, 1], [74900, 2, 1], [74901, 2, 1], [74902, 2, 1], [74903, 2, 1], [74904, 2, 1], [74905, 2, 1], [74906, 2, 1], [74907, 2, 1], [74908, 2, 1], [74909, 2, 1], [74910, 2, 1], [74911, 2, 1], [74912, 2, 1], [74913, 2, 1], [74914, 2, 1], [74915, 2, 1], [74916, 2, 1], [74917, 2, 1], [74918, 2, 1], [74919, 2, 1], [74920, 2, 1], [74921, 2, 1]], "shape": [74922, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/02-clustering_fastidious.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering_fastidious.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,149844 @@\n+>Cluster_1 reference=JF747094_SH197643.07FU_refs position=1..249 errors=112%A\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_2 reference=DQ898183_SH216206.07FU_refs position=1..249 errors=21%G\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3 reference=JN711441_SH022548.07FU_refs_singleton position=1..248 errors=206%T\n+AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_4 reference=AF456924_SH097201.07FU_refs position=1..250\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_5 reference=JX399009_SH268556.07FU_refs position=1..249 errors=185%C\n+CATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_6 reference=KM668101_SH491630.07FU_refs_singleton position=1..250\n+AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\n+>Cluster_7 reference=JF417478_SH216679.07FU_refs position=1..250 errors=99%T\n+CCGAGTGAGGGTCCCCTTTGCGGGCCCGACCTCCCACCCGTGTCTACCGTACCGTGTTGCTTCGGCGGGCCCGCCAGGGGGGCTCCTGTCCCTGGCCGCCGGGGGGCCATCTCCCGTGCCTCCGGGCCCGTGCCCGCCGGAGACCCTCGTGAACGCTGTCTTGAACAAAGGTTGCGGTCTGAGTGGAAAACACAATCGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_8 reference=EU837224_SH182725.07FU_refs position=1..249 errors=132%T\n+TTGAATTCTATGGAGGGGGGAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCTTCCTTTCTCTCATACACACACCTGTGCACCTGTTGTAGGTCCTCGAAAGAGGAGCTATGTTTTTCACATCACACCCCGTCGTATGTCTATAGAATGTGTTGAAAACGTCGACCTGTTTGACAGGCCGGCGGACAATAAAATTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_9 reference=JQ621972_SH177703.07FU_refs position=1..250\n+TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_10 reference=HQ714785_SH330547.07FU_refs position=1..250 errors=136%A\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11 reference=AB594796_SH278638.07FU_refs position=1..248 errors=111%C\n+GATCATTACAGAGTTATCTAACTCCCAAACCCATGTGAACTTACCATTTGTTGCCTCGGCAGAGGCTACCCGGTACCTACCCTGGAGCAGCTACCCTGTAGCTACCCTGGAACGGCCTACCCTGTAGCGCATCCTGCCGGTGGACCTTTAAACTCTTGTTATTTTAAAGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_12 reference=JX118731_SH218995.07FU_refs position=1..250 errors=164%A\n+GGCTCTTCGGGGCATGTGCTCGCCTGTCACCTTTATCTTTCCACCTGTGCACACACTGTAGTCCTGGATACCTCTCGCCGCAAGGCGGATGCAGAGACTGCTGCTCAGCCTCCGAAAGGGGGAGGACGGCTATCTTTGAATTTCCAGGTCTACGATTATCACATACCCCAATTGAATGTTACAGAATGTTATCAAAGGGCCTTGTGCCTATAAACCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGA'..b'TTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_7577_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=178%T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=95+A\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTTAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATTGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_50507_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=157+G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=42%A\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCGATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCTACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_50479_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=126%G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=75+C\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTGCTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_18841_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=101+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=15%G\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAATAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCCATGAAGAACGCAGC\n+>Cluster_47898_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=52+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=82%C\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCGTTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/02-clustering_fastidious.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering_fastidious.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,42 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/clustering.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/clustering.py --distance 1 --fastidious --input-fasta res_3.2.2/01-prepro-vsearch.fasta --input-count res_3.2.2/01-prepro-vsearch.tsv --output-biom res_3.2.2/02-clustering_fastidious.biom --output-fasta res_3.2.2/02-clustering_fastidious.fasta --output-compo res_3.2.2/02-clustering_fastidious_compo.tsv --log-file res_3.2.2/02-clustering_fastidious.log --nb-cpus 2
+
+########################################################################################################
+# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0)
+Command:
+ sortAbundancies.py --size-separator ';size=' --input-file res_3.2.2/01-prepro-vsearch.fasta --output-file res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted.fasta
+
+Execution:
+ start: 01 Apr 2021 15:58:52
+ end:   01 Apr 2021 15:58:55
+
+repalce 100 N tags by 50A-50C in: res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted.fasta out : res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted_NtoA.fasta
+########################################################################################################
+# Clustering sequences. (swarm version : 3.0.0)
+Command:
+ swarm --differences 1 --fastidious  --threads 2 --log res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_swarm_log.txt --output-file res_3.2.2/02-clustering_fastidious_compo.tsv res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted_NtoA.fasta
+
+Execution:
+ start: 01 Apr 2021 15:58:56
+ end:   01 Apr 2021 15:59:10
+
+########################################################################################################
+# Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0)
+Command:
+ swarm2biom.py --clusters-file res_3.2.2/02-clustering_fastidious_compo.tsv --count-file res_3.2.2/01-prepro-vsearch.tsv --output-file res_3.2.2/02-clustering_fastidious.biom
+
+Execution:
+ start: 01 Apr 2021 15:59:10
+ end:   01 Apr 2021 15:59:13
+
+########################################################################################################
+# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1)
+Command:
+ extractSwarmsFasta.py --input-fasta res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted_NtoA.fasta --input-swarms res_3.2.2/02-clustering_fastidious_compo.tsv --output-fasta res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_final_seeds.fasta
+
+Execution:
+ start: 01 Apr 2021 15:59:13
+ end:   01 Apr 2021 15:59:14
+
+replace 50A-50C  tags by N. in: res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_final_seeds.fasta out : res_3.2.2/02-clustering_fastidious.fasta

diff -r 000000000000 -r 834843ebe569 test-data/references/02-clustering_fastidious_compo.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering_fastidious_compo.tsv Thu Apr 08 14:30:48 2021 +0000

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diff -r 000000000000 -r 834843ebe569 test-data/references/03-chimera.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/03-chimera.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54"}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546"}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59"}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81"}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25"}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803"}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_38"}}, {"id": "Cluster_8", "metadata": {"comment": [], "seed_id": "01_90"}}, {"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_97858"}}, {"id": "Cluster_10", "metadata": {"comment": [], "seed_id": "01_259"}}, {"id": "Cluster_11", "metadata": {"comment": [], "seed_id": "01_90304"}}, {"id": 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newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/03-chimera.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/03-chimera.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,149840 @@\n+>Cluster_1 reference=JF747094_SH197643.07FU_refs position=1..249 errors=112%A\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_2 reference=DQ898183_SH216206.07FU_refs position=1..249 errors=21%G\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3 reference=JN711441_SH022548.07FU_refs_singleton position=1..248 errors=206%T\n+AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_4 reference=AF456924_SH097201.07FU_refs position=1..250\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_5 reference=JX399009_SH268556.07FU_refs position=1..249 errors=185%C\n+CATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_6 reference=KM668101_SH491630.07FU_refs_singleton position=1..250\n+AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\n+>Cluster_7 reference=JF417478_SH216679.07FU_refs position=1..250 errors=99%T\n+CCGAGTGAGGGTCCCCTTTGCGGGCCCGACCTCCCACCCGTGTCTACCGTACCGTGTTGCTTCGGCGGGCCCGCCAGGGGGGCTCCTGTCCCTGGCCGCCGGGGGGCCATCTCCCGTGCCTCCGGGCCCGTGCCCGCCGGAGACCCTCGTGAACGCTGTCTTGAACAAAGGTTGCGGTCTGAGTGGAAAACACAATCGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_8 reference=EU837224_SH182725.07FU_refs position=1..249 errors=132%T\n+TTGAATTCTATGGAGGGGGGAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCTTCCTTTCTCTCATACACACACCTGTGCACCTGTTGTAGGTCCTCGAAAGAGGAGCTATGTTTTTCACATCACACCCCGTCGTATGTCTATAGAATGTGTTGAAAACGTCGACCTGTTTGACAGGCCGGCGGACAATAAAATTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_9 reference=JQ621972_SH177703.07FU_refs position=1..250\n+TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_10 reference=HQ714785_SH330547.07FU_refs position=1..250 errors=136%A\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11 reference=AB594796_SH278638.07FU_refs position=1..248 errors=111%C\n+GATCATTACAGAGTTATCTAACTCCCAAACCCATGTGAACTTACCATTTGTTGCCTCGGCAGAGGCTACCCGGTACCTACCCTGGAGCAGCTACCCTGTAGCTACCCTGGAACGGCCTACCCTGTAGCGCATCCTGCCGGTGGACCTTTAAACTCTTGTTATTTTAAAGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_12 reference=JX118731_SH218995.07FU_refs position=1..250 errors=164%A\n+GGCTCTTCGGGGCATGTGCTCGCCTGTCACCTTTATCTTTCCACCTGTGCACACACTGTAGTCCTGGATACCTCTCGCCGCAAGGCGGATGCAGAGACTGCTGCTCAGCCTCCGAAAGGGGGAGGACGGCTATCTTTGAATTTCCAGGTCTACGATTATCACATACCCCAATTGAATGTTACAGAATGTTATCAAAGGGCCTTGTGCCTATAAACCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGA'..b'TTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_7577_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=178%T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=95+A\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTTAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATTGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_50507_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=157+G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=42%A\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCGATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCTACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_50479_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=126%G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=75+C\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTGCTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_18841_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=101+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=15%G\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAATAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCCATGAAGAACGCAGC\n+>Cluster_47898_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=52+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=82%C\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCGTTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/03-chimera.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/03-chimera.html Thu Apr 08 14:30:48 2021 +0000

[

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HTMLTable Library\n+\t\t\t *\n+\t\t\t * Copyright (c) 2015 Escudie Frederic\n+\t\t\t * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.\n+\t\t\t */\n+\t\t\tfunction HTMLtable(e){'..b'a": [24947, 49999, 1, 1, 1, 1, 1, 1]}, {"name": "03_subsample", "data": [24960, 49999, 1, 1, 1, 1, 1, 1]}] ;\n+\t\t\t\tvar remove_info = {"nb_removed": 2, "nb_kept": 74920, "abundance_removed": 2, "abundance_kept": 149998, "nb_ambiguous": 0, "abundance_ambiguous": 0} ;\n+\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Radializes colors\n+\t\t\t\tHighcharts.setOptions({\n+\t\t\t\t\t colors : [\'#8EADAC\', \'#DE9F73\'] ,\n+\t\t\t\t\t lang: {thousandsSep: \',\'}\n+\t\t\t\t\t});\n+\t\t\t\t\tHighcharts.SVGRenderer.prototype.symbols.download = function (x, y, w, h) {\n+\t\t\t\t\tvar path = [\n+\t\t\t\t\t\t// Arrow stem\n+\t\t\t\t\t\t\'M\', x + w * 0.5, y,\n+\t\t\t\t\t\t\'L\', x + w * 0.5, y + h * 0.7,\n+\t\t\t\t\t\t// Arrow head\n+\t\t\t\t\t\t\'M\', x + w * 0.3, y + h * 0.5,\n+\t\t\t\t\t\t\'L\', x + w * 0.5, y + h * 0.7,\n+\t\t\t\t\t\t\'L\', x + w * 0.7, y + h * 0.5,\n+\t\t\t\t\t\t// Box\n+\t\t\t\t\t\t\'M\', x, y + h * 0.9,\n+\t\t\t\t\t\t\'L\', x, y + h,\n+\t\t\t\t\t\t\'L\', x + w, y + h,\n+\t\t\t\t\t\t\'L\', x + w, y + h * 0.9\n+\t\t\t\t\t];\n+\t\t\t\t\treturn path;\n+\t\t\t\t};\n+\t\t\t\t/* Radial gradient ?*/\n+\t\t\t Highcharts.getOptions().colors = Highcharts.map(Highcharts.getOptions().colors, function (color) {\n+\t\t\t return {\n+\t\t\t radialGradient: { cx: 0.5, cy: 0.3, r: 0.7 },\n+\t\t\t stops: [\n+\t\t\t [0, color],\n+\t\t\t [1, Highcharts.Color(color).brighten(-0.1).get(\'rgb\')] // darken\n+\t\t\t ]\n+\t\t\t };\n+\t\t\t });\n+\t\t\t\t\n+\t\t\t \t// Display chimera remove data\n+\t\t\t\tvar nb_filtered_data = [\n+\t\t\t\t\t[\'Kept\', remove_info[\'nb_kept\']],\n+\t\t\t\t\t[\'Removed\', remove_info[\'nb_removed\']]\n+\t\t\t\t];\n+\t\t\t\t$(\'#nb-filtered\').highcharts( pie_param(\'Clusters\', nb_filtered_data, \'Clusters\') );\n+\t\t\t\tvar abundance_filtered_data = [\n+ \t\t\t\t\t[\'Kept\', remove_info[\'abundance_kept\']],\n+ \t\t\t\t\t[\'Removed\', remove_info[\'abundance_removed\']]\n+ \t\t\t\t];\n+\t\t\t\t$(\'#abundance-filtered\').highcharts( pie_param(\'Abundance\', abundance_filtered_data, \'Sequences\') );\n+\t\t\t\t\n+\t\t\t\t// Display chimera detection data\n+\t\t\t\tvar table_categories = detection_categories.slice() ;\n+\t\t\t\ttable_categories.unshift( "Sample" );\n+\t\t\t\tvar table_series = new Array();\n+\t\t\t\tfor( var spl_idx = 0 ; spl_idx < detection_series.length ; spl_idx++ ){\n+\t\t\t\t\tvar nb_by_step = detection_series[spl_idx][\'data\'].slice() ;\n+\t\t\t\t\tnb_by_step.unshift( detection_series[spl_idx][\'name\'] );\n+\t\t\t\t\ttable_series.push( nb_by_step );\n+\t\t\t\t};\n+\t\t\t\t$(\'#filter-log\').append( table("Chimera detection by sample", table_categories, table_series) );\n+\t\t\t\t$(\'#filter-log table\').prop( \'id\', \'details-table\' );\n+\t\t\t\t$(\'#filter-log table\').DataTable({\n+\t\t\t\t\tdom: \t"<\'#details-csv-export\'><\'row\'<\'col-sm-5\'l><\'col-sm-7\'f>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-12\'tr>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-5\'i><\'col-sm-7\'p>>",\n+\t\t\t\t\t\'lengthMenu\': [[10, 25, 50, 100, -1], [10, 25, 50, 100, "All"]],\n+\t\t\t\t});\n+\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>\' );\n+\t\t\t\t$(\'#details-csv-export\').addClass( \'dataTables_filter\' );\n+\t\t\t\t$(\'#details-csv-export\').datatableExport({\n+\t\t\t\t\t\'table_id\': "details-table"\n+\t\t\t\t});\n+\t\t\t});\n+\t\t</script>\n+\t</head>\n+\t<body>\n+\t\t\n+\t\t<p id="js-alert" class="alert alert-warning">\n+\t\t\tjavascript is needed to display data.<br />\n+\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+\t\t\n+\t\t<div id="content" class="hidden">\n+\t\t\t<div id="filter-summary">\n+ \t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Remove summary</h2>\n+ \t\t<div class="row">\n+\t \t\t<div id="nb-filtered" class="col-md-6"></div> \n+\t \t\t<div id="abundance-filtered" class="col-md-6"></div>\n+ \t\t</div>\n+\t\t\t</div>\n+\t\t\t<div id="filter-log">\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Chimera detection by sample</h2>\n+\t\t\t\t<p>Chimera are first detected by sample, and finally only clusters always detected as chimera in all samples including thoses clusters are removed.</p>\n+\t\t\t</div>\n+\t\t</div>\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/03-chimera.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/03-chimera.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,49 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/remove_chimera.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/remove_chimera.py --input-fasta res_3.2.2/02-clustering_fastidious.fasta --input-biom res_3.2.2/02-clustering_fastidious.biom --non-chimera res_3.2.2/03-chimera.fasta --out-abundance res_3.2.2/03-chimera.biom --summary res_3.2.2/03-chimera.html --log-file res_3.2.2/03-chimera.log --nb-cpus 2
+
+########################################################################################################
+# Removes PCR chimera by samples. (parallelChimera.py version : 0.7.2 [vsearch v2.17.0_linux_x86_64])
+Command:
+ parallelChimera.py --lenient-filter --nb-cpus 2 --sequences res_3.2.2/02-clustering_fastidious.fasta --biom res_3.2.2/02-clustering_fastidious.biom --non-chimera res_3.2.2/03-chimera.fasta --out-abundance res_3.2.2/03-chimera.biom --summary res_3.2.2/1617285647.872855_16058_03-chimera.fasta_summary.tsv --log-file res_3.2.2/1617285647.872855_16058_03-chimera.fasta_tmp.log
+
+Execution:
+ start: 01 Apr 2021 16:00:47
+ end: 01 Apr 2021 16:02:01
+
+
+
+##Sample : 01_subsample
+## Vsearch command: vsearch --uchime_denovo res_3.2.2/1617285648.0228698_16063_01_subsample.fasta.tmp --nonchimeras res_3.2.2/1617285648.0228698_16063_01_subsample.fasta --uchimeout res_3.2.2/1617285648.0228698_16063_01_subsample.fasta.log
+##Results
+sample_name: 01_subsample
+nb_chimera: 0
+chimera_abun: 0
+max_chimera_abun: 0
+nb_non_chimera: 25127
+non_chimera_abun: 50000
+
+##Sample : 02_subsample
+## Vsearch command: vsearch --uchime_denovo res_3.2.2/1617285648.0228698_16063_02_subsample.fasta.tmp --nonchimeras res_3.2.2/1617285648.0228698_16063_02_subsample.fasta --uchimeout res_3.2.2/1617285648.0228698_16063_02_subsample.fasta.log
+##Results
+sample_name: 02_subsample
+nb_chimera: 1
+chimera_abun: 1
+max_chimera_abun: 1
+nb_non_chimera: 24947
+non_chimera_abun: 49999
+
+##Sample : 03_subsample
+## Vsearch command: vsearch --uchime_denovo res_3.2.2/1617285648.0228698_16063_03_subsample.fasta.tmp --nonchimeras res_3.2.2/1617285648.0228698_16063_03_subsample.fasta --uchimeout res_3.2.2/1617285648.0228698_16063_03_subsample.fasta.log
+##Results
+sample_name: 03_subsample
+nb_chimera: 1
+chimera_abun: 1
+max_chimera_abun: 1
+nb_non_chimera: 24960
+non_chimera_abun: 49999
+
+
+## Removes the chimera observation from BIOM.
+
+

diff -r 000000000000 -r 834843ebe569 test-data/references/04-filters.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/04-filters.biom Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,1 @@
+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54"}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546"}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59"}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81"}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25"}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803"}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_38"}}, {"id": "Cluster_8", "metadata": {"comment": [], "seed_id": "01_90"}}, {"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_97858"}}, {"id": "Cluster_10", "metadata": {"comment": [], "seed_id": "01_259"}}, {"id": "Cluster_11", "metadata": {"comment": [], "seed_id": "01_90304"}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_22"}}, {"id": "Cluster_13", "metadata": {"comment": [], "seed_id": "01_94"}}, {"id": "Cluster_14", "metadata": {"comment": [], "seed_id": "01_76"}}, {"id": "Cluster_15", "metadata": {"comment": [], "seed_id": "01_60934"}}, {"id": "Cluster_16", "metadata": {"comment": [], "seed_id": "01_85419"}}, {"id": "Cluster_17", "metadata": {"comment": [], "seed_id": "01_54589"}}, {"id": "Cluster_18", "metadata": {"comment": [], "seed_id": "01_40"}}, {"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_66"}}, {"id": "Cluster_20", "metadata": {"comment": [], "seed_id": "01_51488"}}, {"id": "Cluster_21", "metadata": {"comment": [], "seed_id": "01_54706"}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_155"}}, {"id": "Cluster_23", "metadata": {"comment": [], "seed_id": "01_101"}}, {"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_10"}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_97506"}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_151"}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_108"}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_71661"}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id": "01_201"}}, {"id": "Cluster_30", "metadata": {"comment": [], "seed_id": "01_66997"}}, {"id": "Cluster_31", "metadata": {"comment": [], "seed_id": "01_190"}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_96725"}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_103"}}, {"id": "Cluster_34", "metadata": {"comment": [], "seed_id": "01_67"}}, {"id": "Cluster_35", "metadata": {"comment": [], "seed_id": "01_76743"}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_48", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": {"comment": [], "seed_id": "01_1953"}}, {"id": "Cluster_53", "metadata": {"comment": [], "seed_id": "01_4641"}}, {"id": "Cluster_54", "metadata": {"comment": [], "seed_id": "01_3904"}}, {"id": "Cluster_55", "metadata": {"comment": [], "seed_id": "01_67609"}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 484], [7, 2, 513], [8, 0, 526], [8, 1, 494], [8, 2, 551], [9, 0, 511], [9, 1, 529], [9, 2, 479], [10, 0, 469], [10, 1, 520], [10, 2, 516], [11, 0, 542], [11, 1, 531], [11, 2, 537], [12, 0, 527], [12, 1, 543], [12, 2, 506], [13, 0, 495], [13, 1, 511], [13, 2, 528], [14, 0, 508], [14, 1, 527], 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1, 508], [38, 2, 486], [39, 0, 534], [39, 1, 524], [39, 2, 514], [40, 0, 518], [40, 1, 517], [40, 2, 494], [41, 0, 540], [41, 1, 524], [41, 2, 516], [42, 0, 497], [42, 1, 505], [42, 2, 514], [43, 0, 511], [43, 1, 518], [43, 2, 502], [44, 0, 530], [44, 1, 513], [44, 2, 541], [45, 0, 507], [45, 1, 530], [45, 2, 498], [46, 0, 499], [46, 1, 513], [46, 2, 520], [47, 0, 177], [47, 1, 203], [47, 2, 164], [48, 0, 80], [48, 1, 83], [48, 2, 82], [49, 0, 526], [49, 1, 518], [49, 2, 553], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}
\ No newline at end of file

diff -r 000000000000 -r 834843ebe569 test-data/references/04-filters.excluded
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/04-filters.excluded Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,74866 @@\n+#Present in less than 3 samples\tAbundance < 0.005% (i.e 8 sequences )\tPresent in databank of contaminants\n+Cluster_57_FROGS_combined\tCluster_56\t\n+Cluster_58_FROGS_combined\tCluster_57_FROGS_combined\t\n+Cluster_59_FROGS_combined\tCluster_58_FROGS_combined\t\n+Cluster_60_FROGS_combined\tCluster_59_FROGS_combined\t\n+Cluster_61_FROGS_combined\tCluster_60_FROGS_combined\t\n+Cluster_62_FROGS_combined\tCluster_61_FROGS_combined\t\n+Cluster_63_FROGS_combined\tCluster_62_FROGS_combined\t\n+Cluster_64_FROGS_combined\tCluster_63_FROGS_combined\t\n+Cluster_65_FROGS_combined\tCluster_64_FROGS_combined\t\n+Cluster_66_FROGS_combined\tCluster_65_FROGS_combined\t\n+Cluster_67_FROGS_combined\tCluster_66_FROGS_combined\t\n+Cluster_68_FROGS_combined\tCluster_67_FROGS_combined\t\n+Cluster_69_FROGS_combined\tCluster_68_FROGS_combined\t\n+Cluster_70_FROGS_combined\tCluster_69_FROGS_combined\t\n+Cluster_71_FROGS_combined\tCluster_70_FROGS_combined\t\n+Cluster_72_FROGS_combined\tCluster_71_FROGS_combined\t\n+Cluster_73_FROGS_combined\tCluster_72_FROGS_combined\t\n+Cluster_74_FROGS_combined\tCluster_73_FROGS_combined\t\n+Cluster_75_FROGS_combined\tCluster_74_FROGS_combined\t\n+Cluster_76_FROGS_combined\tCluster_75_FROGS_combined\t\n+Cluster_77_FROGS_combined\tCluster_76_FROGS_combined\t\n+Cluster_78_FROGS_combined\tCluster_77_FROGS_combined\t\n+Cluster_79_FROGS_combined\tCluster_78_FROGS_combined\t\n+Cluster_80_FROGS_combined\tCluster_79_FROGS_combined\t\n+Cluster_81_FROGS_combined\tCluster_80_FROGS_combined\t\n+Cluster_82_FROGS_combined\tCluster_81_FROGS_combined\t\n+Cluster_83_FROGS_combined\tCluster_82_FROGS_combined\t\n+Cluster_84_FROGS_combined\tCluster_83_FROGS_combined\t\n+Cluster_85_FROGS_combined\tCluster_84_FROGS_combined\t\n+Cluster_86_FROGS_combined\tCluster_85_FROGS_combined\t\n+Cluster_87_FROGS_combined\tCluster_86_FROGS_combined\t\n+Cluster_88_FROGS_combined\tCluster_87_FROGS_combined\t\n+Cluster_89_FROGS_combined\tCluster_88_FROGS_combined\t\n+Cluster_90_FROGS_combined\tCluster_89_FROGS_combined\t\n+Cluster_91_FROGS_combined\tCluster_90_FROGS_combined\t\n+Cluster_92_FROGS_combined\tCluster_91_FROGS_combined\t\n+Cluster_93_FROGS_combined\tCluster_92_FROGS_combined\t\n+Cluster_94_FROGS_combined\tCluster_93_FROGS_combined\t\n+Cluster_95_FROGS_combined\tCluster_94_FROGS_combined\t\n+Cluster_96_FROGS_combined\tCluster_95_FROGS_combined\t\n+Cluster_97_FROGS_combined\tCluster_96_FROGS_combined\t\n+Cluster_98_FROGS_combined\tCluster_97_FROGS_combined\t\n+Cluster_99_FROGS_combined\tCluster_98_FROGS_combined\t\n+Cluster_100_FROGS_combined\tCluster_99_FROGS_combined\t\n+Cluster_101_FROGS_combined\tCluster_100_FROGS_combined\t\n+Cluster_102_FROGS_combined\tCluster_101_FROGS_combined\t\n+Cluster_103_FROGS_combined\tCluster_102_FROGS_combined\t\n+Cluster_104_FROGS_combined\tCluster_103_FROGS_combined\t\n+Cluster_105_FROGS_combined\tCluster_104_FROGS_combined\t\n+Cluster_106_FROGS_combined\tCluster_105_FROGS_combined\t\n+Cluster_107_FROGS_combined\tCluster_106_FROGS_combined\t\n+Cluster_108_FROGS_combined\tCluster_107_FROGS_combined\t\n+Cluster_109_FROGS_combined\tCluster_108_FROGS_combined\t\n+Cluster_110_FROGS_combined\tCluster_109_FROGS_combined\t\n+Cluster_111_FROGS_combined\tCluster_110_FROGS_combined\t\n+Cluster_112_FROGS_combined\tCluster_111_FROGS_combined\t\n+Cluster_113_FROGS_combined\tCluster_112_FROGS_combined\t\n+Cluster_114_FROGS_combined\tCluster_113_FROGS_combined\t\n+Cluster_115_FROGS_combined\tCluster_114_FROGS_combined\t\n+Cluster_116_FROGS_combined\tCluster_115_FROGS_combined\t\n+Cluster_117_FROGS_combined\tCluster_116_FROGS_combined\t\n+Cluster_118_FROGS_combined\tCluster_117_FROGS_combined\t\n+Cluster_119_FROGS_combined\tCluster_118_FROGS_combined\t\n+Cluster_120_FROGS_combined\tCluster_119_FROGS_combined\t\n+Cluster_121_FROGS_combined\tCluster_120_FROGS_combined\t\n+Cluster_122_FROGS_combined\tCluster_121_FROGS_combined\t\n+Cluster_123_FROGS_combined\tCluster_122_FROGS_combined\t\n+Cluster_124_FROGS_combined\tCluster_123_FROGS_combined\t\n+Cluster_125_FROGS_combined\tCluster_124_FROGS_combined\t\n+Cluster_126_FROGS_combined\tCluster_125_FROGS_combined\t\n+Cluster_127_FROGS_combined\tCluster_126_FROGS_combined'..b'bined\t\n+Cluster_74857_FROGS_combined\tCluster_74856_FROGS_combined\t\n+Cluster_74858_FROGS_combined\tCluster_74857_FROGS_combined\t\n+Cluster_74859_FROGS_combined\tCluster_74858_FROGS_combined\t\n+Cluster_74860_FROGS_combined\tCluster_74859_FROGS_combined\t\n+Cluster_74861_FROGS_combined\tCluster_74860_FROGS_combined\t\n+Cluster_74862_FROGS_combined\tCluster_74861_FROGS_combined\t\n+Cluster_74863_FROGS_combined\tCluster_74862_FROGS_combined\t\n+Cluster_74864_FROGS_combined\tCluster_74863_FROGS_combined\t\n+Cluster_74865_FROGS_combined\tCluster_74864_FROGS_combined\t\n+Cluster_74866_FROGS_combined\tCluster_74865_FROGS_combined\t\n+Cluster_74867_FROGS_combined\tCluster_74866_FROGS_combined\t\n+Cluster_74868_FROGS_combined\tCluster_74867_FROGS_combined\t\n+Cluster_74869_FROGS_combined\tCluster_74868_FROGS_combined\t\n+Cluster_74870_FROGS_combined\tCluster_74869_FROGS_combined\t\n+Cluster_74871_FROGS_combined\tCluster_74870_FROGS_combined\t\n+Cluster_74872_FROGS_combined\tCluster_74871_FROGS_combined\t\n+Cluster_74873_FROGS_combined\tCluster_74872_FROGS_combined\t\n+Cluster_74874_FROGS_combined\tCluster_74873_FROGS_combined\t\n+Cluster_74875_FROGS_combined\tCluster_74874_FROGS_combined\t\n+Cluster_74876_FROGS_combined\tCluster_74875_FROGS_combined\t\n+Cluster_74877_FROGS_combined\tCluster_74876_FROGS_combined\t\n+Cluster_74878_FROGS_combined\tCluster_74877_FROGS_combined\t\n+Cluster_74879_FROGS_combined\tCluster_74878_FROGS_combined\t\n+Cluster_74880_FROGS_combined\tCluster_74879_FROGS_combined\t\n+Cluster_74881_FROGS_combined\tCluster_74880_FROGS_combined\t\n+Cluster_74882_FROGS_combined\tCluster_74881_FROGS_combined\t\n+Cluster_74883_FROGS_combined\tCluster_74882_FROGS_combined\t\n+Cluster_74884_FROGS_combined\tCluster_74883_FROGS_combined\t\n+Cluster_74885_FROGS_combined\tCluster_74884_FROGS_combined\t\n+Cluster_74886_FROGS_combined\tCluster_74885_FROGS_combined\t\n+Cluster_74887_FROGS_combined\tCluster_74886_FROGS_combined\t\n+Cluster_74888_FROGS_combined\tCluster_74887_FROGS_combined\t\n+Cluster_74889_FROGS_combined\tCluster_74888_FROGS_combined\t\n+Cluster_74890_FROGS_combined\tCluster_74889_FROGS_combined\t\n+Cluster_74891_FROGS_combined\tCluster_74890_FROGS_combined\t\n+Cluster_74892_FROGS_combined\tCluster_74891_FROGS_combined\t\n+Cluster_74893_FROGS_combined\tCluster_74892_FROGS_combined\t\n+Cluster_74894_FROGS_combined\tCluster_74893_FROGS_combined\t\n+Cluster_74895_FROGS_combined\tCluster_74894_FROGS_combined\t\n+Cluster_74896_FROGS_combined\tCluster_74895_FROGS_combined\t\n+Cluster_74897_FROGS_combined\tCluster_74896_FROGS_combined\t\n+Cluster_74898_FROGS_combined\tCluster_74897_FROGS_combined\t\n+Cluster_74899_FROGS_combined\tCluster_74898_FROGS_combined\t\n+Cluster_74900_FROGS_combined\tCluster_74899_FROGS_combined\t\n+Cluster_74901_FROGS_combined\tCluster_74900_FROGS_combined\t\n+Cluster_74902_FROGS_combined\tCluster_74901_FROGS_combined\t\n+Cluster_74903_FROGS_combined\tCluster_74902_FROGS_combined\t\n+Cluster_74904_FROGS_combined\tCluster_74903_FROGS_combined\t\n+Cluster_74905_FROGS_combined\tCluster_74904_FROGS_combined\t\n+Cluster_74906_FROGS_combined\tCluster_74905_FROGS_combined\t\n+Cluster_74907_FROGS_combined\tCluster_74906_FROGS_combined\t\n+Cluster_74908_FROGS_combined\tCluster_74907_FROGS_combined\t\n+Cluster_74909_FROGS_combined\tCluster_74908_FROGS_combined\t\n+Cluster_74910_FROGS_combined\tCluster_74909_FROGS_combined\t\n+Cluster_74911_FROGS_combined\tCluster_74910_FROGS_combined\t\n+Cluster_74912_FROGS_combined\tCluster_74911_FROGS_combined\t\n+Cluster_74913_FROGS_combined\tCluster_74912_FROGS_combined\t\n+Cluster_74914_FROGS_combined\tCluster_74913_FROGS_combined\t\n+Cluster_74915_FROGS_combined\tCluster_74914_FROGS_combined\t\n+Cluster_74916_FROGS_combined\tCluster_74915_FROGS_combined\t\n+Cluster_74917_FROGS_combined\tCluster_74916_FROGS_combined\t\n+Cluster_74918_FROGS_combined\tCluster_74917_FROGS_combined\t\n+Cluster_74919_FROGS_combined\tCluster_74918_FROGS_combined\t\n+Cluster_74920_FROGS_combined\tCluster_74919_FROGS_combined\t\n+Cluster_74921_FROGS_combined\tCluster_74920_FROGS_combined\t\n+Cluster_74922_FROGS_combined\tCluster_74921_FROGS_combined\t\n+\tCluster_74922_FROGS_combined\t\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/04-filters.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/04-filters.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,110 @@\n+>Cluster_1 reference=JF747094_SH197643.07FU_refs position=1..249 errors=112%A\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_2 reference=DQ898183_SH216206.07FU_refs position=1..249 errors=21%G\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3 reference=JN711441_SH022548.07FU_refs_singleton position=1..248 errors=206%T\n+AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_4 reference=AF456924_SH097201.07FU_refs position=1..250\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_5 reference=JX399009_SH268556.07FU_refs position=1..249 errors=185%C\n+CATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_6 reference=KM668101_SH491630.07FU_refs_singleton position=1..250\n+AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\n+>Cluster_7 reference=JF417478_SH216679.07FU_refs position=1..250 errors=99%T\n+CCGAGTGAGGGTCCCCTTTGCGGGCCCGACCTCCCACCCGTGTCTACCGTACCGTGTTGCTTCGGCGGGCCCGCCAGGGGGGCTCCTGTCCCTGGCCGCCGGGGGGCCATCTCCCGTGCCTCCGGGCCCGTGCCCGCCGGAGACCCTCGTGAACGCTGTCTTGAACAAAGGTTGCGGTCTGAGTGGAAAACACAATCGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_8 reference=EU837224_SH182725.07FU_refs position=1..249 errors=132%T\n+TTGAATTCTATGGAGGGGGGAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCTTCCTTTCTCTCATACACACACCTGTGCACCTGTTGTAGGTCCTCGAAAGAGGAGCTATGTTTTTCACATCACACCCCGTCGTATGTCTATAGAATGTGTTGAAAACGTCGACCTGTTTGACAGGCCGGCGGACAATAAAATTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_9 reference=JQ621972_SH177703.07FU_refs position=1..250\n+TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_10 reference=HQ714785_SH330547.07FU_refs position=1..250 errors=136%A\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11 reference=AB594796_SH278638.07FU_refs position=1..248 errors=111%C\n+GATCATTACAGAGTTATCTAACTCCCAAACCCATGTGAACTTACCATTTGTTGCCTCGGCAGAGGCTACCCGGTACCTACCCTGGAGCAGCTACCCTGTAGCTACCCTGGAACGGCCTACCCTGTAGCGCATCCTGCCGGTGGACCTTTAAACTCTTGTTATTTTAAAGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_12 reference=JX118731_SH218995.07FU_refs position=1..250 errors=164%A\n+GGCTCTTCGGGGCATGTGCTCGCCTGTCACCTTTATCTTTCCACCTGTGCACACACTGTAGTCCTGGATACCTCTCGCCGCAAGGCGGATGCAGAGACTGCTGCTCAGCCTCCGAAAGGGGGAGGACGGCTATCTTTGAATTTCCAGGTCTACGATTATCACATACCCCAATTGAATGTTACAGAATGTTATCAAAGGGCCTTGTGCCTATAAACCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGA'..b'TATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_46 reference=JQ716403_SH219241.07FU_refs position=1..250\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_47 reference=EU623745_SH215851.07FU_refs position=1..250 errors=191%C\n+GCGGAAGGATCATTACTGAATTGAAATGCGTTAGTTAGTTGAGCTGACCTTCTCCCTTTAATGGGGGGGGGAGTAGTATGTGCTCGCTATATCGCTTTTTCTAACTCCCCACTGTGCACCTCTATTGTAGGCTACGAGTGACTCTCAAGTAGACACACTCCCATAACACACCCTTTGTGCGCAGAAGGGGGGGGAAAAGGGTCTATTTGGGTTTAAGAAGGCTTATCGGGCATCCATTTTGCTTGCTTTCGACTTTGTAGCCTATGATCTTACAACAAACTACTTTGATAAAGTCTTGATGAATGATAGATTGGTCTTTTGAACCAATATAAAAGTTGTACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_48 reference=GQ169315_SH195598.07FU_refs position=1..245 errors=79%A\n+TGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_49 reference=GQ159830_SH222371.07FU_refs position=1..244\n+TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_50_FROGS_combined R1_desc:reference=JF419897_SH181470.07FU_refs position=1..250;R2_desc=R2_desc=reference=JF419897_SH181470.07FU_refs position=1..250\n+GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_51 reference=AJ786644_SH470265.07FU_refs_singleton position=1..243 errors=78%G\n+CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_52 reference=EF669607_SH109271.07FU_refs_singleton position=1..243\n+CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_53 reference=FJ860822_SH177722.07FU_refs position=1..242 errors=22%A\n+CATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_54 reference=UDB016470_SH189377.07FU_refs position=1..242 errors=108%A\n+CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_55 reference=UDB011541_SH194446.07FU_refs position=1..241 errors=109%G\n+GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/04-filters.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/04-filters.html Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,694 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>FROGS OTU Filters</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="3.2.2">\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#venn-filters {\n+\t\t\t\tpadding: 10px;\n+\t\t\t\tbackground-color: #FFF;\n+\t\t\t\tbackground-clip: padding-box;\n+\t\t\t\tborder: 1px solid rgba(0, 0, 0, 0.15);\n+\t\t\t\tborder-radius: 4px;\n+\t\t\t\tbox-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#byFilters-jvenn {\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#venn-filters ul {\n+\t\t\t\tlist-style-type: none;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t\n+\t\t\t\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAF;\n+\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n+\t\t\t}\n+\t\t\ta {\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\ta:hover{\n+\t\t\t\tcolor:#648a89;\n+\t\t\t}\n+\t\t\t\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 35px;\n+\t\t\t\tmargin-bottom: 12px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 25px;\n+\t\t\t\twidth: 25px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue background */\n+\t'..b'], \'count\': 10},\n+\t\t\t\t\t{\'filters\':[\'filterB\'], \'count\': 20},\n+\t\t\t\t\t{\'filters\':[\'filterC\'], \'count\': 30},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterB\'], \'count\': 1},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterC\'], \'count\': 2},\n+\t\t\t\t\t{\'filters\':[\'filterB\', \'filterC\'], \'count\': 3},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterB\', \'filterC\'], \'count\': 4}\n+\t\t\t\t];\n+\t\t\t*/\n+\t\t\t\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Main\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t$(function() {\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Load active tab\n+\t\t\t\tglobal_filters_load();\n+\t\t\t\tintersections_filters_load();\n+\t\t\t\t\n+\t\t\t\t// Add tab listener\n+\t\t\t\t$(\'.nav-item a\').click(function (e) {\n+\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t$(this).tab(\'show\');\n+\t\t\t\t\tif( $(this).attr(\'href\') == "#view-by-samples" && $(\'#view-by-samples\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#view-by-samples\').removeClass(\'disabled\')\n+\t\t\t\t\t\tsamples_filters_load( "filter-log" );\n+\t\t\t\t\t}\n+\t\t\t\t})\n+\t\t\t});\n+\t\t</script>\n+\n+\t</head>\n+\t<body>\n+\t\t\n+\t\t<p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+ \n+ <div id="content" class="hidden">\n+ \t<ul class="nav nav-tabs">\n+\t\t\t\t<li class="nav-item active"><a class="nav-link active" href="#view-by-filters">Filters by OTUs</a></li>\n+\t\t\t\t<li class="nav-item"><a class="nav-link" href="#view-by-samples">Filters by samples</a></li>\n+\t\t\t</ul>\n+\n+\t\t\t<div id="tab-content" class="tab-content">\n+\t\t\t\t<div id="view-by-filters" role="tabpanel" class="tab-pane active">\n+\t\t\t\t\t<div id="filter-summary">\n+\t\t \t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Filters summary</h2>\n+\t\t \t\t<div class="row">\n+\t\t\t \t\t<div id="nb-filtered" class="col-md-6"></div> \n+\t\t\t \t\t<div id="abundance-filtered" class="col-md-6"></div>\n+\t\t \t\t</div>\n+\t\t\t\t\t</div>\n+\t\t\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Filters intersections</h2>\n+\t\t \t\t<div class="row">\n+\t\t \t\t\t<div class="col-md-2 col-ld-3"></div>\n+\t\t\t\t\t\t<div id="venn-filters" class="col-md-8 col-ld-6">\n+\t\t <p> Draw a Venn to see which OTUs had been deleted by the filters chosen (Maximum 6 options): </p>\n+\t\t <ul id="byFilters-jvenn-chkbx"></ul>\n+\t\t <button id="byFilters-jvenn-btn" class="btn d-block mx-auto" disabled><span class="fa fa-gears" aria-hidden="true"> Venn</span></button>\n+\t\t </div>\n+\t\t <div class="col-md-2 col-ld-3"></div>\n+\t\t </div>\n+\t\t </div>\n+\t\t \n+ <div id="view-by-samples" role="tabpanel" class="tab-pane disabled">\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Details by samples</h2>\n+\t\t <div id="filter-log"></div>\n+ </div>\n+ </div>\n+ </div>\n+\n+\t\t\n+\t\t\n+\t\t<div class="modal fade" id="byFilters-venn-modal" tabindex="-1" role="dialog" aria-labelledby="modal-venn" aria-hidden="true">\n+\t\t <div class="modal-dialog modal-lg">\n+\t\t\t<div class="modal-content">\n+\t\t\t <div class="modal-header">\n+\t\t\t\t<h4 class="modal-title">Venn on removed OTUs</h4>\n+\t\t\t\t<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+\t\t\t </div>\n+\t\t\t <div class="modal-body">\n+\t\t\t\t<div id="byFilters-jvenn"></div>\n+\t\t\t </div>\n+\t\t\t <div class="modal-footer">\n+\t\t\t\t<button type="button" class="btn btn-default" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span></button>\n+\t\t\t </div>\n+\t\t\t</div>\n+\t\t </div>\n+\t\t</div>\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/04-filters.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/04-filters.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,26 @@
+## Application
+Software: otu_filters.py (version: 3.2.2)
+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/otu_filters.py --min-abundance 0.00005 --min-sample-presence 3 --contaminant data/phi.fa --nb-cpus 2 --input-biom res_3.2.2/03-chimera.biom --input-fasta res_3.2.2/03-chimera.fasta --output-fasta res_3.2.2/04-filters.fasta --output-biom res_3.2.2/04-filters.biom --excluded res_3.2.2/04-filters.excluded --summary res_3.2.2/04-filters.html --log-file res_3.2.2/04-filters.log
+
+########################################################################################################
+# Removes contaminant sequences. (removeConta.py version : 1.0)
+Command:
+ removeConta.py --nb-cpus 2 --word-size 40 --min-identity 0.8 --min-coverage 0.8 --input-fasta res_3.2.2/03-chimera.fasta --contaminant-db data/phi.fa --input-biom res_3.2.2/03-chimera.biom --clean-fasta res_3.2.2/1617285721.9659483_16080_cleaned_sequences.fasta --clean-biom res_3.2.2/1617285721.9659483_16080_cleaned_abundance.biom --conta-fasta res_3.2.2/1617285721.9659483_16080_contaminated_sequences.fasta --log-file res_3.2.2/1617285721.9659483_16080_clean.log
+
+Execution:
+ start: 01 Apr 2021 16:02:05
+ end: 01 Apr 2021 16:02:31
+
+Results:
+ number of processed sequences: 74920
+ number of removed contaminated sequences: 0
+
+########################################################################################################
+# Updates fasta file based on sequence in biom file. (biomFastaUpdate.py version : 1.0.1)
+Command:
+ biomFastaUpdate.py --input-biom res_3.2.2/04-filters.biom --input-fasta res_3.2.2/03-chimera.fasta --output-file res_3.2.2/04-filters.fasta --log res_3.2.2/1617285721.9659483_16080_update_fasta_log.txt
+
+Execution:
+ start: 01 Apr 2021 16:02:32
+ end: 01 Apr 2021 16:02:32
+

diff -r 000000000000 -r 834843ebe569 test-data/references/05-itsx.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/05-itsx.biom Thu Apr 08 14:30:48 2021 +0000

[

diff -r 000000000000 -r 834843ebe569 test-data/references/05-itsx.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/05-itsx.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,110 @@\n+>Cluster_1 reference=JF747094_SH197643.07FU_refs position=1..249 errors=112%A\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCA\n+>Cluster_2 reference=DQ898183_SH216206.07FU_refs position=1..249 errors=21%G\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTA\n+>Cluster_3 reference=JN711441_SH022548.07FU_refs_singleton position=1..248 errors=206%T\n+AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAA\n+>Cluster_4 reference=AF456924_SH097201.07FU_refs position=1..250\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCA\n+>Cluster_5 reference=JX399009_SH268556.07FU_refs position=1..249 errors=185%C\n+CATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCA\n+>Cluster_6 reference=KM668101_SH491630.07FU_refs_singleton position=1..250\n+AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAA\n+>Cluster_7 reference=JF417478_SH216679.07FU_refs position=1..250 errors=99%T\n+CCGAGTGAGGGTCCCCTTTGCGGGCCCGACCTCCCACCCGTGTCTACCGTACCGTGTTGCTTCGGCGGGCCCGCCAGGGGGGCTCCTGTCCCTGGCCGCCGGGGGGCCATCTCCCGTGCCTCCGGGCCCGTGCCCGCCGGAGACCCTCGTGAACGCTGTCTTGAACAAAGGTTGCGGTCTGAGTGGAAAACACAATCGTCA\n+>Cluster_8 reference=EU837224_SH182725.07FU_refs position=1..249 errors=132%T\n+TTGAATTCTATGGAGGGGGGAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCTTCCTTTCTCTCATACACACACCTGTGCACCTGTTGTAGGTCCTCGAAAGAGGAGCTATGTTTTTCACATCACACCCCGTCGTATGTCTATAGAATGTGTTGAAAACGTCGACCTGTTTGACAGGCCGGCGGACAATAAAATTATA\n+>Cluster_9 reference=JQ621972_SH177703.07FU_refs position=1..250\n+TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCA\n+>Cluster_10 reference=HQ714785_SH330547.07FU_refs position=1..250 errors=136%A\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATA\n+>Cluster_11 reference=AB594796_SH278638.07FU_refs position=1..248 errors=111%C\n+GATCATTACAGAGTTATCTAACTCCCAAACCCATGTGAACTTACCATTTGTTGCCTCGGCAGAGGCTACCCGGTACCTACCCTGGAGCAGCTACCCTGTAGCTACCCTGGAACGGCCTACCCTGTAGCGCATCCTGCCGGTGGACCTTTAAACTCTTGTTATTTTAAAGTAATCTGAGCGTCTTATTTTAATAAGTCA\n+>Cluster_12 reference=JX118731_SH218995.07FU_refs position=1..250 errors=164%A\n+GGCTCTTCGGGGCATGTGCTCGCCTGTCACCTTTATCTTTCCACCTGTGCACACACTGTAGTCCTGGATACCTCTCGCCGCAAGGCGGATGCAGAGACTGCTGCTCAGCCTCCGAAAGGGGGAGGACGGCTATCTTTGAATTTCCAGGTCTACGATTATCACATACCCCAATTGAATGTTACAGAATGTTATCAAAGGGCCTTGTGCCTATAAACCTATA\n+>Cluster_13 reference=GU234142_SH201120.07FU_refs position=1..250\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATA\n+>Cluster_14 reference=AF118139_SH214931.07FU_refs position=1..250\n+ACGAGTTTCGTACTCCAAACCCTTTGTGAACATACCTGTTTTCGTTGCTTCGGCAGGTGAAGGCGGAGGGCCTCCGGGCCTGAAGCCGCCGCCGGGCGGACCCCTCGCGGGGCGCTGCCGGGTGGGCCTGCCGGAGGGCACAGACTCTGTATTACAACGTACCTCTCTGAGTTATATTTTACAAACAAGTAA\n+>Cluster_15 reference=JX536175_SH183774.'..b'AGGAACGGAAGGGACTGTCGCTGGCCTTTGGAAACGAAGGCATGTGCACGTCTCGAAGTCTTACTTTTTTAGTATCTCGATCTCTTTCCTTTCGTGAGACCCTTTTCTTACACCTGTGCACCTATTGTAGGTCCCGCGAGGGATCTATGTCTCTATCTACTCTAAAACGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTCGGTTGGCGGCAGTAAAGAACTTTATA\n+>Cluster_45 reference=JQ279537_SH175098.07FU_refs position=1..250\n+CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATA\n+>Cluster_46 reference=JQ716403_SH219241.07FU_refs position=1..250\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATA\n+>Cluster_47 reference=EU623745_SH215851.07FU_refs position=1..250 errors=191%C\n+GCGGAAGGATCATTACTGAATTGAAATGCGTTAGTTAGTTGAGCTGACCTTCTCCCTTTAATGGGGGGGGGAGTAGTATGTGCTCGCTATATCGCTTTTTCTAACTCCCCACTGTGCACCTCTATTGTAGGCTACGAGTGACTCTCAAGTAGACACACTCCCATAACACACCCTTTGTGCGCAGAAGGGGGGGGAAAAGGGTCTATTTGGGTTTAAGAAGGCTTATCGGGCATCCATTTTGCTTGCTTTCGACTTTGTAGCCTATGATCTTACAACAAACTACTTTGATAAAGTCTTGATGAATGATAGATTGGTCTTTTGAACCAATATAAAAGTTGTA\n+>Cluster_48 reference=GQ169315_SH195598.07FU_refs position=1..245 errors=79%A\n+TGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTA\n+>Cluster_49 reference=GQ159830_SH222371.07FU_refs position=1..244\n+TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATA\n+>Cluster_50_FROGS_combined R1_desc:reference=JF419897_SH181470.07FU_refs position=1..250;R2_desc=R2_desc=reference=JF419897_SH181470.07FU_refs position=1..250\n+GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTA\n+>Cluster_51 reference=AJ786644_SH470265.07FU_refs_singleton position=1..243 errors=78%G\n+CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTA\n+>Cluster_52 reference=EF669607_SH109271.07FU_refs_singleton position=1..243\n+CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTA\n+>Cluster_53 reference=FJ860822_SH177722.07FU_refs position=1..242 errors=22%A\n+CATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCA\n+>Cluster_54 reference=UDB016470_SH189377.07FU_refs position=1..242 errors=108%A\n+CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATA\n+>Cluster_55 reference=UDB011541_SH194446.07FU_refs position=1..241 errors=109%G\n+GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATA\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/05-itsx.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/05-itsx.html Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,403 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>FROGS ITSx</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="3.2.2">\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t\n+ \n+ \n+\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\t\t\t\n+\t\t\t\n+\t\t\t\n+\t\t</style>\n+\t\t<script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script>\n+\t\t<script type="text/javascript" src="https://code.highcharts.com/8.2.0/highcharts.js"></script>\n+\t\t<script type="text/javascript" src="https://code.highcharts.com/8.2.0/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>\n+\t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script>\n+\t\t<script type="text/javascript">\n+\t\t\t/***************************************************************\n+\t\t\t* Copyright notice\n+\t\t\t*\n+\t\t\t* (c) 2014 PF bioinformatique de Toulouse\n+\t\t\t* All rights reserved\n+\t\t\t* \n+\t\t\t*\n+\t\t\t* This script is an adaptation of the venny script developed by\n+\t\t\t* Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:\n+\t\t\t* Oliveros, J.C. (2007) VENNY. An interactive tool for comparing \n+\t\t\t* lists with Venn Diagrams.\n+\t\t\t* https://bioinfogp.cnb.csic.es/tools/venny/index.html.\n+\t\t\t* It is distributed under the terms of the GNU General Public \n+\t\t\t* License as published by the Free Software Foundation; either \n+\t\t\t* version 2 of the License, or (at your option) any later version.\n+\t\t\t*\n+\t\t\t* The GNU General Public License can be found at\n+\t\t\t* https://www.gnu.org/copyleft/gpl.html.\n+\t\t\t*\n+\t\t\t* This script is distributed in the hope that it will be useful,\n+\t\t\t* but WITHOUT ANY WARRANTY; without even the implied warranty of\n+\t\t\t* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+\t\t\t* GNU General Public License for more details.\n+\t\t\t*\n+\t\t\t* This copyright notice MUST APPEAR in all copies of the script!\n+\t\t\t***************************************************************/\n+\t\t\t!function(){"use strict";function s(s,t){var e,l=Object.keys(t);for(e=0;e<l.length;e++)s=s.replace(new RegExp("\\\\{"+l[e]+"\\\\}","gi"),t[l[e]]);return s}function t(s){var t,e,l;if(!s)throw new Error("cannot create a random attribute name for a'..b' pie_param(\'Abundance\', abundance_filtered_data, \'Sequences\') );\n+\t\t\t}\n+\t\t\t\n+\t\t\tvar samples_filters_load = function( container_id ){\n+\t\t\t\tvar sample_table_titles = ["Sample name", "Initial", "Kept", "Initial abundance", "Kept abundance"];\n+\t\t\t\tvar sample_table_data = new Array();\n+\t\t\t\tfor( var sample in by_samples_results ){\n+\t\t\t\t\tsample_data = [sample, by_samples_results[sample][\'initial\'], by_samples_results[sample][\'kept\'], by_samples_results[sample][\'initial_ab\'], by_samples_results[sample][\'kept_ab\']] ;\n+\t\t\t\t\t\n+\t\t\t\t\t\n+\t\t\t\t\tsample_table_data.push( sample_data );\n+\t\t\t\t}\n+\t\t\t\t$(\'#\' + container_id).append( table("OTUs removed by sample", sample_table_titles, sample_table_data) );\n+\t\t\t\t$(\'#\' + container_id + \' table\').prop( \'id\', \'details-table\' );\n+\t\t\t\t$(\'#\' + container_id + \' table\').DataTable({\n+\t\t\t\t\t"sDom": \'<"top"<"#details-csv-export"><"clear">lf>rt<"bottom"ip><"clear">\'\n+\t\t\t\t});\n+\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>\' );\n+\t\t\t\t$(\'#details-csv-export\').addClass( \'dataTables_filter\' );\n+\t\t\t\t$(\'#details-csv-export\').datatableExport({\n+\t\t\t\t\t\'table_id\': "details-table"\n+\t\t\t\t});\n+\t\t\t}\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Data\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t\n+\t\t\tvar global_results = {"nb_clstr_kept": 55, "nb_clstr_ini": 55, "nb_seq_kept": 75128, "nb_seq_ini": 75128} ; \n+\t\t\t/* Example: \n+\t\t\t\t{\n+\t\t\t\t\t\'nb_clstr_kept\': 100,\n+\t\t\t\t\t\'nb_clstr_ini\': 300,\n+\t\t\t\t\t\'nb_seq_kept\': 100,\n+\t\t\t\t\t\'nb_seq_ini\': 100000\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\tvar by_samples_results = {"01_subsample": {"initial": 55, "filtered": {}, "kept": 55, "initial_ab": 24927, "kept_ab": 24927}, "02_subsample": {"initial": 55, "filtered": {}, "kept": 55, "initial_ab": 25107, "kept_ab": 25107}, "03_subsample": {"initial": 55, "filtered": {}, "kept": 55, "initial_ab": 25094, "kept_ab": 25094}} ;\n+\t\t\t/* Example:\n+\t\t\t\t{\n+\t\t\t\t\t\'sampleA\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterA\': 10,\n+\t\t\t\t\t\t\t\'filterB\': 20\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 75,\n+\t\t\t\t\t\t\'kept\': 50\n+\t\t\t\t\t},\n+\t\t\t\t\t\'sampleB\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterB\': 20,\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 110,\n+\t\t\t\t\t\t\'kept\': 90\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\t\n+\t\t\t\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Main\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t$(function() {\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Load active tab\n+\t\t\t\tglobal_filters_load();\n+\t\t\t\tsamples_filters_load( "filter-log" );\n+\t\t\t\t\n+\t\t\t});\n+\t\t</script>\n+\n+\t</head>\n+\t<body>\n+\t\t\n+\t\t<p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+ \n+ <div id="content" class="hidden">\n+\t\t\t\n+\t\t\t<div id="tab-content" class="tab-content">\n+\t\t\t\t<div id="view-by-filters" role="tabpanel" class="tab-pane active">\n+\t\t\t\t\t<div id="filter-summary">\n+\t\t \t\t<h1 class="pb-2 mt-4 mb-2 border-bottom">Filters (ITSx) summary</h1>\n+\t\t \t\t<div class="row">\n+\t\t\t \t\t<div id="nb-filtered" class="col-md-6"></div> \n+\t\t\t \t\t<div id="abundance-filtered" class="col-md-6"></div>\n+\t\t \t\t</div>\n+\t\t \t\t<h1 class="pb-2 mt-4 mb-2 border-bottom">Filters (ITSx) by samples</h1>\n+\t\t \t\t<div id="view-by-samples" role="tabpanel" class="tab-pane">\n+\t\t\t\t\t\t\t<div id="filter-log"></div>\n+\t\t\t\t\t\t</div>\n+\t\t\t\t\t</div>\n+\t\t </div>\n+ </div>\n+ </div>\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/05-itsx.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/05-itsx.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,35 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/itsx.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/itsx.py --input-fasta res_3.2.2/04-filters.fasta --input-biom res_3.2.2/04-filters.biom --region ITS1 --nb-cpus 2 --out-abundance res_3.2.2/05-itsx.biom --summary res_3.2.2/05-itsx.html --log-file res_3.2.2/05-itsx.log --out-fasta res_3.2.2/05-itsx.fasta --out-removed res_3.2.2/05-itsx-excluded.fasta
+
+########################################################################################################
+# identifies ITS sequences and extracts the ITS region (parallelITSx.py version : 1.0.0 [ITSx 1.1.2])
+Command:
+ parallelITSx.py -f res_3.2.2/04-filters.fasta -b res_3.2.2/04-filters.biom --nb-cpus 2 --its ITS1 --organism-groups F -o res_3.2.2/05-itsx.fasta -m res_3.2.2/05-itsx-excluded.fasta -a res_3.2.2/05-itsx.biom --log-file res_3.2.2/1617285755.6009042_16135_ITSx.log
+
+Execution:
+ start: 01 Apr 2021 16:02:35
+ end: 01 Apr 2021 16:02:43
+
+Results:
+
+# split res_3.2.2/04-filters.fasta in 1 fasta files
+Results
+ Wrote 55 records to res_3.2.2/1617285755.838389_16140_04-filters.fasta_0
+
+## Input file : 1617285755.838389_16140_04-filters.fasta_0
+## in working directory: res_3.2.2/1617285755.838389_16140_1617285755.838389_16140_04-filters.fasta_0
+## ITSx command: ITSx -i /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285755.838389_16140_04-filters.fasta_0 -o 1617285755.838389_16140_04-filters --preserve T -t F --save_regions all
+##Results
+ nb LSU (removed): 0
+ nb 5_8S (removed): 0
+ nb SSU (removed): 1
+ nb full (removed): 0
+ nb no_detections (removed): 0
+ nb ITS2 (removed): 0
+ nb ITS1 (kept): 55
+
+
+## Removes the observations after ITSx.
+
+

diff -r 000000000000 -r 834843ebe569 test-data/references/06-affiliation.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/06-affiliation.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54", "blast_affiliations": [{"subject": "JF747094_SH197643.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546", "blast_affiliations": [{"subject": "DQ898183_SH216206.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59", "blast_affiliations": [{"subject": "JN711441_SH022548.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "evalue": "8.06e-132", "aln_length": 248, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81", "blast_affiliations": [{"subject": "AF456924_SH097201.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "evalue": "4.90e-134", "aln_length": 252, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25", "blast_affiliations": [{"subject": "JX399009_SH268556.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed'..b' 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_54", "metadata": {"comment": [], "seed_id": "01_3904", "blast_affiliations": [{"subject": "UDB016470_SH189377.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "evalue": "1.70e-128", "aln_length": 242, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_55", "metadata": {"comment": [], "seed_id": "01_67609", "blast_affiliations": [{"subject": "UDB011541_SH194446.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "evalue": "6.09e-128", "aln_length": 241, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 484], [7, 2, 513], [8, 0, 526], [8, 1, 494], [8, 2, 551], [9, 0, 511], [9, 1, 529], [9, 2, 479], [10, 0, 469], [10, 1, 520], [10, 2, 516], [11, 0, 542], [11, 1, 531], [11, 2, 537], [12, 0, 527], [12, 1, 543], [12, 2, 506], [13, 0, 495], [13, 1, 511], [13, 2, 528], [14, 0, 508], [14, 1, 527], [14, 2, 530], [15, 0, 535], [15, 1, 512], [15, 2, 517], [16, 0, 508], [16, 1, 504], [16, 2, 490], [17, 0, 490], [17, 1, 531], [17, 2, 495], [18, 0, 499], [18, 1, 490], [18, 2, 476], [19, 0, 526], [19, 1, 498], [19, 2, 494], [20, 0, 514], [20, 1, 507], [20, 2, 499], [21, 0, 504], [21, 1, 483], [21, 2, 536], [22, 0, 510], [22, 1, 472], [22, 2, 518], [23, 0, 515], [23, 1, 500], [23, 2, 515], [24, 0, 491], [24, 1, 506], [24, 2, 533], [25, 0, 494], [25, 1, 513], [25, 2, 509], [26, 0, 536], [26, 1, 490], [26, 2, 547], [27, 0, 545], [27, 1, 507], [27, 2, 493], [28, 0, 498], [28, 1, 515], [28, 2, 524], [29, 0, 525], [29, 1, 530], [29, 2, 510], [30, 0, 511], [30, 1, 550], [30, 2, 469], [31, 0, 509], [31, 1, 522], [31, 2, 515], [32, 0, 508], [32, 1, 544], [32, 2, 545], [33, 0, 480], [33, 1, 504], [33, 2, 515], [34, 0, 525], [34, 1, 499], [34, 2, 483], [35, 0, 536], [35, 1, 534], [35, 2, 521], [36, 0, 499], [36, 1, 538], [36, 2, 539], [37, 0, 473], [37, 1, 528], [37, 2, 524], [38, 0, 518], [38, 1, 508], [38, 2, 486], [39, 0, 534], [39, 1, 524], [39, 2, 514], [40, 0, 518], [40, 1, 517], [40, 2, 494], [41, 0, 540], [41, 1, 524], [41, 2, 516], [42, 0, 497], [42, 1, 505], [42, 2, 514], [43, 0, 511], [43, 1, 518], [43, 2, 502], [44, 0, 530], [44, 1, 513], [44, 2, 541], [45, 0, 507], [45, 1, 530], [45, 2, 498], [46, 0, 499], [46, 1, 513], [46, 2, 520], [47, 0, 177], [47, 1, 203], [47, 2, 164], [48, 0, 80], [48, 1, 83], [48, 2, 82], [49, 0, 526], [49, 1, 518], [49, 2, 553], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/06-affiliation.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/06-affiliation.html Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,548 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>FROGS Affiliation</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="3.2.2">\n+\t\t\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"></link>\n+\t\t<style type="text/css">\n+ #js-alert {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ #content {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ .clear {\n+ clear: both;\n+ height: 0px;\n+ width: 100%;\n+ float: none !important;\n+ }\n+ ul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 0px;\n+\t\t\t\tmargin-bottom: 15px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 20px;\n+\t\t\t\twidth: 20px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue background */\n+\t\t\t.container input:checked ~ .checkmark {\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\topacity:1;\n+\t\t\t}\n+\n+\t\t\t/* Create the checkmark/indicator (hidden when not checked) */\n+\t\t\t.checkmark:after {\n+\t\t\t\tcontent: "";\n+\t\t\t\tposition: absolute;\n+\t\t\t\tdisplay: none;\n+\t\t\t}\n+\n+\t\t\t/* Show the checkmark when checked */\n+\t\t\t.container input:checked ~ .checkmark:after {\n+\t\t\t\tdisplay: block;\n+\t\t\t}\n+\n+\t\t\t/* Style the checkmark/indicator */\n+\t\t\t.container .checkmark:after {\n+\t\t\t\tleft: 7px;\n+\t\t\t\ttop: 3px;\n+\t\t\t\twidth: 6px;\n+\t\t\t\theight: 10px;\n+\t\t\t\tborder: solid white;\n+\t\t\t\tborder-width: 0 3px 3px 0;\n+\t\t\t\t-webkit-transform: rotate(45deg);\n+'..b': [\n+\t\t\t [0, color],\n+\t\t\t [1, Highcharts.Color(color).brighten(-0.3).get(\'rgb\')] // darken\n+\t\t\t ]\n+\t\t\t };\n+\t\t\t });\n+\t\t\t \n+\t\t\t\tvar pie_series = [\n+\t\t\t\t\t["With affiliation", global_results["nb_clstr_with_affi"]],\n+\t\t\t\t\t["Without affiliation", (global_results["nb_clstr"] - global_results["nb_clstr_with_affi"])]\n+\t\t\t\t]\n+\t\t\t\t$(\'#clstr-ratio-affi\').highcharts( pie_param("OTUs affiliation", pie_series, \'OTUs\') );\n+\t\t\t\t\n+\t\t\t\tvar pie_series = [\n+\t\t\t\t\t["With affiliation", global_results["nb_seq_with_affi"]],\n+\t\t\t\t\t["Without affiliation", (global_results["nb_seq"] - global_results["nb_seq_with_affi"])]\n+\t\t\t\t]\n+\t\t\t\t$(\'#seq-ratio-affi\').highcharts( pie_param("Sequences affiliation", pie_series, \'sequences\') );\n+\t\t\t\t\n+\t\t\t\tHighcharts.getOptions().colors = std_color ;\n+\t\t\t\t\n+\t\t\t\tvar histogram_series = [\n+\t\t\t\t\t{\n+\t\t\t\t\t\t\'name\': \'OTUs\',\n+\t\t\t\t\t\t\'data\': global_results["nb_clstr_ambiguous"].map(function(num) {\n+\t\t\t\t\t\t\tvar prct = (num/global_results["nb_clstr"])*10000/100 ;\n+\t\t\t\t\t\t\treturn( parseFloat(numberDisplay(prct)) );\n+\t\t\t\t\t\t})\n+\t\t\t\t\t}, {\n+\t\t\t\t\t\t\'name\': \'Sequences\',\n+\t\t\t\t\t\t\'data\': global_results["nb_seq_ambiguous"].map(function(num) {\n+\t\t\t\t\t\t\tvar prct = (num/global_results["nb_seq"])*10000/100 ;\n+\t\t\t\t\t\t\treturn( parseFloat(numberDisplay(prct)) );\n+\t\t\t\t\t\t})\n+\t\t\t\t\t}\n+\t\t\t\t];\n+\t\t\t\t$(\'#clstr-multi-affi\').highcharts( histogram_param(\'Multi-affiliation by taxonomic rank\', \'% of multi-affiliated\', taxonomy_ranks, histogram_series, \'%\') );\n+\t\t\t\t\n+\t\t\t\t// Display data by sample\n+\t\t\t\tvar table_categories = [ \'Sample\', \'Nb OTUs\', \'% OTUs affiliated by blast\', \'Nb seq\', \'% seq affiliated by blast\' ];\n+\t\t\t\tvar table_series = new Array();\n+\t\t\t\tfor( var sample_name in sample_results ){\n+\t\t\t\t\ttable_series.push([\n+\t\t\t\t\t\tsample_name,\n+\t\t\t\t\t\tsample_results[sample_name][\'nb_clstr\'],\n+\t\t\t\t\t\tMath.round(((sample_results[sample_name][\'nb_clstr_with_affi\']/sample_results[sample_name][\'nb_clstr\'])*10000)/100),\n+\t\t\t\t\t\tsample_results[sample_name][\'nb_seq\'],\n+\t\t\t\t\t\tMath.round(((sample_results[sample_name][\'nb_seq_with_affi\']/sample_results[sample_name][\'nb_seq\'])*10000)/100)\n+\t\t\t\t\t]);\n+\t\t\t\t};\n+\t\t\t\t$(\'#samples-details\').append( table("Blast affiliation by sample", table_categories, table_series) );\n+\t\t\t\t$(\'#samples-details table\').prop( \'id\', \'details-table\' );\n+\t\t\t\t$(\'#samples-details table\').DataTable({\n+\t\t\t\t\t//"sDom": \'<"top"<"#details-csv-export"><"clear">lf>rt<"bottom"ip><"clear">\'\n+\t\t\t\t\tdom: \t"<\'#details-csv-export\'><\'row\'<\'col-sm-5\'l><\'col-sm-7\'f>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-12\'tr>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-5\'i><\'col-sm-7\'p>>",\n+\t\t\t\t\t\t\t"pagingType": "simple"\n+\t\t\t\t});\n+\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn btn-primary" ><span class="fa fa-download" aria-hidden="true"> CSV</span></button>\' );\n+\t\t\t\t$(\'#details-csv-export\').addClass( \'dataTables_filter\' );\n+\t\t\t\t$(\'#details-csv-export\').datatableExport({\n+\t\t\t\t\t\'table_id\': "details-table"\n+\t\t\t\t});\n+\t\t\t});\n+\t\t</script>\n+\t</head>\n+\t<body>\n+\t\t<p id="js-alert" class="alert alert-warning">\n+\t\t\tjavascript is needed to display data.<br />\n+\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t<div id="content" class="hidden">\n+\t\t\t<div id="global-summary">\n+\t\t\t\t<h2 class="pb-2-first mt-4 mb-2 border-bottom" style="margin-top: 1rem">Blast affiliation summary</h2>\n+\t\t\t\t<div class="row">\n+\t\t\t\t\t<div class="col-md-1"></div>\n+\t\t\t\t\t<div id="clstr-ratio-affi" class="col-md-5"></div>\n+\t\t\t\t\t<div id="seq-ratio-affi" class="col-md-5"></div>\n+\t\t\t\t\t<div class="col-md-1"></div>\n+\t\t\t\t</div>\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Blast multi-affiliation summary</h2>\n+\t\t\t\t<div class="row">\n+\t\t\t\t\t<div class="col-md-1"></div>\n+\t\t\t\t\t<div id="clstr-multi-affi" class="col-md-10"></div>\n+\t\t\t\t\t<div class="col-md-1"></div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t\t<div id="samples-details">\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Blast affiliation by sample</h2>\n+\t\t\t</div>\n+\t\t</div>\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/06-affiliation.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/06-affiliation.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,106 @@
+## Application
+Software: affiliation_OTU.py (version: 3.2.2)
+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_OTU.py --reference data/ITS1.rdp.fasta --input-fasta res_3.2.2/04-filters.fasta --input-biom res_3.2.2/04-filters.biom --output-biom res_3.2.2/06-affiliation.biom --summary res_3.2.2/06-affiliation.html --log-file res_3.2.2/06-affiliation.log --nb-cpus 2 --java-mem 2 --rdp
+
+Nb seq : 55
+ with nb seq artificially combined :1
+
+########################################################################################################
+# split res_3.2.2/04-filters.fasta in smaller fasta files
+Results
+ Wrote 55 records to res_3.2.2/1617285763.8139765_17240_04-filters.fasta_0
+########################################################################################################
+# Split on tag. (combine_and_split.py version : 1.0.0)
+Command:
+ combine_and_split.py  --reads1 res_3.2.2/1617285763.8139765_17240_04-filters.fasta_FROGS_combined -s NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --split-output1 res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R1.fasta --split-output2 res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R2.fasta
+
+Execution:
+ start: 01 Apr 2021 16:02:46
+ end:   01 Apr 2021 16:02:46
+
+########################################################################################################
+# blast taxonomic affiliation (blastn version : 2.10.1+)
+Command:
+ blastn -num_threads 2 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R1.fasta -out res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R1.fasta.blast -db data/ITS1.rdp.fasta
+
+Execution:
+ start: 01 Apr 2021 16:02:46
+ end:   01 Apr 2021 16:02:46
+
+########################################################################################################
+# blast taxonomic affiliation (blastn version : 2.10.1+)
+Command:
+ blastn -num_threads 2 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R2.fasta -out res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R2.fasta.blast -db data/ITS1.rdp.fasta
+
+Execution:
+ start: 01 Apr 2021 16:02:46
+ end:   01 Apr 2021 16:02:46
+
+########################################################################################################
+# Reduced reference fasta file based on R1 and R2 100 best score blast alignment (reduce_ref_for_needleall.py version : 1.0)
+Command:
+ reduce_ref_for_needleall.py  -r data/ITS1.rdp.fasta --query-blast-R1 res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R1.fasta.blast --query-blast-R2 res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R2.fasta.blast -f res_3.2.2/1617285763.8139765_17240_reduced_ITS1.rdp.fasta -l res_3.2.2/1617285763.8139765_17240_reduced_ITS1.rdp.fasta.log
+
+Execution:
+ start: 01 Apr 2021 16:02:46
+ end:   01 Apr 2021 16:02:46
+
+ # Parsing blast alignment results to reduce reference databse
+ Reducing reference databases from 102 to 32 sequences
+
+
+########################################################################################################
+# split res_3.2.2/1617285763.8139765_17240_04-filters.fasta_FROGS_combined in smaller fasta files
+Results
+ Generate -1 fasta files of 10 reads
+ Generate 1 fasta file of 1 reads
+
+########################################################################################################
+# rdp taxonomic affiliation (classifier.jar version : unknown)
+Command:
+ java -Xmx2g -jar /home/maria/miniconda3/envs/frogs@3.2.2/bin/classifier.jar classify -c 0.0 -t data/ITS1.rdp.fasta.properties -o res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_0.rdp res_3.2.2/1617285763.8139765_17240_04-filters.fasta_0
+
+Execution:
+ start: 01 Apr 2021 16:02:43
+ end:   01 Apr 2021 16:02:46
+
+
+########################################################################################################
+# Perform global alignment (needleall version : EMBOSS:6.6.0.0)
+Command:
+ needleall  -asequence res_3.2.2/1617285763.8139765_17240_reduced_ITS1.rdp.fasta -bsequence res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0 -outfile res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.sam -aformat3 sam -gapopen 10.0 -gapextend 0.5 -errfile res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.log
+
+Execution:
+ start: 01 Apr 2021 16:02:47
+ end:   01 Apr 2021 16:02:47
+
+########################################################################################################
+# convert NeedleAll Sam output in blast like tsv output sorted by bitscore (needleallSam_to_tsv.py version : 1.0.0)
+Command:
+ needleallSam_to_tsv.py -n res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.sam -r res_3.2.2/1617285763.8139765_17240_reduced_ITS1.rdp.fasta -b res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.blast_like
+
+Execution:
+ start: 01 Apr 2021 16:02:47
+ end:   01 Apr 2021 16:02:47
+
+
+########################################################################################################
+# blast taxonomic affiliation (blastn version : 2.10.1+)
+Command:
+ blastn -num_threads 2 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res_3.2.2/1617285763.8139765_17240_04-filters.fasta_FROGS_full_length -out res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_full_length.blast -db data/ITS1.rdp.fasta
+
+Execution:
+ start: 01 Apr 2021 16:02:47
+ end:   01 Apr 2021 16:02:47
+
+
+
+########################################################################################################
+# Add Blast and/or RDP affiliation to biom (addAffiliation2biom.py version : 2.3.0)
+Command:
+ addAffiliation2biom.py -f data/ITS1.rdp.fasta -i res_3.2.2/04-filters.biom -o res_3.2.2/06-affiliation.biom -b res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_full_length.blast res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.blast_like -r res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_0.rdp
+
+Execution:
+ start: 01 Apr 2021 16:02:48
+ end:   01 Apr 2021 16:02:48
+

diff -r 000000000000 -r 834843ebe569 test-data/references/06-affiliation2.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/06-affiliation2.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54", "blast_affiliations": [{"subject": "JF747094_SH197643.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"]}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546", "blast_affiliations": [{"subject": "DQ898183_SH216206.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"]}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59", "blast_affiliations": [{"subject": "JN711441_SH022548.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "evalue": "8.06e-132", "aln_length": 248, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"]}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81", "blast_affiliations": [{"subject": "AF456924_SH097201.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "evalue": "4.90e-134", "aln_length": 252, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"]}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25", "blast_affiliations": [{"subject": "JX399009_SH268556.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"]}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803", "blast_affiliations": [{"subject": "KM668101_SH491630.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "evalue": "3.94e-140", "aln_length": 263, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"]}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_38", "blast_affiliations": [{"subject": "JF417478_SH216679.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "evalue": "1.75e-133", "aln_length": 251, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"]}}, {"id": "'..b'SH177722.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_rhododendri"], "evalue": "1.70e-128", "aln_length": 242, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_rhododendri"]}}, {"id": "Cluster_54", "metadata": {"comment": [], "seed_id": "01_3904", "blast_affiliations": [{"subject": "UDB016470_SH189377.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "evalue": "1.70e-128", "aln_length": 242, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"]}}, {"id": "Cluster_55", "metadata": {"comment": [], "seed_id": "01_67609", "blast_affiliations": [{"subject": "UDB011541_SH194446.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "evalue": "6.09e-128", "aln_length": 241, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 484], [7, 2, 513], [8, 0, 526], [8, 1, 494], [8, 2, 551], [9, 0, 511], [9, 1, 529], [9, 2, 479], [10, 0, 469], [10, 1, 520], [10, 2, 516], [11, 0, 542], [11, 1, 531], [11, 2, 537], [12, 0, 527], [12, 1, 543], [12, 2, 506], [13, 0, 495], [13, 1, 511], [13, 2, 528], [14, 0, 508], [14, 1, 527], [14, 2, 530], [15, 0, 535], [15, 1, 512], [15, 2, 517], [16, 0, 508], [16, 1, 504], [16, 2, 490], [17, 0, 490], [17, 1, 531], [17, 2, 495], [18, 0, 499], [18, 1, 490], [18, 2, 476], [19, 0, 526], [19, 1, 498], [19, 2, 494], [20, 0, 514], [20, 1, 507], [20, 2, 499], [21, 0, 504], [21, 1, 483], [21, 2, 536], [22, 0, 510], [22, 1, 472], [22, 2, 518], [23, 0, 515], [23, 1, 500], [23, 2, 515], [24, 0, 491], [24, 1, 506], [24, 2, 533], [25, 0, 494], [25, 1, 513], [25, 2, 509], [26, 0, 536], [26, 1, 490], [26, 2, 547], [27, 0, 545], [27, 1, 507], [27, 2, 493], [28, 0, 498], [28, 1, 515], [28, 2, 524], [29, 0, 525], [29, 1, 530], [29, 2, 510], [30, 0, 511], [30, 1, 550], [30, 2, 469], [31, 0, 509], [31, 1, 522], [31, 2, 515], [32, 0, 508], [32, 1, 544], [32, 2, 545], [33, 0, 480], [33, 1, 504], [33, 2, 515], [34, 0, 525], [34, 1, 499], [34, 2, 483], [35, 0, 536], [35, 1, 534], [35, 2, 521], [36, 0, 499], [36, 1, 538], [36, 2, 539], [37, 0, 473], [37, 1, 528], [37, 2, 524], [38, 0, 518], [38, 1, 508], [38, 2, 486], [39, 0, 534], [39, 1, 524], [39, 2, 514], [40, 0, 518], [40, 1, 517], [40, 2, 494], [41, 0, 540], [41, 1, 524], [41, 2, 516], [42, 0, 497], [42, 1, 505], [42, 2, 514], [43, 0, 511], [43, 1, 518], [43, 2, 502], [44, 0, 530], [44, 1, 513], [44, 2, 541], [45, 0, 507], [45, 1, 530], [45, 2, 498], [46, 0, 499], [46, 1, 513], [46, 2, 520], [47, 0, 177], [47, 1, 203], [47, 2, 164], [48, 0, 80], [48, 1, 83], [48, 2, 82], [49, 0, 526], [49, 1, 518], [49, 2, 553], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/06-affiliation2.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/06-affiliation2.html Thu Apr 08 14:30:48 2021 +0000

[

diff -r 000000000000 -r 834843ebe569 test-data/references/06-affiliation2.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/06-affiliation2.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,92 @@
+## Application
+Software: affiliation_OTU.py (version: 3.2.2)
+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_OTU.py --reference data/ITS1.rdp.fasta --input-fasta res_3.2.2/04-filters.fasta --input-biom res_3.2.2/04-filters.biom --output-biom res_3.2.2/06-affiliation2.biom --summary res_3.2.2/06-affiliation2.html --log-file res_3.2.2/06-affiliation2.log --nb-cpus 2 --java-mem 2
+
+Nb seq : 55
+ with nb seq artificially combined :1
+
+########################################################################################################
+# Split on tag. (combine_and_split.py version : 1.0.0)
+Command:
+ combine_and_split.py  --reads1 res_3.2.2/1617285768.1955829_17320_04-filters.fasta_FROGS_combined -s NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --split-output1 res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R1.fasta --split-output2 res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R2.fasta
+
+Execution:
+ start: 01 Apr 2021 16:02:48
+ end:   01 Apr 2021 16:02:48
+
+########################################################################################################
+# blast taxonomic affiliation (blastn version : 2.10.1+)
+Command:
+ blastn -num_threads 2 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R1.fasta -out res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R1.fasta.blast -db data/ITS1.rdp.fasta
+
+Execution:
+ start: 01 Apr 2021 16:02:48
+ end:   01 Apr 2021 16:02:48
+
+########################################################################################################
+# blast taxonomic affiliation (blastn version : 2.10.1+)
+Command:
+ blastn -num_threads 2 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R2.fasta -out res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R2.fasta.blast -db data/ITS1.rdp.fasta
+
+Execution:
+ start: 01 Apr 2021 16:02:48
+ end:   01 Apr 2021 16:02:48
+
+########################################################################################################
+# Reduced reference fasta file based on R1 and R2 100 best score blast alignment (reduce_ref_for_needleall.py version : 1.0)
+Command:
+ reduce_ref_for_needleall.py  -r data/ITS1.rdp.fasta --query-blast-R1 res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R1.fasta.blast --query-blast-R2 res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R2.fasta.blast -f res_3.2.2/1617285768.1955829_17320_reduced_ITS1.rdp.fasta -l res_3.2.2/1617285768.1955829_17320_reduced_ITS1.rdp.fasta.log
+
+Execution:
+ start: 01 Apr 2021 16:02:48
+ end:   01 Apr 2021 16:02:48
+
+ # Parsing blast alignment results to reduce reference databse
+ Reducing reference databases from 102 to 32 sequences
+
+
+########################################################################################################
+# split res_3.2.2/1617285768.1955829_17320_04-filters.fasta_FROGS_combined in smaller fasta files
+Results
+ Generate -1 fasta files of 10 reads
+ Generate 1 fasta file of 1 reads
+
+########################################################################################################
+# Perform global alignment (needleall version : EMBOSS:6.6.0.0)
+Command:
+ needleall  -asequence res_3.2.2/1617285768.1955829_17320_reduced_ITS1.rdp.fasta -bsequence res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0 -outfile res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.sam -aformat3 sam -gapopen 10.0 -gapextend 0.5 -errfile res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.log
+
+Execution:
+ start: 01 Apr 2021 16:02:48
+ end:   01 Apr 2021 16:02:48
+
+########################################################################################################
+# convert NeedleAll Sam output in blast like tsv output sorted by bitscore (needleallSam_to_tsv.py version : 1.0.0)
+Command:
+ needleallSam_to_tsv.py -n res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.sam -r res_3.2.2/1617285768.1955829_17320_reduced_ITS1.rdp.fasta -b res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.blast_like
+
+Execution:
+ start: 01 Apr 2021 16:02:49
+ end:   01 Apr 2021 16:02:49
+
+
+########################################################################################################
+# blast taxonomic affiliation (blastn version : 2.10.1+)
+Command:
+ blastn -num_threads 2 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res_3.2.2/1617285768.1955829_17320_04-filters.fasta_FROGS_full_length -out res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_full_length.blast -db data/ITS1.rdp.fasta
+
+Execution:
+ start: 01 Apr 2021 16:02:49
+ end:   01 Apr 2021 16:02:49
+
+
+
+########################################################################################################
+# Add Blast and/or RDP affiliation to biom (addAffiliation2biom.py version : 2.3.0)
+Command:
+ addAffiliation2biom.py -f data/ITS1.rdp.fasta -i res_3.2.2/04-filters.biom -o res_3.2.2/06-affiliation2.biom -b res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_full_length.blast res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.blast_like
+
+Execution:
+ start: 01 Apr 2021 16:02:49
+ end:   01 Apr 2021 16:02:49
+

diff -r 000000000000 -r 834843ebe569 test-data/references/07-affiliation_deleted.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-affiliation_deleted.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "FROGS_affiliation_filters", "date": "2021-04-01T16:02:50", "rows": [{"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_10", "blast_affiliations": [{"subject": "UDB003291_SH182302.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Hydnellum", "s__Hydnellum_peckii"], "evalue": "7.05e-153", "aln_length": 286, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Hydnellum", "s__Hydnellum_peckii"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Hydnellum", "s__Hydnellum_peckii"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_97506", "blast_affiliations": [{"subject": "KC992854_SH220410.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "evalue": "2.53e-152", "aln_length": 285, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_151", "blast_affiliations": [{"subject": "JX179268_SH178540.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "evalue": "2.53e-152", "aln_length": 285, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_108", "blast_affiliations": [{"subject": "KF732310_SH222414.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"], "evalue": "5.49e-154", "aln_length": 288, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_71661", "blast_affiliations": [{"subject": "UDB001581_SH219736.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "evalue": "1.97e-153", "aln_length": 287, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id"'..b'idiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485", "blast_affiliations": [{"subject": "JQ716403_SH219241.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "evalue": "7.94e-178", "aln_length": 331, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410", "blast_affiliations": [{"subject": "EU623745_SH215851.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "evalue": "0.0", "aln_length": 390, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined", "blast_affiliations": [{"subject": "JF419897_SH181470.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "evalue": "-1", "aln_length": 1017, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 515], [0, 1, 500], [0, 2, 515], [1, 0, 491], [1, 1, 506], [1, 2, 533], [2, 0, 494], [2, 1, 513], [2, 2, 509], [3, 0, 536], [3, 1, 490], [3, 2, 547], [4, 0, 545], [4, 1, 507], [4, 2, 493], [5, 0, 498], [5, 1, 515], [5, 2, 524], [6, 0, 525], [6, 1, 530], [6, 2, 510], [7, 0, 511], [7, 1, 550], [7, 2, 469], [8, 0, 509], [8, 1, 522], [8, 2, 515], [9, 0, 508], [9, 1, 544], [9, 2, 545], [10, 0, 480], [10, 1, 504], [10, 2, 515], [11, 0, 525], [11, 1, 499], [11, 2, 483], [12, 0, 536], [12, 1, 534], [12, 2, 521], [13, 0, 499], [13, 1, 538], [13, 2, 539], [14, 0, 473], [14, 1, 528], [14, 2, 524], [15, 0, 518], [15, 1, 508], [15, 2, 486], [16, 0, 534], [16, 1, 524], [16, 2, 514], [17, 0, 518], [17, 1, 517], [17, 2, 494], [18, 0, 540], [18, 1, 524], [18, 2, 516], [19, 0, 497], [19, 1, 505], [19, 2, 514], [20, 0, 511], [20, 1, 518], [20, 2, 502], [21, 0, 530], [21, 1, 513], [21, 2, 541], [22, 0, 507], [22, 1, 530], [22, 2, 498], [23, 0, 499], [23, 1, 513], [23, 2, 520], [24, 0, 526], [24, 1, 518], [24, 2, 553]], "shape": [25, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/07-affiliation_deleted.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-affiliation_deleted.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,50 @@\n+>Cluster_25 reference=KC992854_SH220410.07FU_refs position=1..250\n+ATCTATGGTGTTGGTTGTAGCTGGCTTCTCGGAGCATGTGCACACCCGCCATTTTTATCTTTCCACCTGTGCACTTAATGTAGATCTGGATAACTCTCGCTTTCACGAGCGGATGCAAGGATTGCTGTGTCGCAAGACCGGCTTTCTTTGAACTTCCAGGTCTATGTACCCTTACACACCCCAATTGTATGATGAAGAATGTAGTCAATGGGCTTTATGCCTATAAAACAAAATACAACTTTTAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_24 reference=UDB003291_SH182302.07FU_refs position=1..250 errors=113%G\n+GGACTGCGGAGGACATTAATGAAATCGACGTTTCGGGAAAGGTTGTTGCTGGCCCCACGGCATGTGCACGCCTTTACCGGATGTATTCGTCCTTTCTTTACACCTGTGCACGATCTGTAGCTAGGGATGATCACGGAGCCTGTCGGTTCCGAATGCCCTGGCTATGAACGTTTTTATACCCTCTTATAAAGTTTTTTTTGAATGTTTGTCCTGCGTGTAACAGCGCGAATGAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_26 reference=JX179268_SH178540.07FU_refs position=1..250 errors=128%C\n+TCATTATTGAATAAATATGGTAGGTTGTAGCTGGCTTTGTGAAGCATGTGCACGCCTACTGTCTTTATCTATCCCTCTGTGCATCATTTGTAGTCCTGGAGAGCAAGCCCCCTGCATTGGAAAGAAGTAATTCTTTTTCTTGGGGGTGTCTGATCCAGGTCTATGTATTTTCCATAGACAATGCAGTATGTTACCGAATGTAATCAATGGGTCATTGTGCCTATAAAACTTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_28 reference=UDB001581_SH219736.07FU_refs position=1..250 errors=177%C\n+TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_27 reference=KF732310_SH222414.07FU_refs position=1..250 errors=173%G\n+TTGAAATAAACCTGATGAGTTGCTGCTGGCTCTCTTGGGAGCATGTGCACACTTGTCGTCTTTATATCTCCACCTGTGCACCTTTTGTAGACTTTGGATATCTTTCTGAGTGCTTGTCACTCAGGTTCTTGAGGATTGACTTTACGTCTCTCTTTACATTTCCAAGTCTATGTTTCTTCATATACTCAATGTATGTCTTAGAGTGTAATTAATGGGCCATTGTGCCTATAAACTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_29 reference=KF732603_SH223051.07FU_refs position=1..250 errors=238%C\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_30 reference=KC992888_SH220378.07FU_refs position=1..250\n+ATGAATATCTATGGCGGTGGTTGTAGCTGGCTTCTAGGAGCATATGTGCACACCCGTCATTCATATCTTTCCACCTGTGAACCTAATGTAGATCTGGATAACTCTCGCTTTCTGAGCGGAAACAGGGATTGCTGTGTCGCAAGGCCAGCTCTCTTTGAATTTCCAGGTCTATGTCCTTTACACACCCCAATTGAATGATGAAGAATGTAGTCAATGGGCTCTAAGCCCATAAAACACAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_31 reference=KF732272_SH222375.07FU_refs position=1..250\n+TTGAAATAAATCTGATAAGTTGCTGCTGGTTCTCTAGGGAGCAATGTGCACACTTGTCATCTTTGTATCTTCACCTGTGCACCTTTTGTAGACCTGAGTATCTCTCTGAATTGCTTATAGCATTCAGGATTGAGAATTGACTTCTTGTCTCTTCTTATATTTTCAGGTCTATGTTTCTTCATATACCCCAATGTATGTTTATAGAATGTAATTAATGGGCCTTTGTGCCTATAAACCTTTACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_32 reference=KF732249_SH136099.07FU_refs_singleton position=1..250\n+TTGAAATAAACCTGATGAGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACACTCGTCATCTTTGTATATTCACCTGTGCATCTTTTGTAGACCCTTGGGTATCTCTCTGATTGCTTTTAGCACTCAGGATTGAGGATTGACTTCCTGTCTCTTCTTACATTTCCAGGTCTATGTTTCTTAATATACCCTAATGTATGTTTATAGAATGTAATTAATGGGCCTTTGTGCCTATAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_33 reference=HG007976_SH219743.07FU_refs position=1..250 errors=127%C,210%A\n+AAGGATCATTATTGAATGAACTTGGCGTGGTTGTTGCTGGTCCTCTCGGGGGCATGTGCACACCCGTCATCTTTATCTTTCCACCTGTGCACGTTTTGTAGGTCCAAAAAATTTTTCCGAGGCAACTCGTTTTAGGGGACTGGCGTTCGTTACTGTCGCCTTTCCCTGGATTTTAGGCCTATGTTTTCACATACACCATAACAATGTAATAGAATGTTATTAATGGGCTTTATTGCCTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_34 reference=UDB016091_SH210668.07FU_refs position=1..250 errors=238%A\n+ATGAAATCAAAACTTTCATTGAAAGGTTGTTGCTGATATATATATATATATGTGCACACCTGGATTTGAAAGTCTTCATCCTTTACCTCCCTTGTGCACGATCTGTAGCTTTGGGATGATTACAGAGTTTACTCTTTTTATTAGAGGATTCTGAATGCCCTTTGCTATGAACGTTTTTACACACACAAATGTTTATTAGAATGTATGCTCGAGCGTGTAACA'..b'01086_SH222381.07FU_refs position=1..250 errors=99%G\n+CTGCGGAAGGATCATTATTGAAATAAATCTGATGAGTTGCTGCTGGTTCTCTTAGGGAGCATGTGCACACTTGTCATCTTTATATTCTCCACCTTGTGCACCTTTTGTAGACCTGGATATCTCTCTGAGTGCTTTTAGCACTCAGGTTTGGAGGATTGACTTTTCTGTCTTTCCTTACCTTTCCCGGCCTATGTTTCTTCAAATACCCAATGTGTATGTCATTAGAATGTAATAAATGGGCTTTTGTGCCTTATAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_41 reference=UDB011569_SH190415.07FU_refs position=1..250 errors=166%T\n+GTGACTGCGGAGGATCATTATTGAAATAAAGCTTGGTTAGGTTGTTGCTGGCTCTTCGGGGCATGTGCACACCTGACACCAACTTTTCTTACCACCTGTGCACTTTTTGTAGACTTTGGAATACCTCTCGAGGAAACTCGGTTTTGAGGACTGCTGTGCGCAAGCCGGCTTTCCTTACATTTTCCGGTCTATGTTTTTCTATATACCCTATAGTATGTCACAGAATGTCATTTTAATGGGCTTAATTGCCTTTAAACCTATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_42 reference=UDB015350_SH176685.07FU_refs position=1..250 errors=205%A\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_43 reference=HQ714696_SH221416.07FU_refs position=1..250\n+ATCCGGAGGGGAGATGAAGAGGGAATTTAGTAGGAACCGTAGGCATTGTCGCTGGCCTTTGGAAACAAACGCATGTGCACATCTCGAAAGTCTTACTTAGTACCTCGATCTCTTTCCTTTTGTGAACCCCTTTTCTTACACCTGTGCACCCATTGTAGGTCCCGCGAGGGATCCTATGTCTCTATCTACTCTTAAATGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTTGGTTGGCGGCAGTAAAGAACCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_44 reference=HQ714699_SH221418.07FU_refs position=1..250 errors=112%A\n+ATCCGGAGGGGGGGAGACGAGAGAAATTTGGGGTAGGAACGGAAGGGACTGTCGCTGGCCTTTGGAAACGAAGGCATGTGCACGTCTCGAAGTCTTACTTTTTTAGTATCTCGATCTCTTTCCTTTCGTGAGACCCTTTTCTTACACCTGTGCACCTATTGTAGGTCCCGCGAGGGATCTATGTCTCTATCTACTCTAAAACGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTCGGTTGGCGGCAGTAAAGAACTTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_45 reference=JQ279537_SH175098.07FU_refs position=1..250\n+CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_46 reference=JQ716403_SH219241.07FU_refs position=1..250\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_47 reference=EU623745_SH215851.07FU_refs position=1..250 errors=191%C\n+GCGGAAGGATCATTACTGAATTGAAATGCGTTAGTTAGTTGAGCTGACCTTCTCCCTTTAATGGGGGGGGGAGTAGTATGTGCTCGCTATATCGCTTTTTCTAACTCCCCACTGTGCACCTCTATTGTAGGCTACGAGTGACTCTCAAGTAGACACACTCCCATAACACACCCTTTGTGCGCAGAAGGGGGGGGAAAAGGGTCTATTTGGGTTTAAGAAGGCTTATCGGGCATCCATTTTGCTTGCTTTCGACTTTGTAGCCTATGATCTTACAACAAACTACTTTGATAAAGTCTTGATGAATGATAGATTGGTCTTTTGAACCAATATAAAAGTTGTACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_50_FROGS_combined R1_desc:reference=JF419897_SH181470.07FU_refs position=1..250;R2_desc=R2_desc=reference=JF419897_SH181470.07FU_refs position=1..250\n+GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/07-affiliation_deleted.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-affiliation_deleted.html Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,754 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>FROGS Affiliation Filters</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="3.2.2">\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#venn-filters {\n+\t\t\t\tpadding: 10px;\n+\t\t\t\tbackground-color: #FFF;\n+\t\t\t\tbackground-clip: padding-box;\n+\t\t\t\tborder: 1px solid rgba(0, 0, 0, 0.15);\n+\t\t\t\tborder-radius: 4px;\n+\t\t\t\tbox-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#byFilters-jvenn {\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#venn-filters ul {\n+\t\t\t\tlist-style-type: none;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t\n+\t\t\t\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAF;\n+\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n+\t\t\t}\n+\t\t\ta {\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\ta:hover{\n+\t\t\t\tcolor:#648a89;\n+\t\t\t}\n+\t\t\t\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 35px;\n+\t\t\t\tmargin-bottom: 12px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 25px;\n+\t\t\t\twidth: 25px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue backgrou'..b'///////////////////\n+\t\t\t$(function() {\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Load active tab\n+\t\t\t\tglobal_filters_load();\n+\t\t\t\tintersections_filters_load();\n+\t\t\t\t\n+\t\t\t\t// Add tab listener\n+\t\t\t\t$(\'.nav-item a\').click(function (e) {\n+\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t$(this).tab(\'show\');\n+\t\t\t\t\tif( $(this).attr(\'href\') == "#view-by-samples" && $(\'#view-by-samples\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#view-by-samples\').removeClass(\'disabled\')\n+\t\t\t\t\t\tsamples_filters_load( "filter-log" );\n+\t\t\t\t\t}\n+\t\t\t\t})\n+\t\t\t});\n+\t\t</script>\n+\n+\t</head>\n+\t<body>\n+\t\t\n+\t\t<p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+ \n+ <div id="content" class="hidden">\n+ \t<ul class="nav nav-tabs">\n+\t\t\t\t<li class="nav-item active"><a class="nav-link active" href="#view-by-filters">Filters by OTUs</a></li>\n+\t\t\t\t<li class="nav-item"><a class="nav-link" href="#view-by-samples">Filters by samples</a></li>\n+\t\t\t</ul>\n+\n+\t\t\t<div id="tab-content" class="tab-content">\n+\t\t\t\t<div id="view-by-filters" role="tabpanel" class="tab-pane active">\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Filters summary</h2>\n+\t\t\t\t\t<div id="filter-summary">\n+\t\t \t\t<div class="row">\n+\t\t\t \t\t<div id="nb-filtered" class="col-md-6"></div> \n+\t\t\t \t\t<div id="abundance-filtered" class="col-md-6"></div>\n+\t\t \t\t</div>\n+\t\t\t\t\t</div>\n+\t\t\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Taxon lost summary</h2>\n+\t\t\t\t\tFiltering criteria are applied by affiliation. So for blast, filters are not only applied on the blast consensus taxonomy but on each blast hit (cf multihit.tsv file).<br>\n+\t\t\t\t\tFor each OTU, none, part or all blast affiliations may be removed, resulting in unchanged / updated or deleted blast consensus taxonomy.<br>\n+\t\t\t\t\tThe detailed number of lost affiliations (not only the consensus) by rank are summarised. It may also precise if blast consensus multi-affiliation are lost.<br><br>\n+\t\t <div id="taxon_lost"></div>\n+\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Filters intersections</h2>\n+\t\t \t\t<div class="row">\n+\t\t \t\t\t<div class="col-md-2 col-ld-3"></div>\n+\t\t\t\t\t\t<div id="venn-filters" class="col-md-8 col-ld-6">\n+\t\t <p> Draw a Venn to see which OTUs had been deleted by the filters chosen (Maximum 6 options): </p>\n+\t\t <ul id="byFilters-jvenn-chkbx"></ul>\n+\t\t <button id="byFilters-jvenn-btn" class="btn d-block mx-auto" disabled><span class="fa fa-gears" aria-hidden="true"> Venn</span></button>\n+\t\t </div>\n+\t\t <div class="col-md-2 col-ld-3"></div>\n+\t\t </div>\n+\t\t </div>\n+\t\t \n+ <div id="view-by-samples" role="tabpanel" class="tab-pane disabled">\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Details by samples of removed OTUs</h2>\n+\t\t <div id="filter-log"></div>\n+ </div>\n+ </div>\n+ </div>\n+\n+\t\t\n+\t\t\n+\t\t<div class="modal fade" id="byFilters-venn-modal" tabindex="-1" role="dialog" aria-labelledby="modal-venn" aria-hidden="true">\n+\t\t <div class="modal-dialog modal-lg">\n+\t\t\t<div class="modal-content">\n+\t\t\t <div class="modal-header">\n+\t\t\t\t<h4 class="modal-title">Venn on removed OTUs</h4>\n+\t\t\t\t<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+\t\t\t </div>\n+\t\t\t <div class="modal-body">\n+\t\t\t\t<div id="byFilters-jvenn"></div>\n+\t\t\t </div>\n+\t\t\t <div class="modal-footer">\n+\t\t\t\t<button type="button" class="btn btn-default" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span></button>\n+\t\t\t </div>\n+\t\t\t</div>\n+\t\t </div>\n+\t\t</div>\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/07-affiliation_filter_delMode.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-affiliation_filter_delMode.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,26 @@
+## Application
+Software: affiliation_filters.py (version: 3.2.2)
+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_filters.py --input-biom res_3.2.2/06-affiliation.biom --input-fasta res_3.2.2/04-filters.fasta --output-biom res_3.2.2/07-affiliation_deleted.biom --output-fasta res_3.2.2/07-affiliation_deleted.fasta --summary res_3.2.2/07-affiliation_deleted.html --impacted res_3.2.2/07-impacted_OTU_deleted.tsv --impacted-multihit res_3.2.2/07-impacted_OTU_deleted_multihit.tsv --log-file res_3.2.2/07-affiliation_filter_delMode.log --min-rdp-bootstrap Species:0.8 --min-blast-length 150 --min-blast-identity 1.0 --min-blast-coverage 1.0 --max-blast-evalue 1e-150 --ignore-blast-taxa "g__Sarcodon" "s__Trichoderma" --delete --taxonomic-ranks Domain Phylum Class Order Family Genus Species
+
+Identify OTU with :
+ - Blast evalue > 1e-150 : 30
+ - Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma : 6
+ - Blast identity < 1.0 : 1
+########################################################################################################
+# Convert a biom file into tsv file (biom_to_tsv.py version : 3.2.2)
+Command:
+ biom_to_tsv.py  --input-biom res_3.2.2/1617285770.1797566_17379_impacted.biom --input-fasta res_3.2.2/04-filters.fasta --output-tsv res_3.2.2/07-impacted_OTU_deleted.tsv --output-multi-affi res_3.2.2/07-impacted_OTU_deleted_multihit.tsv --log-file  res_3.2.2/1617285770.1797566_17379_impacted.biom2tsv.log
+
+Execution:
+ start: 01 Apr 2021 16:02:50
+ end:   01 Apr 2021 16:02:50
+
+########################################################################################################
+# Updates fasta file based on sequence in biom file. (biomFastaUpdate.py version : 1.0.1)
+Command:
+ biomFastaUpdate.py --input-biom res_3.2.2/07-affiliation_deleted.biom --input-fasta res_3.2.2/04-filters.fasta --output-file res_3.2.2/07-affiliation_deleted.fasta --log res_3.2.2/1617285770.1797566_17379_update_fasta_log.txt
+
+Execution:
+ start: 01 Apr 2021 16:02:50
+ end:   01 Apr 2021 16:02:50
+

diff -r 000000000000 -r 834843ebe569 test-data/references/07-affiliation_filter_maskMode.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-affiliation_filter_maskMode.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,17 @@
+## Application
+Software: affiliation_filters.py (version: 3.2.2)
+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_filters.py --input-biom res_3.2.2/06-affiliation.biom --input-fasta res_3.2.2/04-filters.fasta --output-biom res_3.2.2/07-affiliation_masked.biom --summary res_3.2.2/07-affiliation_masked.html --impacted res_3.2.2/07-impacted_OTU_masked.tsv --impacted-multihit res_3.2.2/07-impacted_OTU_masked_multihit.tsv --log-file res_3.2.2/07-affiliation_filter_maskMode.log --min-rdp-bootstrap Species:0.8 --min-blast-length 150 --min-blast-identity 1.0 --min-blast-coverage 1.0 --max-blast-evalue 1e-150 --ignore-blast-taxa "g__Sarcodon" "s__Trichoderma" --mask --taxonomic-ranks Domain Phylum Class Order Family Genus Species
+
+Identify OTU with :
+ - Blast evalue > 1e-150 : 30
+ - Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma : 6
+ - Blast identity < 1.0 : 1
+########################################################################################################
+# Convert a biom file into tsv file (biom_to_tsv.py version : 3.2.2)
+Command:
+ biom_to_tsv.py --input-biom res_3.2.2/1617285769.6536694_17365_impacted.biom --input-fasta res_3.2.2/04-filters.fasta --output-tsv res_3.2.2/07-impacted_OTU_masked.tsv --output-multi-affi res_3.2.2/07-impacted_OTU_masked_multihit.tsv --log-file res_3.2.2/1617285769.6536694_17365_impacted.biom2tsv.log
+
+Execution:
+ start: 01 Apr 2021 16:02:49
+ end: 01 Apr 2021 16:02:50
+

diff -r 000000000000 -r 834843ebe569 test-data/references/07-affiliation_masked.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-affiliation_masked.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "FROGS_affiliation_filters", "date": "2021-04-01T16:02:49", "rows": [{"id": "Cluster_1", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_54", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_2", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_92546", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_3", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_59", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_4", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_81", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_5", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_25", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_6", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_74803", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_7", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_38", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_8", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_90", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Suillaceae", "g__Truncocolumella", "s__Truncocolumella_rubra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_9", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_97858", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_mienum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_10", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_259", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_cyathuliformis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.99]}}, {"id": "Cluster_11", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_90304", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__A'..b'dp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_52", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_1953", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_53", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_4641", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_rhododendri"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_54", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_3904", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_55", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_67609", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 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"sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/07-affiliation_masked.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-affiliation_masked.html Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,753 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>FROGS Affiliation Filters</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="3.2.2">\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#venn-filters {\n+\t\t\t\tpadding: 10px;\n+\t\t\t\tbackground-color: #FFF;\n+\t\t\t\tbackground-clip: padding-box;\n+\t\t\t\tborder: 1px solid rgba(0, 0, 0, 0.15);\n+\t\t\t\tborder-radius: 4px;\n+\t\t\t\tbox-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#byFilters-jvenn {\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#venn-filters ul {\n+\t\t\t\tlist-style-type: none;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t\n+\t\t\t\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAF;\n+\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n+\t\t\t}\n+\t\t\ta {\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\ta:hover{\n+\t\t\t\tcolor:#648a89;\n+\t\t\t}\n+\t\t\t\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 35px;\n+\t\t\t\tmargin-bottom: 12px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 25px;\n+\t\t\t\twidth: 25px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue backgrou'..b'/////////////////////////////////////////////\n+\t\t\t$(function() {\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Load active tab\n+\t\t\t\tglobal_filters_load();\n+\t\t\t\tintersections_filters_load();\n+\t\t\t\t\n+\t\t\t\t// Add tab listener\n+\t\t\t\t$(\'.nav-item a\').click(function (e) {\n+\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t$(this).tab(\'show\');\n+\t\t\t\t\tif( $(this).attr(\'href\') == "#view-by-samples" && $(\'#view-by-samples\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#view-by-samples\').removeClass(\'disabled\')\n+\t\t\t\t\t\tsamples_filters_load( "filter-log" );\n+\t\t\t\t\t}\n+\t\t\t\t})\n+\t\t\t});\n+\t\t</script>\n+\n+\t</head>\n+\t<body>\n+\t\t\n+\t\t<p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+ \n+ <div id="content" class="hidden">\n+ \t<ul class="nav nav-tabs">\n+\t\t\t\t<li class="nav-item active"><a class="nav-link active" href="#view-by-filters">Filters by OTUs</a></li>\n+\t\t\t\t<li class="nav-item"><a class="nav-link" href="#view-by-samples">Filters by samples</a></li>\n+\t\t\t</ul>\n+\n+\t\t\t<div id="tab-content" class="tab-content">\n+\t\t\t\t<div id="view-by-filters" role="tabpanel" class="tab-pane active">\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Filters summary</h2>\n+\t\t\t\t\t<div id="filter-summary">\n+\t\t \t\t<div class="row">\n+\t\t\t \t\t<div id="nb-filtered" class="col-md-6"></div> \n+\t\t\t \t\t<div id="abundance-filtered" class="col-md-6"></div>\n+\t\t \t\t</div>\n+\t\t\t\t\t</div>\n+\t\t\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Taxon lost summary</h2>\n+\t\t\t\t\tFiltering criteria are applied by affiliation. So for blast, filters are not only applied on the blast consensus taxonomy but on each blast hit (cf multihit.tsv file).<br>\n+\t\t\t\t\tFor each OTU, none, part or all blast affiliations may be removed, resulting in unchanged / updated or deleted blast consensus taxonomy.<br>\n+\t\t\t\t\tThe detailed number of lost affiliations (not only the consensus) by rank are summarised. It may also precise if blast consensus multi-affiliation are lost.<br><br>\n+\t\t <div id="taxon_lost"></div>\n+\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Filters intersections</h2>\n+\t\t \t\t<div class="row">\n+\t\t \t\t\t<div class="col-md-2 col-ld-3"></div>\n+\t\t\t\t\t\t<div id="venn-filters" class="col-md-8 col-ld-6">\n+Draw a Venn to see which OTUs had its taxonomy masked by the filters chosen (Maximum 6 options): \t\t <ul id="byFilters-jvenn-chkbx"></ul>\n+\t\t <button id="byFilters-jvenn-btn" class="btn d-block mx-auto" disabled><span class="fa fa-gears" aria-hidden="true"> Venn</span></button>\n+\t\t </div>\n+\t\t <div class="col-md-2 col-ld-3"></div>\n+\t\t </div>\n+\t\t </div>\n+\t\t \n+ <div id="view-by-samples" role="tabpanel" class="tab-pane disabled">\n+\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Details by samples of masked OTUs</h2>\n+\t\t <div id="filter-log"></div>\n+ </div>\n+ </div>\n+ </div>\n+\n+\t\t\n+\t\t\n+\t\t<div class="modal fade" id="byFilters-venn-modal" tabindex="-1" role="dialog" aria-labelledby="modal-venn" aria-hidden="true">\n+\t\t <div class="modal-dialog modal-lg">\n+\t\t\t<div class="modal-content">\n+\t\t\t <div class="modal-header">\n+\t\t\t\t<h4 class="modal-title">Venn on removed OTUs</h4>\n+\t\t\t\t<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+\t\t\t </div>\n+\t\t\t <div class="modal-body">\n+\t\t\t\t<div id="byFilters-jvenn"></div>\n+\t\t\t </div>\n+\t\t\t <div class="modal-footer">\n+\t\t\t\t<button type="button" class="btn btn-default" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span></button>\n+\t\t\t </div>\n+\t\t\t</div>\n+\t\t </div>\n+\t\t</div>\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/07-impacted_OTU_deleted.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-impacted_OTU_deleted.tsv Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,31 @@\n+#comment\tstatus\trdp_tax_and_bootstrap\tblast_taxonomy\tblast_subject\tblast_perc_identity\tblast_perc_query_coverage\tblast_evalue\tblast_aln_length\tseed_id\tseed_sequence\tobservation_name\tobservation_sum\t01_subsample\t02_subsample\t03_subsample\n+blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Chaetothyriales;(1.0);f__Herpotrichiellaceae;(1.0);g__Exophiala;(1.0);s__Exophiala_equina;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Chaetothyriales;f__Herpotrichiellaceae;g__Exophiala;s__Exophiala_equina\tJF747094_SH197643.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_54\tATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_1\t1561\t512\t515\t534\n+blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Pezizomycetes;(1.0);o__Pezizales;(1.0);f__Tuberaceae;(1.0);g__Tuber;(1.0);s__Tuber_latisporum;(1.0);\tk__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Tuberaceae;g__Tuber;s__Tuber_latisporum\tDQ898183_SH216206.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_92546\tCCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\tCluster_2\t1556\t508\t512\t536\n+blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Elaphomycetaceae;(1.0);g__Elaphomyces;(1.0);s__Elaphomyces_compleximurus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Elaphomycetaceae;g__Elaphomyces;s__Elaphomyces_compleximurus\tJN711441_SH022548.07FU_refs_singleton\t100.0\t100.0\t8.06e-132\t248\t01_59\tAGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_3\t1550\t514\t502\t534\n+blast_eval_gt_1e-150;undesired_tax_in_blast\tOTU_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Hypocreales;(1.0);f__Hypocreaceae;(1.0);g__Trichoderma;(1.0);s__Trichoderma_aggressivum;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum\tAF456924_SH097201.07FU_refs\t100.0\t100.0\t4.90e-134\t252\t01_81\tCCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_4\t1564\t503\t515\t546\n+blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Xylariales;(1.0);f__Amphisphaeriaceae;(1.0);g__Pestalotiopsis;(1.0);s__Pestalotiopsis_diversiseta;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Pestalotiopsis;s__Pestalotiopsis_diversiseta\tJX399009_SH268556.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_25\tCATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_5\t1544\t521\t550\t473\n+blast_eval_gt_1e-150;undesired_tax_in_blast\tOTU_deleted\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Bankeraceae;(1.0);g__Sarcodon;(1.0);s__Sarcodon_quercophilus;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Sarcodon;s__Sarcodon_quercophilus\tKM668101_SH491630.07FU_refs_singleton\t100.0\t100.0\t3.94e-140\t263\t01_74803\tAGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTT'..b'GTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_48\t544\t177\t203\t164\n+blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Cortinariaceae;(1.0);g__Cortinarius;(1.0);s__Cortinarius_parkeri;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_parkeri\tGQ159830_SH222371.07FU_refs\t100.0\t100.0\t1.33e-129\t244\t01_88865\tTGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_49\t245\t80\t83\t82\n+blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Dothideomycetes;(1.0);o__Pleosporales;(1.0);f__Leptosphaeriaceae;(1.0);g__Leptosphaeria;(1.0);s__Leptosphaeria_polylepidis;(1.0);\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Leptosphaeriaceae;g__Leptosphaeria;s__Leptosphaeria_polylepidis\tAJ786644_SH470265.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_210\tCATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_51\t83\t22\t28\t33\n+blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Trichocomaceae;(1.0);g__Aspergillus;(1.0);s__Aspergillus_microcysticus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_microcysticus\tEF669607_SH109271.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_1953\tCGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_52\t59\t26\t16\t17\n+blast_eval_gt_1e-150;undesired_tax_in_blast\tOTU_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Hypocreales;(1.0);f__Hypocreaceae;(1.0);g__Trichoderma;(1.0);s__Trichoderma_rhododendri;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rhododendri\tFJ860822_SH177722.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_4641\tCATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_53\t45\t17\t12\t16\n+blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Thelephoraceae;(1.0);g__Thelephora;(1.0);s__Thelephora_atra;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Thelephoraceae;g__Thelephora;s__Thelephora_atra\tUDB016470_SH189377.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_3904\tCCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_54\t37\t9\t13\t15\n+blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Amanitaceae;(1.0);g__Amanita;(1.0);s__Amanita_friabilis;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_friabilis\tUDB011541_SH194446.07FU_refs\t100.0\t100.0\t6.09e-128\t241\t01_67609\tGGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\tCluster_55\t10\t2\t6\t2\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/07-impacted_OTU_deleted_multihit.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-impacted_OTU_deleted_multihit.tsv Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,1 @@
+#observation_name blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length

diff -r 000000000000 -r 834843ebe569 test-data/references/07-impacted_OTU_masked.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-impacted_OTU_masked.tsv Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,31 @@\n+#comment\tstatus\trdp_tax_and_bootstrap\tblast_taxonomy\tblast_subject\tblast_perc_identity\tblast_perc_query_coverage\tblast_evalue\tblast_aln_length\tseed_id\tseed_sequence\tobservation_name\tobservation_sum\t01_subsample\t02_subsample\t03_subsample\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Chaetothyriales;(1.0);f__Herpotrichiellaceae;(1.0);g__Exophiala;(1.0);s__Exophiala_equina;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Chaetothyriales;f__Herpotrichiellaceae;g__Exophiala;s__Exophiala_equina\tJF747094_SH197643.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_54\tATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_1\t1561\t512\t515\t534\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Pezizomycetes;(1.0);o__Pezizales;(1.0);f__Tuberaceae;(1.0);g__Tuber;(1.0);s__Tuber_latisporum;(1.0);\tk__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Tuberaceae;g__Tuber;s__Tuber_latisporum\tDQ898183_SH216206.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_92546\tCCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\tCluster_2\t1556\t508\t512\t536\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Elaphomycetaceae;(1.0);g__Elaphomyces;(1.0);s__Elaphomyces_compleximurus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Elaphomycetaceae;g__Elaphomyces;s__Elaphomyces_compleximurus\tJN711441_SH022548.07FU_refs_singleton\t100.0\t100.0\t8.06e-132\t248\t01_59\tAGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_3\t1550\t514\t502\t534\n+blast_eval_gt_1e-150;undesired_tax_in_blast\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Hypocreales;(1.0);f__Hypocreaceae;(1.0);g__Trichoderma;(1.0);s__Trichoderma_aggressivum;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum\tAF456924_SH097201.07FU_refs\t100.0\t100.0\t4.90e-134\t252\t01_81\tCCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_4\t1564\t503\t515\t546\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Xylariales;(1.0);f__Amphisphaeriaceae;(1.0);g__Pestalotiopsis;(1.0);s__Pestalotiopsis_diversiseta;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Pestalotiopsis;s__Pestalotiopsis_diversiseta\tJX399009_SH268556.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_25\tCATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_5\t1544\t521\t550\t473\n+blast_eval_gt_1e-150;undesired_tax_in_blast\tAffiliation_masked\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Bankeraceae;(1.0);g__Sarcodon;(1.0);s__Sarcodon_quercophilus;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Sarcodon;s__Sarcodon_quercophilus\tKM668101_SH491630.07FU_refs_singleton\t100.0\t100.0\t3.94e-140\t263\t01_74803\tAGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAA'..b'CGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_48\t544\t177\t203\t164\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Cortinariaceae;(1.0);g__Cortinarius;(1.0);s__Cortinarius_parkeri;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_parkeri\tGQ159830_SH222371.07FU_refs\t100.0\t100.0\t1.33e-129\t244\t01_88865\tTGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_49\t245\t80\t83\t82\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Dothideomycetes;(1.0);o__Pleosporales;(1.0);f__Leptosphaeriaceae;(1.0);g__Leptosphaeria;(1.0);s__Leptosphaeria_polylepidis;(1.0);\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Leptosphaeriaceae;g__Leptosphaeria;s__Leptosphaeria_polylepidis\tAJ786644_SH470265.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_210\tCATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_51\t83\t22\t28\t33\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Trichocomaceae;(1.0);g__Aspergillus;(1.0);s__Aspergillus_microcysticus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_microcysticus\tEF669607_SH109271.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_1953\tCGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_52\t59\t26\t16\t17\n+blast_eval_gt_1e-150;undesired_tax_in_blast\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Hypocreales;(1.0);f__Hypocreaceae;(1.0);g__Trichoderma;(1.0);s__Trichoderma_rhododendri;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rhododendri\tFJ860822_SH177722.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_4641\tCATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_53\t45\t17\t12\t16\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Thelephoraceae;(1.0);g__Thelephora;(1.0);s__Thelephora_atra;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Thelephoraceae;g__Thelephora;s__Thelephora_atra\tUDB016470_SH189377.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_3904\tCCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_54\t37\t9\t13\t15\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Amanitaceae;(1.0);g__Amanita;(1.0);s__Amanita_friabilis;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_friabilis\tUDB011541_SH194446.07FU_refs\t100.0\t100.0\t6.09e-128\t241\t01_67609\tGGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\tCluster_55\t10\t2\t6\t2\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/07-impacted_OTU_masked_multihit.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-impacted_OTU_masked_multihit.tsv Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,1 @@
+#observation_name blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length

diff -r 000000000000 -r 834843ebe569 test-data/references/08-affiliation_postprocessed.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/08-affiliation_postprocessed.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "FROGS_aggregate_affiliated_otu", "date": "2021-04-01T16:02:51", "rows": [{"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803", "blast_affiliations": [{"subject": "KM668101_SH491630.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "evalue": "3.94e-140", "aln_length": 263, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_22", "blast_affiliations": [{"subject": "JX118731_SH218995.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "evalue": "5.20e-144", "aln_length": 270, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_103", "blast_affiliations": [{"subject": "HG007976_SH219743.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Pholiota", "s__Pholiota_highlandensis"], "evalue": "1.22e-160", "aln_length": 300, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Pholiota", "s__Pholiota_highlandensis"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Pholiota", "s__Pholiota_highlandensis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined", "blast_affiliations": [{"subject": "JF419897_SH181470.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "evalue": "-1", "aln_length": 1017, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222", "blast_affiliations": [{"subject": "UDB002317_SH221025.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "evalue": "9.52e-162", "aln_length": 302, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_boots'..b' 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_54", "metadata": {"comment": [], "seed_id": "01_3904", "blast_affiliations": [{"subject": "UDB016470_SH189377.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "evalue": "1.70e-128", "aln_length": 242, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_55", "metadata": {"comment": [], "seed_id": "01_67609", "blast_affiliations": [{"subject": "UDB011541_SH194446.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "evalue": "6.09e-128", "aln_length": 241, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 574], [0, 2, 545], [1, 0, 542], [1, 1, 531], [1, 2, 537], [2, 0, 508], [2, 1, 544], [2, 2, 545], [3, 0, 526], [3, 1, 518], [3, 2, 553], [4, 0, 536], [4, 1, 534], [4, 2, 521], [5, 0, 530], [5, 1, 513], [5, 2, 541], [6, 0, 540], [6, 1, 524], [6, 2, 516], [7, 0, 527], [7, 1, 543], [7, 2, 506], [8, 0, 499], [8, 1, 538], [8, 2, 539], [9, 0, 536], [9, 1, 490], [9, 2, 547], [10, 0, 534], [10, 1, 524], [10, 2, 514], [11, 0, 526], [11, 1, 494], [11, 2, 551], [12, 0, 508], [12, 1, 527], [12, 2, 530], [13, 0, 525], [13, 1, 530], [13, 2, 510], [14, 0, 503], [14, 1, 515], [14, 2, 546], [15, 0, 535], [15, 1, 512], [15, 2, 517], [16, 0, 512], [16, 1, 515], [16, 2, 534], [17, 0, 508], [17, 1, 512], [17, 2, 536], [18, 0, 514], [18, 1, 502], [18, 2, 534], [19, 0, 509], [19, 1, 522], [19, 2, 515], [20, 0, 545], [20, 1, 507], [20, 2, 493], [21, 0, 521], [21, 1, 550], [21, 2, 473], [22, 0, 498], [22, 1, 515], [22, 2, 524], [23, 0, 507], [23, 1, 530], [23, 2, 498], [24, 0, 495], [24, 1, 511], [24, 2, 528], [25, 0, 509], [25, 1, 492], [25, 2, 532], [26, 0, 499], [26, 1, 513], [26, 2, 520], [27, 0, 511], [27, 1, 518], [27, 2, 502], [28, 0, 515], [28, 1, 500], [28, 2, 515], [29, 0, 491], [29, 1, 506], [29, 2, 533], [30, 0, 511], [30, 1, 550], [30, 2, 469], [31, 0, 518], [31, 1, 517], [31, 2, 494], [32, 0, 473], [32, 1, 528], [32, 2, 524], [33, 0, 526], [33, 1, 484], [33, 2, 513], [34, 0, 504], [34, 1, 483], [34, 2, 536], [35, 0, 514], [35, 1, 507], [35, 2, 499], [36, 0, 511], [36, 1, 529], [36, 2, 479], [37, 0, 526], [37, 1, 498], [37, 2, 494], [38, 0, 490], [38, 1, 531], [38, 2, 495], [39, 0, 494], [39, 1, 513], [39, 2, 509], [40, 0, 497], [40, 1, 505], [40, 2, 514], [41, 0, 518], [41, 1, 508], [41, 2, 486], [42, 0, 525], [42, 1, 499], [42, 2, 483], [43, 0, 469], [43, 1, 520], [43, 2, 516], [44, 0, 508], [44, 1, 504], [44, 2, 490], [45, 0, 510], [45, 1, 472], [45, 2, 518], [46, 0, 480], [46, 1, 504], [46, 2, 515], [47, 0, 499], [47, 1, 490], [47, 2, 476], [48, 0, 177], [48, 1, 203], [48, 2, 164], [49, 0, 80], [49, 1, 83], [49, 2, 82], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/08-affiliation_postprocessed.compo.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/08-affiliation_postprocessed.compo.tsv Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,55 @@
+Cluster_6
+Cluster_12
+Cluster_33
+Cluster_50_FROGS_combined
+Cluster_36
+Cluster_45
+Cluster_42
+Cluster_13
+Cluster_37
+Cluster_27
+Cluster_40
+Cluster_9
+Cluster_15
+Cluster_30
+Cluster_4
+Cluster_16
+Cluster_1
+Cluster_2
+Cluster_3
+Cluster_32
+Cluster_28
+Cluster_5
+Cluster_29
+Cluster_46
+Cluster_14
+Cluster_7
+Cluster_47
+Cluster_44
+Cluster_24
+Cluster_25
+Cluster_31
+Cluster_41
+Cluster_38
+Cluster_8
+Cluster_22
+Cluster_21
+Cluster_10
+Cluster_20
+Cluster_18
+Cluster_26
+Cluster_43
+Cluster_39
+Cluster_35
+Cluster_11
+Cluster_17
+Cluster_23
+Cluster_34
+Cluster_19
+Cluster_48
+Cluster_49
+Cluster_51
+Cluster_52
+Cluster_53
+Cluster_54
+Cluster_55

diff -r 000000000000 -r 834843ebe569 test-data/references/08-affiliation_postprocessed.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/08-affiliation_postprocessed.fasta Thu Apr 08 14:30:48 2021 +0000

diff -r 000000000000 -r 834843ebe569 test-data/references/08-affiliation_postprocessed.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/08-affiliation_postprocessed.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,31 @@
+## Application
+Software: affiliation_postprocess.py (version: 3.2.2)
+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_postprocess.py --input-biom res_3.2.2/06-affiliation.biom --input-fasta res_3.2.2/04-filters.fasta --reference data/Unite_extract_ITS1.fasta --output-biom res_3.2.2/08-affiliation_postprocessed.biom --output-compo res_3.2.2/08-affiliation_postprocessed.compo.tsv --output-fasta res_3.2.2/08-affiliation_postprocessed.fasta --log-file res_3.2.2/08-affiliation_postprocessed.log
+
+########################################################################################################
+# Select smallest reference as affiliation. (select_inclusive_amplicon.py version : 1.0)
+Command:
+ select_inclusive_amplicon.py  --ITS-reference data/Unite_extract_ITS1.fasta -b res_3.2.2/06-affiliation.biom -o res_3.2.2/1617285770.775001_17397_06-affiliation.biom_resolve_inclusiv_its.biom --log-file res_3.2.2/1617285770.775001_17397_06-affiliation.biom_resolve_inclusiv_its.log
+
+Execution:
+ start: 01 Apr 2021 16:02:50
+ end:   01 Apr 2021 16:02:50
+
+ # nb OTU : 55
+ # nb OTU with multiaffiliations : 0
+ # nb OTU with multiaffiliations resolved : 0
+ # nb multiaffiliations removed : 0
+
+########################################################################################################
+# Aggregate OTU that share taxonomic affiliation with at least I% identity and C% coverage (aggregate_affiliated_otus.py version : 1.0.0)
+Command:
+ aggregate_affiliated_otus.py  -b res_3.2.2/1617285770.775001_17397_06-affiliation.biom_resolve_inclusiv_its.biom -f res_3.2.2/04-filters.fasta --identity 99.0 --coverage 99.0 --output-biom res_3.2.2/08-affiliation_postprocessed.biom --output-compo res_3.2.2/08-affiliation_postprocessed.compo.tsv --output-fasta res_3.2.2/08-affiliation_postprocessed.fasta --log-file res_3.2.2/1617285770.775001_17397_06-affiliation.biom_aggregation.log
+
+Execution:
+ start: 01 Apr 2021 16:02:51
+ end:   01 Apr 2021 16:02:51
+
+ # nb OTU in : 55
+ # nb OTU out : 55
+ # nb OTU aggregated : 0
+

diff -r 000000000000 -r 834843ebe569 test-data/references/09-normalisation.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/09-normalisation.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "Sampling 100 elements by sample from res_3.2.2/08-affiliation_postprocessed.biom", "date": "2021-04-01T16:02:51", "rows": [{"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_66", "blast_affiliations": [{"subject": "JX118682_SH219010.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_candidolanata"], "evalue": "5.05e-139", "aln_length": 261, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_candidolanata"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_candidolanata"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_22", "blast_affiliations": [{"subject": "JX118731_SH218995.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "evalue": "5.20e-144", "aln_length": 270, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_155", "blast_affiliations": [{"subject": "UDB000320_SH220111.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_semisanguifluus"], "evalue": "1.45e-144", "aln_length": 271, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_semisanguifluus"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_semisanguifluus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410", "blast_affiliations": [{"subject": "EU623745_SH215851.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "evalue": "0.0", "aln_length": 390, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222", "blast_affiliations": [{"subject": "UDB002317_SH221025.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "evalue": "9.52e-162", "aln_length": 302, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_bootstrap":'..b' 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_38", "blast_affiliations": [{"subject": "JF417478_SH216679.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "evalue": "1.75e-133", "aln_length": 251, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_71661", "blast_affiliations": [{"subject": "UDB001581_SH219736.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "evalue": "1.97e-153", "aln_length": 287, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_96725", "blast_affiliations": [{"subject": "KF732249_SH136099.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_amnicola"], "evalue": "1.19e-155", "aln_length": 291, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_amnicola"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_amnicola"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 3], [0, 1, 3], [1, 0, 4], [1, 1, 3], [1, 2, 3], [2, 0, 3], [2, 1, 2], [2, 2, 3], [3, 0, 5], [3, 1, 1], [3, 2, 3], [4, 0, 3], [4, 1, 2], [4, 2, 3], [5, 0, 1], [5, 1, 3], [5, 2, 2], [6, 0, 2], [6, 1, 2], [6, 2, 3], [7, 0, 4], [7, 2, 2], [8, 0, 4], [8, 1, 2], [8, 2, 1], [9, 0, 3], [9, 1, 3], [9, 2, 4], [10, 0, 2], [10, 1, 5], [10, 2, 1], [11, 0, 4], [11, 1, 6], [11, 2, 2], [12, 0, 5], [12, 1, 1], [12, 2, 1], [13, 0, 2], [13, 1, 2], [14, 0, 2], [14, 1, 2], [14, 2, 2], [15, 0, 3], [15, 1, 3], [16, 0, 2], [16, 2, 1], [17, 0, 3], [17, 1, 1], [17, 2, 2], [18, 0, 2], [18, 2, 3], [19, 0, 1], [20, 0, 2], [20, 1, 2], [20, 2, 4], [21, 0, 3], [21, 1, 2], [21, 2, 1], [22, 0, 4], [22, 2, 1], [23, 0, 3], [23, 1, 1], [24, 0, 3], [24, 1, 3], [24, 2, 2], [25, 0, 2], [25, 1, 1], [26, 0, 2], [26, 1, 4], [26, 2, 1], [27, 0, 1], [27, 1, 2], [27, 2, 1], [28, 0, 1], [28, 1, 1], [29, 0, 4], [29, 1, 1], [29, 2, 3], [30, 0, 2], [30, 1, 4], [30, 2, 1], [31, 0, 1], [31, 1, 3], [31, 2, 3], [32, 0, 2], [32, 2, 4], [33, 0, 2], [33, 1, 1], [33, 2, 3], [34, 0, 1], [34, 1, 1], [34, 2, 2], [35, 0, 1], [35, 1, 8], [35, 2, 4], [36, 0, 3], [36, 1, 3], [37, 0, 2], [37, 1, 2], [37, 2, 2], [38, 0, 1], [38, 1, 3], [38, 2, 2], [39, 0, 1], [39, 2, 4], [40, 0, 1], [40, 2, 3], [41, 1, 2], [41, 2, 1], [42, 1, 3], [42, 2, 5], [43, 1, 2], [43, 2, 2], [44, 1, 2], [44, 2, 1], [45, 1, 1], [45, 2, 5], [46, 1, 2], [46, 2, 2], [47, 1, 2], [47, 2, 1], [48, 1, 1], [48, 2, 3], [49, 1, 2], [49, 2, 3]], "shape": [50, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/09-normalisation.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/09-normalisation.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,100 @@\n+>Cluster_1 reference=JF747094_SH197643.07FU_refs position=1..249 errors=112%A\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_2 reference=DQ898183_SH216206.07FU_refs position=1..249 errors=21%G\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3 reference=JN711441_SH022548.07FU_refs_singleton position=1..248 errors=206%T\n+AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_4 reference=AF456924_SH097201.07FU_refs position=1..250\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_5 reference=JX399009_SH268556.07FU_refs position=1..249 errors=185%C\n+CATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_6 reference=KM668101_SH491630.07FU_refs_singleton position=1..250\n+AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\n+>Cluster_7 reference=JF417478_SH216679.07FU_refs position=1..250 errors=99%T\n+CCGAGTGAGGGTCCCCTTTGCGGGCCCGACCTCCCACCCGTGTCTACCGTACCGTGTTGCTTCGGCGGGCCCGCCAGGGGGGCTCCTGTCCCTGGCCGCCGGGGGGCCATCTCCCGTGCCTCCGGGCCCGTGCCCGCCGGAGACCCTCGTGAACGCTGTCTTGAACAAAGGTTGCGGTCTGAGTGGAAAACACAATCGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_8 reference=EU837224_SH182725.07FU_refs position=1..249 errors=132%T\n+TTGAATTCTATGGAGGGGGGAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCTTCCTTTCTCTCATACACACACCTGTGCACCTGTTGTAGGTCCTCGAAAGAGGAGCTATGTTTTTCACATCACACCCCGTCGTATGTCTATAGAATGTGTTGAAAACGTCGACCTGTTTGACAGGCCGGCGGACAATAAAATTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_9 reference=JQ621972_SH177703.07FU_refs position=1..250\n+TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_10 reference=HQ714785_SH330547.07FU_refs position=1..250 errors=136%A\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11 reference=AB594796_SH278638.07FU_refs position=1..248 errors=111%C\n+GATCATTACAGAGTTATCTAACTCCCAAACCCATGTGAACTTACCATTTGTTGCCTCGGCAGAGGCTACCCGGTACCTACCCTGGAGCAGCTACCCTGTAGCTACCCTGGAACGGCCTACCCTGTAGCGCATCCTGCCGGTGGACCTTTAAACTCTTGTTATTTTAAAGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_12 reference=JX118731_SH218995.07FU_refs position=1..250 errors=164%A\n+GGCTCTTCGGGGCATGTGCTCGCCTGTCACCTTTATCTTTCCACCTGTGCACACACTGTAGTCCTGGATACCTCTCGCCGCAAGGCGGATGCAGAGACTGCTGCTCAGCCTCCGAAAGGGGGAGGACGGCTATCTTTGAATTTCCAGGTCTACGATTATCACATACCCCAATTGAATGTTACAGAATGTTATCAAAGGGCCTTGTGCCTATAAACCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGA'..b'TATGTTTTTCTATATACCCTATAGTATGTCACAGAATGTCATTTTAATGGGCTTAATTGCCTTTAAACCTATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_42 reference=UDB015350_SH176685.07FU_refs position=1..250 errors=205%A\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_43 reference=HQ714696_SH221416.07FU_refs position=1..250\n+ATCCGGAGGGGAGATGAAGAGGGAATTTAGTAGGAACCGTAGGCATTGTCGCTGGCCTTTGGAAACAAACGCATGTGCACATCTCGAAAGTCTTACTTAGTACCTCGATCTCTTTCCTTTTGTGAACCCCTTTTCTTACACCTGTGCACCCATTGTAGGTCCCGCGAGGGATCCTATGTCTCTATCTACTCTTAAATGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTTGGTTGGCGGCAGTAAAGAACCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_44 reference=HQ714699_SH221418.07FU_refs position=1..250 errors=112%A\n+ATCCGGAGGGGGGGAGACGAGAGAAATTTGGGGTAGGAACGGAAGGGACTGTCGCTGGCCTTTGGAAACGAAGGCATGTGCACGTCTCGAAGTCTTACTTTTTTAGTATCTCGATCTCTTTCCTTTCGTGAGACCCTTTTCTTACACCTGTGCACCTATTGTAGGTCCCGCGAGGGATCTATGTCTCTATCTACTCTAAAACGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTCGGTTGGCGGCAGTAAAGAACTTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_45 reference=JQ279537_SH175098.07FU_refs position=1..250\n+CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_46 reference=JQ716403_SH219241.07FU_refs position=1..250\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_47 reference=EU623745_SH215851.07FU_refs position=1..250 errors=191%C\n+GCGGAAGGATCATTACTGAATTGAAATGCGTTAGTTAGTTGAGCTGACCTTCTCCCTTTAATGGGGGGGGGAGTAGTATGTGCTCGCTATATCGCTTTTTCTAACTCCCCACTGTGCACCTCTATTGTAGGCTACGAGTGACTCTCAAGTAGACACACTCCCATAACACACCCTTTGTGCGCAGAAGGGGGGGGAAAAGGGTCTATTTGGGTTTAAGAAGGCTTATCGGGCATCCATTTTGCTTGCTTTCGACTTTGTAGCCTATGATCTTACAACAAACTACTTTGATAAAGTCTTGATGAATGATAGATTGGTCTTTTGAACCAATATAAAAGTTGTACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_48 reference=GQ169315_SH195598.07FU_refs position=1..245 errors=79%A\n+TGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_49 reference=GQ159830_SH222371.07FU_refs position=1..244\n+TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_50_FROGS_combined R1_desc:reference=JF419897_SH181470.07FU_refs position=1..250;R2_desc=R2_desc=reference=JF419897_SH181470.07FU_refs position=1..250\n+GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/09-normalisation.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/09-normalisation.html Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,431 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>FROGS Abundance Normalisation</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="3.2.2">\n+\t\t\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAF;\n+\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n+\t\t\t}\n+\t\t\ta {\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\ta:hover{\n+\t\t\t\tcolor:#648a89;\n+\t\t\t}\n+\t\t\t\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 35px;\n+\t\t\t\tmargin-bottom: 12px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 25px;\n+\t\t\t\twidth: 25px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue background */\n+\t\t\t.container input:checked ~ .checkmark {\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\topacity:1;\n+\t\t\t}\n+\n+\t\t\t/* Create the checkmark/indicator (hidden when not checked) */\n+\t\t\t.checkmark:after {\n+\t\t\t\tcontent: "";\n+\t\t\t\tposition: absolute;\n+\t\t\t\tdisplay: none;\n+\t\t\t}\n+\n+\t\t\t/* Show the checkmark when checked */\n+\t\t\t.container input:checked ~ .checkmark:after {\n+\t\t\t\tdisplay: block;\n+\t\t\t}\n+\n+\t\t\t/* Style the checkmark/indicator */\n+\t\t\t.container .checkmark:after {\n+\t\t\t\tleft: 9px;\n+\t\t\t\ttop: 5px;\n+\t\t\t\twidth: 5px;\n+\t\t\t\theight: 10px;\n+\t\t\t\tborder: solid white;\n+\t\t\t\tborder-width: 0 3px 3px 0;\n+\t\t\t\t-webkit-transform:'..b'ltip: {\n+\t\t\t\t\t\theaderFormat: \'<span style="font-size:10px">{point.key}</span><table>\',\n+\t\t\t\t\t\tpointFormat: \'<tr><td style="color:{series.color};padding:0">{series.name}: </td>\' +\n+\t\t\t\t\t\t\t\'<td style="padding:0"><b>{point.y} \' + unity + \'</b></td></tr>\',\n+\t\t\t\t\t\tfooterFormat: \'</table>\',\n+\t\t\t\t\t\tshared: true,\n+\t\t\t\t\t\tuseHTML: true\n+\t\t\t\t\t},\n+\t\t\t\t\tplotOptions: {\n+\t\t\t\t column: {\n+\t\t\t\t stacking: \'normal\',\n+\t\t\t\t dataLabels: {\n+\t\t\t\t enabled: true,\n+\t\t\t\t useHTML: true,\n+\t\t\t\t style: {\n+\t\t\t\t\t\t\t\t\ttextShadow: false,\n+\t\t\t\t\t\t\t\t\ttextOutline: false,\n+\t\t\t\t \tfontWeight : \'bold\'\n+\t\t\t\t },\n+\t\t\t\t formatter() {\n+\t\t\t\t \tvar pointWidth = this.point.shapeArgs.width + 10;\n+\t\t\t\t \tvar margin_top = this.point.shapeArgs.height < 20 ? -12 : 0;\n+\t\t\t\t \treturn \'<div class="datalabelInside" style="text-shadow:none;color:#8EADAC;position: absolute; margin-top:\'+ margin_top+\'px ;margin-left:\' + pointWidth / 2 + \'px">\' + numberDisplay(this.y) + \'</div>\';\n+\t\t\t\t }\n+\t\n+\t\t\t\t },\n+\t\t\t\t pointPadding: 0.2,\n+ borderWidth: 0\n+\t\t\t\t }\n+ },\n+\t\t\t\t\tcredits: {\n+\t\t\t\t\t\tenabled: false\n+\t\t\t\t\t},\n+\t\t\t\t\texporting:{buttons: {contextButton: { symbol: \'download\' }}},\n+\t\t\t\t\tbuttons: {contextButton: {menuItems: [\'downloadPNG\', \'downloadSVG\']}},\n+\t\t\t\t\tseries: pSeries,\n+\t\t\t\t\tnavigation: {\n+\t\t\t\t\t\t\tbuttonOptions: {\n+\t\t\t\t\t\t\t\ttheme: {\n+\t\t\t\t\t\t\t\t\tr: 4,\n+\t\t\t\t\t\t\t\t\tfill:\'#8EADAC\',\n+\t\t\t\t\t\t\t\t\tstates: {\n+\t\t\t\t\t\t\t\t\t\thover: {\n+\t\t\t\t\t\t\t\t\t\t\tfill: \'rgb(100, 138, 137)\',\n+\t\t\t\t\t\t\t\t\t\t\tstroke:\'#8EADAC\'\n+\t\t\t\t\t\t\t\t\t\t},\n+\t\t\t\t\t\t\t\t\t\tselect: {\n+\t\t\t\t\t\t\t\t\t\t\tstroke: \'#8EADAC\',\n+\t\t\t\t\t\t\t\t\t\t\tfill: \'rgb(100, 138, 137)\',\n+\t\t\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t}\n+\t\t\t\t};\n+\t\t\t\t\n+\t\t\t\treturn param ;\n+\t\t\t}\n+\t\t\t\n+\t\t\t$(function() {\n+\t\t\t\tvar categories = ["Nb OTU before normalisation", "Nb OTU after normalisation"] ;\n+\t\t\t\tvar histogram_series = [55, 50] ;\n+\t\t\t\tvar series_by_sample = [{"name": "01_subsample", "data": [55, 41]}, {"name": "02_subsample", "data": [55, 42]}, {"name": "03_subsample", "data": [55, 42]}] ;\n+\t\t\t\t\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Display summary\n+\t\t\t\tvar global_series = [{ name: \'All samples\', data: histogram_series }];\n+\t\t\t\t$(\'#filter-summary\').highcharts( histogram_param(\'Composition summary\', \'Nb OTUs\', categories, global_series, \'otu\') );\n+\t\t\t\t\n+\t\t\t\t// Display data by sample\n+\t\t\t\tvar table_categories = categories.slice() ;\n+\t\t\t\ttable_categories.unshift( "Sample" );\n+\t\t\t\tvar table_series = new Array();\n+\t\t\t\tfor( var spl_idx = 0 ; spl_idx < series_by_sample.length ; spl_idx++ ){\n+\t\t\t\t\tvar nb_by_step = series_by_sample[spl_idx][\'data\'].slice() ;\n+\t\t\t\t\tnb_by_step.unshift( series_by_sample[spl_idx][\'name\'] );\n+\t\t\t\t\ttable_series.push( nb_by_step );\n+\t\t\t\t};\n+\t\t\t\t$(\'#filter-log\').append( table("Composition by sample", table_categories, table_series) );\n+\t\t\t\t$(\'#filter-log table\').prop( \'id\', \'details-table\' );\n+\t\t\t\t$(\'#filter-log table\').DataTable({\n+\t\t\t\t\tdom: \t"<\'#details-csv-export\'><\'row\'<\'col-sm-5\'l><\'col-sm-7\'f>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-12\'tr>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-5\'i><\'col-sm-7\'p>>"\n+\t\t\t\t});\n+\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>\' );\n+\t\t\t\t$(\'#details-csv-export\').addClass( \'dataTables_filter\' );\n+\t\t\t\t$(\'#details-csv-export\').datatableExport({\n+\t\t\t\t\t\'table_id\': "details-table"\n+\t\t\t\t});\n+\t\t\t});\n+\t\t</script>\n+\t</head>\n+\t<body>\n+\t\t<p id="js-alert" class="alert alert-warning">\n+\t\t\tjavascript is needed to display data.<br />\n+\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t<div id="content" class="hidden">\n+\t\t\t<div id="filter-summary"></div>\n+\t\t\t<div id="filter-log"></div>\n+\t\t</div>\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/09-normalisation.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/09-normalisation.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,34 @@
+## Application
+Software: normalisation.py (version: 3.2.2)
+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/normalisation.py -n 100 --input-biom res_3.2.2/08-affiliation_postprocessed.biom --input-fasta res_3.2.2/08-affiliation_postprocessed.fasta --output-biom res_3.2.2/09-normalisation.biom --output-fasta res_3.2.2/09-normalisation.fasta --summary res_3.2.2/09-normalisation.html --log-file res_3.2.2/09-normalisation.log
+
+Application start: 01 Apr 2021 16:02:51
+
+#Normalisation calculation
+ start: 01 Apr 2021 16:02:51
+########################################################################################################
+# Random sampling in each sample. (biomTools.py version : 0.10.1)
+Command:
+ biomTools.py sampling --nb-sampled 100 --input-file res_3.2.2/08-affiliation_postprocessed.biom --output-file res_3.2.2/09-normalisation.biom
+
+Execution:
+ start: 01 Apr 2021 16:02:51
+ end: 01 Apr 2021 16:02:51
+
+ end: 01 Apr 2021 16:02:51
+
+########################################################################################################
+# Update fasta file based on sequence in biom file (biomFastaUpdate.py version : 1.0.1)
+Command:
+ biomFastaUpdate.py --input-biom res_3.2.2/09-normalisation.biom --input-fasta res_3.2.2/08-affiliation_postprocessed.fasta --output-file res_3.2.2/09-normalisation.fasta --log res_3.2.2/1617285771.1815455_17407_tmp_fasta_update.log
+
+Execution:
+ start: 01 Apr 2021 16:02:51
+ end: 01 Apr 2021 16:02:51
+
+
+#Summarise
+ start: 01 Apr 2021 16:02:51
+ end: 01 Apr 2021 16:02:51
+
+Application end: 01 Apr 2021 16:02:51

diff -r 000000000000 -r 834843ebe569 test-data/references/10-clustersStat.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/10-clustersStat.html Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,915 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>FROGS Cluster stat</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="3.2.2">\n+\t\t\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#hc-graph {\n+\t\t\t\theight: 500px;\n+\t\t\t\toverflow: auto;\n+\t\t\t}\n+\t\t\t#hc-warning {\n+\t\t\t\tmargin-top: 8px;\n+\t\t\t}\n+\t\t\t#hc-newick {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tposition: absolute;\n+\t\t\t\tbackground-color: white;\n+\t\t\t\tborder: 1px solid lightgrey;\n+\t\t\t\tborder-radius:5px;\n+\t\t\t\tpadding: 5px 5px 5px 5px;\n+\t\t\t\tmargin-top: 10px;\n+\t\t\t}\n+\t\t\t#dispersion {\n+\t\t\t\theight: 1000px;\n+\t\t\t}\n+\t\t\t#twofigs{\n+\t\t\t\theight: 600px;\n+\t\t\t}\n+\t\t\t.label-badge {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: -10px;\n+\t\t\t\tleft: -10px;\n+\t\t\t}\n+\t\t\t.badge-primary{\n+\t\t\t\tbackground-color:#8EADAC;\n+\t\t\t}\n+\t\t\t.graph-nb {\n+\t\t\t\tcolor: #95959C;\n+\t\t\t\tfont-style: italic;\n+\t\t\t\ttext-align: center;\n+\t\t\t}\n+\t\t\t.circle {\n+\t\t\t\tborder-style: solid;\n+\t\t\t\tborder-width: 3px;\n+\t\t\t\tborder-radius: 50px;\n+\t\t\t\tbox-shadow: 2px 2px 2px #555;\n+\t\t\t\tborder-color: #648a89;\n+\t\t\t\tbackground: radial-gradient( #8EADAC, #648a89);\n+\t\t\t\tcolor: white;\n+\t\t\t\tpadding: 10px;\n+\t\t\t\twidth: 180px;\n+\t\t\t\theight: 98px;\n+\t\t\t\tline-height: 30px;\n+\t\t\t\ttext-align: center;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-bottom: 10px;\n+\t\t\t\tvertical-align: middle;\n+\t\t\t}\n+\t\t\t.circle-value {\n+\t\t\t\tfont-weight: bold;\n+\t\t\t}\n+\t\t\t.d3-node {\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\t\t\t.d3-node-dot {\n+\t\t\t\tfill: #fff;\n+\t\t\t\tstroke: #8EADAC;\n+\t\t\t\tstroke-width: 3px;\n+\t\t\t}\n+\t\t\t.d3-collapsed-node {\n+\t\t\t\tfill: #8EADAC;\n+\t\t\t\tstroke: #648a89;\n+\t\t\t\tstroke-width: 3px;\n+\t\t\t}\n+\t\t\t.d3-node text {\n+\t\t\t\tfont: 13px sans-serif;\n+\t\t\t}\n+\t\t\t.d3-link {\n+\t\t\t\tfill: none;\n+\t\t\t\tstroke: #648a89;\n+\t\t\t\tstroke-width: 2px;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAF;\n+\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n+\t\t\t}\n+\t\t\ta {\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\ta:hover{\n+\t\t\t\tcolor:#648a89;\n+\t\t\t}\n+\t\t\t.page-link{\n+\t\t\t\tco'..b'td> \' + this.points[i].point.y + \'% </td>\' +\n+\t\t\t\t\t\t\t\t\t\'<td> sequences</td>\' +\n+\t\t\t\t\t\t\t\t \'</tr>\' ;\n+\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\treturn tooltip_head + \'<table>\' + tooltip_body + \'</table>\' ;\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\tshared: true,\n+\t\t\t\t\t\tuseHTML: true\n+\t\t\t\t\t};\n+\t\t\t\t\t$(\'#\' + container_id).append(\'<div></div>\');\n+\t\t\t\t\t$(\'#\' + container_id).highcharts( seq_by_depth );\n+\t\t\t\t\t$(\'#\' + container_id).append(\'<p class="graph-nb">N.B.: Select area to zoom in.</p>\');\n+\t\t\t}\n+\n+\t\t\t\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Data\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\tvar clusters_sizes = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13] ;\n+\t\t\tvar series = [{\n+\t\t\t\t\'name\': "All",\n+\t\t\t\t\'data\': [1, 1, 5, 8, 4, 13, 6, 7, 1, 2, 1, 1]\n+\t\t\t}];\n+\t\t\tvar sum_series = new Array() ;\n+\t\t\tvar samples_distrib = {"01_subsample": {"shared_seq": 99, "shared_observations": 40, "own_seq": 1, "own_observations": 1}, "02_subsample": {"shared_seq": 100, "shared_observations": 42, "own_seq": 0, "own_observations": 0}, "03_subsample": {"shared_seq": 100, "shared_observations": 42, "own_seq": 0, "own_observations": 0}} ;\n+\t\t\tvar newick = "((03_subsample,(01_subsample,02_subsample):0.400):0.425);" ;\n+\n+\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Main\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t$(function() {\t\t\t\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\n+\t\t\t\t// Load active tab\n+\t\t\t\tcluster_distrib_load( "cluster-distrib" );\n+\t\t\t\t\n+\t\t\t\t// Add tab listener\n+\t\t\t\t$(\'.nav-tabs a\').click(function (e) {\n+\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t$(this).tab(\'show\');\n+\t\t\t\t\tif( $(this).attr(\'href\') == "#sequence-distrib" && $(\'#sequence-distrib\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#sequence-distrib\').removeClass("disabled");\n+\t\t\t\t\t\tsequence_distrib_load( "sequence-distrib" );\n+\t\t\t\t\t} else if( $(this).attr(\'href\') == "#samples-distrib" && $(\'#samples-distrib\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#samples-distrib\').removeClass("disabled");\n+\t\t\t\t\t\tsample_table_load( "samples-distrib-table" );\n+\t\t\t\t\t\thierarchical_clustering_load( "samples-distrib-hc" );\n+\t\t\t\t\t}\n+\t\t\t\t})\n+\t\t\t});\n+\t\t</script>\n+\t</head>\n+\t<body>\n+\t\t<p id="js-alert" class="alert alert-warning">\n+\t\t\tjavascript is needed to display data.<br />\n+\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+\t\t<div id="content" class="hidden">\n+\t\t\t<ul class="nav nav-tabs">\n+\t\t\t\t<li class="nav-item active"><a class="nav-link active" href="#cluster-distrib">Clusters distribution</a></li>\n+\t\t\t\t<li class="nav-item active"><a class="nav-link" href="#sequence-distrib">Sequences distribution</a></li>\n+\t\t\t\t<li class="nav-item active"><a class="nav-link" href="#samples-distrib">Samples distribution</a></li>\n+\t\t\t</ul>\n+\t\t\t<div class="tab-content">\n+\t\t\t\t<div id="cluster-distrib" role="tabpanel" class="tab-pane active">\n+\t\t\t\t\t<div class="row">\n+\t\t\t\t\t\t<div class="col-md-2"></div>\n+\t\t\t\t\t\t<div id="nb-clusters" class="col-sm-6 col-md-4"></div>\n+\t\t\t\t\t\t<div id="nb-sequences" class="col-sm-6 col-md-4"></div>\n+\t\t\t\t\t\t<div class="col-md-2"></div>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t\t<div id="sequence-distrib" role="tabpanel" class="tab-pane disabled"></div>\n+\t\t\t\t<div id="samples-distrib" role="tabpanel" class="tab-pane disabled">\n+\t\t\t\t\t<div>\n+\t\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Sequences count</h2>\n+\t\t\t\t\t\t<div id="samples-distrib-table"></div>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div>\n+\t\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Hierarchical clustering</h2>\n+\t\t\t\t\t\t<div id="samples-distrib-hc"></div>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t</div>\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/10-clustersStat.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/10-clustersStat.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,22 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/clusters_stat.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/clusters_stat.py --input-biom res_3.2.2/09-normalisation.biom --output-file res_3.2.2/10-clustersStat.html --log-file res_3.2.2/10-clustersStat.log
+
+########################################################################################################
+# Hierarchical classification on observation proportions. (biomTools.py version : 0.10.1)
+Command:
+ biomTools.py hclassification --distance-method braycurtis --linkage-method average --input-file res_3.2.2/09-normalisation.biom --output-file res_3.2.2/1617285771.5673287_17417_HClassif.newick > res_3.2.2/1617285771.5673287_17417_HClassif_log.txt
+
+Execution:
+ start: 01 Apr 2021 16:02:51
+ end: 01 Apr 2021 16:02:53
+
+########################################################################################################
+# Writes by abundance the number of clusters. (biomTools.py version : 0.10.1)
+Command:
+ biomTools.py obsdepth --input-file res_3.2.2/09-normalisation.biom --output-file res_3.2.2/1617285771.5673287_17417_depths.tsv
+
+Execution:
+ start: 01 Apr 2021 16:02:53
+ end: 01 Apr 2021 16:02:53
+

diff -r 000000000000 -r 834843ebe569 test-data/references/11-affiliationsStat.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/11-affiliationsStat.html Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,1197 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>FROGS Affiliations stat</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="3.2.2">\n+\t\t\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t/*\n+\t\t\t * jDistrib 0.1.0 - CSS jDistrib Library\t\n+\t\t\t *\t\t \n+\t\t\t * Copyright (c) 2015 Escudie Frederic\n+\t\t\t * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.\n+\t\t\t */\n+\t\t\t#sunburst-graph{margin-left:auto;margin-right:auto}.jDistrib-walk-rank{height:100%;margin-right:2px;padding:8px;float:left;border-top-right-radius:7px;border-bottom-right-radius:7px;cursor:pointer;box-shadow:1px 1px 1px #555}.jDistrib-walk-rank-size{margin-left:5px;padding:4px;background-color:#FFF;color:#648a89;border-radius:9px;text-align:center;font-size:10px;font-family:sans-serif}.jDistrib-root-label{font-weight:700;cursor:pointer}.jDistrib-arc-label{cursor:pointer}.jDistrib-arc{cursor:pointer;stroke:#fff;fill-rule:evenodd}.jDistrib-tooltip{position:absolute;padding:10px;font:12px sans-serif;background:#8EADAC;border:0;border-radius:8px;pointer-events:none}.jDistrib-empty-details{color:#fff;background-color:#8EADAC;padding:15px;margin-bottom:20px;border:1px solid transparent;border-radius:4px}.jDistrib-table-details>tbody>tr:nth-of-type(2n+1){background-color:#F5F5F5}.jDistrib-table-details{border:1px solid #DDD;border-radius:8px;border-spacing:1px;border-collapse:separate}.jDistrib-table-details td,th{padding:2px 8px}.jDistrib-table-details .number{text-align:right}.jDistrib-export-toggle{height:30px;width:30px;padding:1px}.jDistrib-export-toggle div{background-color:#636363;border-radius:2px;height:3px;margin-top:2px;margin-bottom:2px}\n+\t\t</style>\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\t.set-datatype {\n+\t\t\t\twidth: 200px;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t}\n+\t\t\t.table-action {\n+\t\t\t\tvertical-align: middle;\n+\t\t\t\tmargin-right: 20px;\n+\t\t\t}\n+\t\t\t.fusion-left {\n+\t\t\t\tposition:relative;\n+\t\t\t\tz-index:2;\t\t\n+\t\t\t\tmargin-right: 0px;\n+\t\t\t\tmargin-bottom: 0px;\n+\t\t\t\tborder-top-left-radius: 4px;\n+\t\t\t\tborder-bottom-left-radius: 4px;\n+\t\t\t}\n+\t\t\t.fusion-right {\n+\t\t\t\tborder-top-left-radius: 0px;\n+\t\t\t\tborder-bottom-left-radius: 0px;\n+\t\t\t\tmargin-left:-6px;\n+\t\t\t}\n+\t\t\tselect.table-action {\n+\t\t\t\tpadding: 6px 12px;\n+\t\t\t\tfont-size: 14px;\n+\t\t\t\tfont-weight: 400;\n+\t\t\t\tline-height: 1.42857;\n+\t\t\t\tbox-shadow: 0px 1px 1px rgba(0, 0, 0, 0.075);\n+\t\t\t\tcolor: #555;\n+\t\t\t\tbackground-color: #FFF;\n+\t\t\t\tbackground-image: none;\n+\t\t\t\tborder: 1px solid #CCC;\n+\t\t\t}\n+\t\t\t#sunburst-detail table {\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t}\t\n+\t\t\t#sunburst-detail p {\n+\t\t\t\ttext-align: center;\n+\t\t\t}\n+\t\t\t#sunburst-menu i'..b'class="nav-item active"><a class="nav-link active" href="#tax-distrib">Taxonomy distribution</a></li>\n+\t\t\t\t<li class="nav-item" id="bootstrap-nav-tab"><a class="nav-link" href="#bootstrap-distrib">Bootstrap distribution</a></li>\n+\t\t\t\t<li class="nav-item" id="alignment-nav-tab"><a class="nav-link" href="#alignment-distrib">Alignment distribution</a></li>\n+\t\t\t</ul>\n+\t\t\t<div id="tab-content" class="tab-content">\n+\t\t\t\t<div id="tax-distrib" role="tabpanel" class="tab-pane active">\n+\t\t\t\t\t<button id="display-global-sunburst" class="btn d-block mx-auto" data-toggle="modal" data-target="#sunburst-modal">\n+\t\t\t\t\t\t<span class="fa fa-pie-chart" aria-hidden="true"> Display global distribution</span>\n+\t\t\t\t\t</button>\n+\t\t\t\t\t<table id="taxBySample-table" class="table table-striped">\n+\t\t\t\t\t\t<thead>\n+\t\t\t\t\t\t</thead>\n+\t\t\t\t\t\t<tbody></tbody>\n+\t\t\t\t\t\t<tfoot>\n+\t\t\t\t\t\t\t<tr>\n+\t\t\t\t\t\t\t\t<th>\n+\t\t\t\t\t\t\t\t\t<span class="table-action">With selection:</span>\n+\t\t\t\t\t\t\t\t\t<select id="rarefaction-level" name="select" class="table-action fusion-left"></select>\n+\t\t\t\t\t\t\t\t\t<button id="display-rarefaction" class="btn table-action fusion-right" disabled data-toggle="modal" data-target="#rarefaction-modal"><span class="fa fa-line-chart" aria-hidden="true"> Display rarefaction</span></button>\n+\t\t\t\t\t\t\t\t\t<button id="display-spl-sunburst" class="btn table-action" disabled data-toggle="modal" data-target="#sunburst-modal"><span class="fa fa-pie-chart" aria-hidden="true"> Display distribution</span></button>\n+\t\t\t\t\t\t\t\t</th>\n+\t\t\t\t\t\t\t</tr>\n+\t\t\t\t\t\t</tfoot>\n+\t\t\t\t\t</table>\n+\t\t\t\t</div>\n+\t\t\t\t<div id="bootstrap-distrib" role="tabpanel" class="tab-pane disabled">\n+\t\t\t\t\t<div id="bootstrap-barplot"></div>\n+\t\t\t\t\t<div id="set-bootstrap-barplot" class="set-datatype">\n+\t\t\t\t\t\t<button id="bootstrap-clstr-btn" type="button" class="btn btn-md btn-block">by OTUs</button>\n+\t\t\t\t\t\t<button id="bootstrap-seq-btn" type="button" class="btn btn-md btn-block">by sequences</button>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t\t<div id="alignment-distrib" role="tabpanel" class="tab-pane disabled">\n+\t\t\t\t\t<div id="alignment-heatmap"></div>\n+\t\t\t\t\t<div id="set-alignment-heatmap" class="set-datatype">\n+\t\t\t\t\t\t<button id="heatmap-clstr-btn" type="button" class="btn btn-md btn-block" disabled>by OTUs</button>\n+\t\t\t\t\t\t<button id="heatmap-seq-btn" type="button" class="btn btn-md btn-block">by sequences</button>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t</div>\n+\t\t\n+\t\t<div class="modal" id="sunburst-modal" tabindex="-1" role="dialog" aria-hidden="true">\n+\t\t\t<div class="modal-dialog modal-lg">\n+\t\t\t\t<div class="modal-content">\n+\t\t\t\t\t<div class="modal-header">\n+\t\t\t\t\t\t<h6 class="modal-title">Taxa distribution</h6>\n+\t\t\t\t\t\t<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div class="modal-body">\n+\t\t\t\t\t\t<div id="sunburst-walktrace"></div>\n+\t\t\t\t\t\t<div id="sunburst-graph"></div>\n+\t\t\t\t\t\t<div>\n+\t\t\t\t\t\t\t</br><h6>Detail on selected:</h6>\n+\t\t\t\t\t\t\t<div id="sunburst-detail"></div>\n+\t\t\t\t\t\t</div>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div class="modal-footer">\n+\t\t\t\t\t\t<span id="sunburst-menu"></span>\n+\t\t\t\t\t\t<button type="button" class="btn btn-default" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t</div>\n+\t\t<div class="modal" id="rarefaction-modal" tabindex="-1" role="dialog" aria-hidden="true">\n+\t\t\t<div class="modal-dialog modal-lg">\n+\t\t\t\t<div class="modal-content">\n+\t\t\t\t\t<div class="modal-header">\n+\t\t\t\t\t\t<h6 class="modal-title">Rarefaction</h6>\n+\t\t\t\t\t\t<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div class="modal-body">\n+\t\t\t\t\t\t<div id="rarefaction-chart"></div>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div class="modal-footer">\n+\t\t\t\t\t\t<button type="button" class="btn btn-default" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t</div>\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/11-affiliationsStat.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/11-affiliationsStat.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,22 @@
+## Application
+Software: affiliations_stat.py (version: 3.2.2)
+Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliations_stat.py --input-biom res_3.2.2/09-normalisation.biom --output-file res_3.2.2/11-affiliationsStat.html --log-file res_3.2.2/11-affiliationsStat.log --tax-consensus-tag blast_taxonomy --identity-tag perc_identity --coverage-tag perc_query_coverage --multiple-tag blast_affiliations --rarefaction-ranks Family Genus Species --taxonomic-ranks Domain Phylum Class Order Family Genus Species
+
+########################################################################################################
+# Writes by sample the rarefaction data for rank(s) 4, 5, 6. (biomTools.py version : 0.10.1)
+Command:
+ biomTools.py rarefaction --input-file res_3.2.2/09-normalisation.biom --output-file-pattern res_3.2.2/1617285773.930201_17428_rarefaction_rank_##RANK##.tsv --taxonomy-key "blast_taxonomy" --step-size 2 --ranks 4 5 6
+
+Execution:
+ start: 01 Apr 2021 16:02:53
+ end: 01 Apr 2021 16:02:54
+
+########################################################################################################
+# Produces a taxonomy tree with counts by sample. (biomTools.py version : 0.10.1)
+Command:
+ biomTools.py treeCount --input-file res_3.2.2/09-normalisation.biom --taxonomy-key "blast_taxonomy" --output-enewick res_3.2.2/1617285773.930201_17428_taxCount.enewick --output-samples res_3.2.2/1617285773.930201_17428_taxCount_ids.tsv
+
+Execution:
+ start: 01 Apr 2021 16:02:54
+ end: 01 Apr 2021 16:02:54
+

diff -r 000000000000 -r 834843ebe569 test-data/references/12-biom2tsv-affiliation_multihit.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/12-biom2tsv-affiliation_multihit.tsv Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,1 @@
+#observation_name blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length

diff -r 000000000000 -r 834843ebe569 test-data/references/12-biom2tsv.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/12-biom2tsv.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,22 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/biom_to_tsv.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/biom_to_tsv.py --input-biom res_3.2.2/09-normalisation.biom --input-fasta res_3.2.2/09-normalisation.fasta --output-tsv res_3.2.2/12-biom2tsv.tsv --output-multi-affi res_3.2.2/12-biom2tsv-affiliation_multihit.tsv --log-file res_3.2.2/12-biom2tsv.log
+
+########################################################################################################
+# Converts a BIOM file in TSV file. (biom2tsv.py version : 1.5.0)
+Command:
+ biom2tsv.py --input-file res_3.2.2/09-normalisation.biom --input-fasta res_3.2.2/09-normalisation.fasta --output-file res_3.2.2/12-biom2tsv.tsv --fields 'comment' '@rdp_tax_and_bootstrap' 'blast_taxonomy' '@blast_subject' '@blast_perc_identity' '@blast_perc_query_coverage' '@blast_evalue' '@blast_aln_length' 'seed_id' '@seed_sequence' '@observation_name' '@observation_sum' '@sample_count'
+
+Execution:
+ start: 01 Apr 2021 16:02:54
+ end: 01 Apr 2021 16:02:54
+
+########################################################################################################
+# Extracts multi-affiliations data from a FROGS BIOM file. (multiAffiFromBiom.py version : 1.3.0)
+Command:
+ multiAffiFromBiom.py --input-file res_3.2.2/09-normalisation.biom --output-file res_3.2.2/12-biom2tsv-affiliation_multihit.tsv
+
+Execution:
+ start: 01 Apr 2021 16:02:54
+ end: 01 Apr 2021 16:02:54
+

diff -r 000000000000 -r 834843ebe569 test-data/references/12-biom2tsv.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/12-biom2tsv.tsv Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,51 @@\n+#comment\trdp_tax_and_bootstrap\tblast_taxonomy\tblast_subject\tblast_perc_identity\tblast_perc_query_coverage\tblast_evalue\tblast_aln_length\tseed_id\tseed_sequence\tobservation_name\tobservation_sum\t01_subsample\t02_subsample\t03_subsample\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Chaetothyriales;(1.0);f__Herpotrichiellaceae;(1.0);g__Exophiala;(1.0);s__Exophiala_equina;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Chaetothyriales;f__Herpotrichiellaceae;g__Exophiala;s__Exophiala_equina\tJF747094_SH197643.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_54\tATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_1\t3\t0\t2\t1\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Pezizomycetes;(1.0);o__Pezizales;(1.0);f__Tuberaceae;(1.0);g__Tuber;(1.0);s__Tuber_latisporum;(1.0);\tk__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Tuberaceae;g__Tuber;s__Tuber_latisporum\tDQ898183_SH216206.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_92546\tCCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\tCluster_2\t7\t4\t2\t1\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Elaphomycetaceae;(1.0);g__Elaphomyces;(1.0);s__Elaphomyces_compleximurus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Elaphomycetaceae;g__Elaphomyces;s__Elaphomyces_compleximurus\tJN711441_SH022548.07FU_refs_singleton\t100.0\t100.0\t8.06e-132\t248\t01_59\tAGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_3\t6\t1\t3\t2\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Hypocreales;(1.0);f__Hypocreaceae;(1.0);g__Trichoderma;(1.0);s__Trichoderma_aggressivum;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum\tAF456924_SH097201.07FU_refs\t100.0\t100.0\t4.90e-134\t252\t01_81\tCCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_4\t8\t4\t1\t3\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Xylariales;(1.0);f__Amphisphaeriaceae;(1.0);g__Pestalotiopsis;(1.0);s__Pestalotiopsis_diversiseta;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Pestalotiopsis;s__Pestalotiopsis_diversiseta\tJX399009_SH268556.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_25\tCATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_5\t4\t0\t2\t2\n+no data\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Bankeraceae;(1.0);g__Sarcodon;(1.0);s__Sarcodon_quercophilus;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Sarcodon;s__Sarcodon_quercophilus\tKM668101_SH491630.07FU_refs_singleton\t100.0\t100.0\t3.94e-140\t263\t01_74803\tAGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\tCluster_6\t6\t0\t1\t5\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes'..b'GCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_45\t6\t2\t0\t4\n+no data\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Hymenochaetales;(1.0);f__Hymenochaetaceae;(1.0);g__Pseudochaete;(1.0);s__Pseudochaete_subrigidula;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Pseudochaete;s__Pseudochaete_subrigidula\tJQ716403_SH219241.07FU_refs\t100.0\t100.0\t7.94e-178\t331\t01_91485\tTCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_46\t4\t1\t1\t2\n+no data\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Marasmiaceae;(1.0);g__Megacollybia;(1.0);s__Megacollybia_subfurfuracea;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Marasmiaceae;g__Megacollybia;s__Megacollybia_subfurfuracea\tEU623745_SH215851.07FU_refs\t100.0\t100.0\t0.0\t390\t01_410\tGCGGAAGGATCATTACTGAATTGAAATGCGTTAGTTAGTTGAGCTGACCTTCTCCCTTTAATGGGGGGGGGAGTAGTATGTGCTCGCTATATCGCTTTTTCTAACTCCCCACTGTGCACCTCTATTGTAGGCTACGAGTGACTCTCAAGTAGACACACTCCCATAACACACCCTTTGTGCGCAGAAGGGGGGGGAAAAGGGTCTATTTGGGTTTAAGAAGGCTTATCGGGCATCCATTTTGCTTGCTTTCGACTTTGTAGCCTATGATCTTACAACAAACTACTTTGATAAAGTCTTGATGAATGATAGATTGGTCTTTTGAACCAATATAAAAGTTGTACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_47\t9\t5\t1\t3\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Trichocomaceae;(1.0);g__Aspergillus;(1.0);s__Aspergillus_caninus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_caninus\tGQ169315_SH195598.07FU_refs\t100.0\t100.0\t3.70e-130\t245\t01_86\tTGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_48\t2\t1\t1\t0\n+no data\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Cortinariaceae;(1.0);g__Cortinarius;(1.0);s__Cortinarius_parkeri;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_parkeri\tGQ159830_SH222371.07FU_refs\t100.0\t100.0\t1.33e-129\t244\t01_88865\tTGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_49\t1\t1\t0\t0\n+FROGS_combined\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Dothideomycetes;(1.0);o__Pleosporales;(1.0);f__Lindgomycetaceae;(1.0);g__Lindgomyces;(1.0);s__Lindgomyces_breviappendiculatus;(1.0);\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Lindgomycetaceae;g__Lindgomyces;s__Lindgomyces_breviappendiculatus\tJF419897_SH181470.07FU_refs\t100.0\t100.0\t-1\t1017\t01_71070_FROGS_combined\tGATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_50_FROGS_combined\t4\t1\t0\t3\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/13-affiliation_multihit.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/13-affiliation_multihit.tsv Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,51 @@\n+#OTUID\ttaxonomy\tsubject\tevalue\tperc_identity\tperc_query_coverage\taln_length\n+Cluster_19\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_candidolanata\tJX118682_SH219010.07FU_refs\t5.05e-139\t100.0\t100.0\t261\n+Cluster_12\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_pachyderma\tJX118731_SH218995.07FU_refs\t5.20e-144\t100.0\t100.0\t270\n+Cluster_22\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_semisanguifluus\tUDB000320_SH220111.07FU_refs\t1.45e-144\t100.0\t100.0\t271\n+Cluster_47\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Marasmiaceae;g__Megacollybia;s__Megacollybia_subfurfuracea\tEU623745_SH215851.07FU_refs\t0.0\t100.0\t100.0\t390\n+Cluster_36\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii\tUDB002317_SH221025.07FU_refs\t9.52e-162\t100.0\t100.0\t302\n+Cluster_18\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rodmanii\tEU330948_SH316773.07FU_refs\t8.56e-142\t100.0\t100.0\t266\n+Cluster_34\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Hydnellum;s__Hydnellum_suaveolens\tUDB016091_SH210668.07FU_refs\t1.97e-153\t100.0\t100.0\t287\n+Cluster_20\tk__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Pezizaceae;g__Terfezia;s__Terfezia_claveryi\tGU474801_SH104786.07FU_refs_singleton\t8.56e-142\t100.0\t100.0\t266\n+Cluster_2\tk__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Tuberaceae;g__Tuber;s__Tuber_latisporum\tDQ898183_SH216206.07FU_refs\t2.25e-132\t100.0\t100.0\t249\n+Cluster_29\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_caesiocolor\tKF732603_SH223051.07FU_refs\t5.49e-154\t100.0\t100.0\t288\n+Cluster_37\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Entolomataceae;g__Entoloma;s__Entoloma_sp\tJQ320113_SH190746.07FU_refs\t2.66e-162\t100.0\t100.0\t303\n+Cluster_16\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Xylariaceae;g__Hypoxylon;s__Hypoxylon_fragiforme\tAY616689_SH196294.07FU_refs\t8.56e-142\t100.0\t100.0\t266\n+Cluster_41\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Tricholoma;s__Tricholoma_portentosum\tUDB011569_SH190415.07FU_refs\t2.72e-167\t100.0\t100.0\t312\n+Cluster_27\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_gentianeus\tKF732310_SH222414.07FU_refs\t5.49e-154\t100.0\t100.0\t288\n+Cluster_11\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Adisciso;s__Adisciso_tricellulare\tAB594796_SH278638.07FU_refs\t8.06e-132\t100.0\t100.0\t248\n+Cluster_26\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Agaricaceae;g__Lepiota;s__Lepiota_geogenia\tJX179268_SH178540.07FU_refs\t2.53e-152\t100.0\t100.0\t285\n+Cluster_24\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Hydnellum;s__Hydnellum_peckii\tUDB003291_SH182302.07FU_refs\t7.05e-153\t100.0\t100.0\t286\n+Cluster_33\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Strophariaceae;g__Pholiota;s__Pholiota_highlandensis\tHG007976_SH219743.07FU_refs\t1.22e-160\t100.0\t100.0\t300\n+Cluster_35\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_aurantiobasis\tJX045670_SH303923.07FU_refs\t1.19e-155\t100.0\t100.0\t291\n+Cluster_49\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_parkeri\tGQ159830_SH222371.07FU_refs\t1.33e-129\t100.0\t100.0\t244\n+Cluster_8\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Suillaceae;g__Truncocolumella;s__Truncocolumella_rubra\tEU837224_SH182725.07FU_refs\t2.25e-132\t100.0\t100.0\t249\n+Cluster_15\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Omphalotaceae;g__Gymnopus;s__Gymnopus_hybridus\tJX536175_SH183774.07FU_refs\t2.39e-142'..b'Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_caninus\tGQ169315_SH195598.07FU_refs\t3.70e-130\t100.0\t100.0\t245\n+Cluster_4\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum\tAF456924_SH097201.07FU_refs\t4.90e-134\t100.0\t100.0\t252\n+Cluster_42\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Inocybaceae;g__Inocybe;s__Inocybe_sindonia\tUDB015350_SH176685.07FU_refs\t4.60e-170\t100.0\t100.0\t317\n+Cluster_10\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_cyathuliformis\tHQ714785_SH330547.07FU_refs\t4.90e-134\t100.0\t100.0\t252\n+Cluster_45\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Hymenochaete;s__Hymenochaete_longispora\tJQ279537_SH175098.07FU_refs\t0.0\t100.0\t100.0\t337\n+Cluster_30\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Psathyrella;s__Psathyrella_multipedata\tKC992888_SH220378.07FU_refs\t1.19e-155\t100.0\t100.0\t291\n+Cluster_46\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Pseudochaete;s__Pseudochaete_subrigidula\tJQ716403_SH219241.07FU_refs\t7.94e-178\t100.0\t100.0\t331\n+Cluster_40\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_limonius\tUDB001086_SH222381.07FU_refs\t7.59e-168\t100.0\t100.0\t313\n+Cluster_38\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_sinapivelus\tGQ890305_SH122869.07FU_refs_singleton\t1.57e-159\t100.0\t100.0\t298\n+Cluster_13\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Gamundia;s__Gamundia_leucophylla\tGU234142_SH201120.07FU_refs\t8.63e-142\t99.627\t100.0\t268\n+Cluster_3\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Elaphomycetaceae;g__Elaphomyces;s__Elaphomyces_compleximurus\tJN711441_SH022548.07FU_refs_singleton\t8.06e-132\t100.0\t100.0\t248\n+Cluster_9\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_mienum\tJQ621972_SH177703.07FU_refs\t2.32e-137\t100.0\t100.0\t258\n+Cluster_50_FROGS_combined\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Lindgomycetaceae;g__Lindgomyces;s__Lindgomyces_breviappendiculatus\tJF419897_SH181470.07FU_refs\t-1\t100.0\t100.0\t1017\n+Cluster_21\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_cremeum\tAY737760_SH296378.07FU_refs\t1.45e-144\t100.0\t100.0\t271\n+Cluster_25\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Psathyrella;s__Psathyrella_sublatispora\tKC992854_SH220410.07FU_refs\t2.53e-152\t100.0\t100.0\t285\n+Cluster_31\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_calojanthinus\tKF732272_SH222375.07FU_refs\t1.19e-155\t100.0\t100.0\t291\n+Cluster_1\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Chaetothyriales;f__Herpotrichiellaceae;g__Exophiala;s__Exophiala_equina\tJF747094_SH197643.07FU_refs\t2.25e-132\t100.0\t100.0\t249\n+Cluster_6\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Sarcodon;s__Sarcodon_quercophilus\tKM668101_SH491630.07FU_refs_singleton\t3.94e-140\t100.0\t100.0\t263\n+Cluster_5\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Pestalotiopsis;s__Pestalotiopsis_diversiseta\tJX399009_SH268556.07FU_refs\t2.25e-132\t100.0\t100.0\t249\n+Cluster_7\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Rasamsonia;s__Rasamsonia_emersonii\tJF417478_SH216679.07FU_refs\t1.75e-133\t100.0\t100.0\t251\n+Cluster_28\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Strophariaceae;g__Hypholoma;s__Hypholoma_capnoides\tUDB001581_SH219736.07FU_refs\t1.97e-153\t100.0\t100.0\t287\n+Cluster_32\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_amnicola\tKF732249_SH136099.07FU_refs_singleton\t1.19e-155\t100.0\t100.0\t291\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/13-affiliation_std.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/13-affiliation_std.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "Sampling 100 elements by sample from res_3.2.2/08-affiliation_postprocessed.biom", "date": "2021-04-01T16:02:51", "rows": [{"id": "Cluster_19", "metadata": {"comment": "", "seed_id": "01_66", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_candidolanata", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_candidolanata", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_candidolanata"]}}, {"id": "Cluster_12", "metadata": {"comment": "", "seed_id": "01_22", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_pachyderma", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_pachyderma", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"]}}, {"id": "Cluster_22", "metadata": {"comment": "", "seed_id": "01_155", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_semisanguifluus", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_semisanguifluus", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_semisanguifluus"]}}, {"id": "Cluster_47", "metadata": {"comment": "", "seed_id": "01_410", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Marasmiaceae;g__Megacollybia;s__Megacollybia_subfurfuracea", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Marasmiaceae;g__Megacollybia;s__Megacollybia_subfurfuracea", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"]}}, {"id": "Cluster_36", "metadata": {"comment": "", "seed_id": "01_222", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"]}}, {"id": "Cluster_18", "metadata": {"comment": "", "seed_id": "01_40", "blast_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rodmanii", "rdp_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rodmanii", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_rodmanii"]}}, {"id": "Cluster_34", "metadata": {"comment": "", "seed_id": "01_67", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Hydnellum;s__Hydnellum_suaveolens", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Hydnellum;s__Hydnellum_suaveolens", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Ban'..b', "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"]}}, {"id": "Cluster_5", "metadata": {"comment": "", "seed_id": "01_25", "blast_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Pestalotiopsis;s__Pestalotiopsis_diversiseta", "rdp_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Pestalotiopsis;s__Pestalotiopsis_diversiseta", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"]}}, {"id": "Cluster_7", "metadata": {"comment": "", "seed_id": "01_38", "blast_taxonomy": "k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Rasamsonia;s__Rasamsonia_emersonii", "rdp_taxonomy": "k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Rasamsonia;s__Rasamsonia_emersonii", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"]}}, {"id": "Cluster_28", "metadata": {"comment": "", "seed_id": "01_71661", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Strophariaceae;g__Hypholoma;s__Hypholoma_capnoides", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Strophariaceae;g__Hypholoma;s__Hypholoma_capnoides", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"]}}, {"id": "Cluster_32", "metadata": {"comment": "", "seed_id": "01_96725", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_amnicola", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_amnicola", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_amnicola"]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 3], [0, 1, 3], [1, 0, 4], [1, 1, 3], [1, 2, 3], [2, 0, 3], [2, 1, 2], [2, 2, 3], [3, 0, 5], [3, 1, 1], [3, 2, 3], [4, 0, 3], [4, 1, 2], [4, 2, 3], [5, 0, 1], [5, 1, 3], [5, 2, 2], [6, 0, 2], [6, 1, 2], [6, 2, 3], [7, 0, 4], [7, 2, 2], [8, 0, 4], [8, 1, 2], [8, 2, 1], [9, 0, 3], [9, 1, 3], [9, 2, 4], [10, 0, 2], [10, 1, 5], [10, 2, 1], [11, 0, 4], [11, 1, 6], [11, 2, 2], [12, 0, 5], [12, 1, 1], [12, 2, 1], [13, 0, 2], [13, 1, 2], [14, 0, 2], [14, 1, 2], [14, 2, 2], [15, 0, 3], [15, 1, 3], [16, 0, 2], [16, 2, 1], [17, 0, 3], [17, 1, 1], [17, 2, 2], [18, 0, 2], [18, 2, 3], [19, 0, 1], [20, 0, 2], [20, 1, 2], [20, 2, 4], [21, 0, 3], [21, 1, 2], [21, 2, 1], [22, 0, 4], [22, 2, 1], [23, 0, 3], [23, 1, 1], [24, 0, 3], [24, 1, 3], [24, 2, 2], [25, 0, 2], [25, 1, 1], [26, 0, 2], [26, 1, 4], [26, 2, 1], [27, 0, 1], [27, 1, 2], [27, 2, 1], [28, 0, 1], [28, 1, 1], [29, 0, 4], [29, 1, 1], [29, 2, 3], [30, 0, 2], [30, 1, 4], [30, 2, 1], [31, 0, 1], [31, 1, 3], [31, 2, 3], [32, 0, 2], [32, 2, 4], [33, 0, 2], [33, 1, 1], [33, 2, 3], [34, 0, 1], [34, 1, 1], [34, 2, 2], [35, 0, 1], [35, 1, 8], [35, 2, 4], [36, 0, 3], [36, 1, 3], [37, 0, 2], [37, 1, 2], [37, 2, 2], [38, 0, 1], [38, 1, 3], [38, 2, 2], [39, 0, 1], [39, 2, 4], [40, 0, 1], [40, 2, 3], [41, 1, 2], [41, 2, 1], [42, 1, 3], [42, 2, 5], [43, 1, 2], [43, 2, 2], [44, 1, 2], [44, 2, 1], [45, 1, 1], [45, 2, 5], [46, 1, 2], [46, 2, 2], [47, 1, 2], [47, 2, 1], [48, 1, 1], [48, 2, 3], [49, 1, 2], [49, 2, 3]], "shape": [50, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/13-biom2stdbiom.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/13-biom2stdbiom.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,4 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/biom_to_stdBiom.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/biom_to_stdBiom.py --input-biom res_3.2.2/09-normalisation.biom --output-biom res_3.2.2/13-affiliation_std.biom --output-metadata res_3.2.2/13-affiliation_multihit.tsv --log-file res_3.2.2/13-biom2stdbiom.log
+

diff -r 000000000000 -r 834843ebe569 test-data/references/14-tsv2biom.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/14-tsv2biom.biom Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "FROGS_tsv2_biom", "date": "2021-04-01T16:02:54", "rows": [{"id": "Cluster_1", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "seed_id": "01_54", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "subject": "JF747094_SH197643.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "2.25e-132", "aln_length": "249"}]}}, {"id": "Cluster_2", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "seed_id": "01_92546", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "subject": "DQ898183_SH216206.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "2.25e-132", "aln_length": "249"}]}}, {"id": "Cluster_3", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "seed_id": "01_59", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "subject": "JN711441_SH022548.07FU_refs_singleton", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "8.06e-132", "aln_length": "248"}]}}, {"id": "Cluster_4", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "seed_id": "01_81", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "subject": "AF456924_SH097201.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "4.90e-134", "aln_length": "252"}]}}, {"id": "Cluster_5", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "seed_id": "01_25", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "subject": "JX399009_SH268556.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "2.25e'..b'_Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_caninus"], "seed_id": "01_86", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_caninus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_caninus"], "subject": "GQ169315_SH195598.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "3.70e-130", "aln_length": "245"}]}}, {"id": "Cluster_49", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"], "seed_id": "01_88865", "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"], "subject": "GQ159830_SH222371.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "1.33e-129", "aln_length": "244"}]}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "seed_id": "01_71070_FROGS_combined", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "subject": "JF419897_SH181470.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "-1", "aln_length": "1017"}]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 1, 2], [0, 2, 1], [1, 0, 4], [1, 1, 2], [1, 2, 1], [2, 0, 1], [2, 1, 3], [2, 2, 2], [3, 0, 4], [3, 1, 1], [3, 2, 3], [4, 1, 2], [4, 2, 2], [5, 1, 1], [5, 2, 5], [6, 1, 2], [6, 2, 1], [7, 0, 2], [7, 1, 2], [7, 2, 4], [8, 0, 1], [8, 2, 4], [9, 0, 1], [9, 1, 3], [9, 2, 3], [10, 0, 2], [10, 1, 2], [10, 2, 2], [11, 0, 4], [11, 1, 3], [11, 2, 3], [12, 0, 2], [12, 1, 2], [12, 2, 2], [13, 0, 3], [13, 1, 1], [14, 0, 3], [14, 1, 2], [14, 2, 1], [15, 0, 4], [15, 1, 6], [15, 2, 2], [16, 0, 1], [16, 1, 2], [16, 2, 1], [17, 0, 1], [17, 1, 3], [17, 2, 2], [18, 0, 3], [18, 1, 3], [19, 0, 4], [19, 2, 2], [20, 1, 2], [20, 2, 1], [21, 0, 3], [21, 1, 2], [21, 2, 3], [22, 0, 4], [22, 2, 1], [23, 1, 3], [23, 2, 5], [24, 0, 2], [24, 2, 1], [25, 0, 3], [25, 1, 3], [26, 1, 1], [26, 2, 3], [27, 0, 2], [27, 1, 2], [28, 0, 3], [28, 1, 3], [28, 2, 4], [29, 0, 2], [29, 1, 1], [29, 2, 3], [30, 1, 2], [30, 2, 2], [31, 1, 2], [31, 2, 3], [32, 0, 3], [32, 1, 1], [32, 2, 2], [33, 0, 2], [33, 1, 2], [33, 2, 3], [34, 0, 2], [34, 2, 3], [35, 0, 3], [35, 1, 2], [35, 2, 3], [36, 0, 2], [36, 1, 5], [36, 2, 1], [37, 0, 3], [37, 1, 3], [38, 0, 2], [38, 1, 4], [38, 2, 1], [39, 0, 1], [39, 1, 8], [39, 2, 4], [40, 0, 5], [40, 1, 1], [40, 2, 1], [41, 0, 2], [41, 1, 4], [41, 2, 1], [42, 0, 2], [42, 1, 1], [43, 0, 3], [43, 1, 3], [43, 2, 2], [44, 0, 2], [44, 2, 4], [45, 0, 1], [45, 1, 1], [45, 2, 2], [46, 0, 5], [46, 1, 1], [46, 2, 3], [47, 0, 1], [47, 1, 1], [48, 0, 1], [49, 0, 1], [49, 2, 3]], "shape": [50, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/14-tsv2biom.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/14-tsv2biom.fasta Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,100 @@\n+>Cluster_1\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_2\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3\n+AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_4\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_5\n+CATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_6\n+AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\n+>Cluster_7\n+CCGAGTGAGGGTCCCCTTTGCGGGCCCGACCTCCCACCCGTGTCTACCGTACCGTGTTGCTTCGGCGGGCCCGCCAGGGGGGCTCCTGTCCCTGGCCGCCGGGGGGCCATCTCCCGTGCCTCCGGGCCCGTGCCCGCCGGAGACCCTCGTGAACGCTGTCTTGAACAAAGGTTGCGGTCTGAGTGGAAAACACAATCGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_8\n+TTGAATTCTATGGAGGGGGGAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCTTCCTTTCTCTCATACACACACCTGTGCACCTGTTGTAGGTCCTCGAAAGAGGAGCTATGTTTTTCACATCACACCCCGTCGTATGTCTATAGAATGTGTTGAAAACGTCGACCTGTTTGACAGGCCGGCGGACAATAAAATTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_9\n+TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_10\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11\n+GATCATTACAGAGTTATCTAACTCCCAAACCCATGTGAACTTACCATTTGTTGCCTCGGCAGAGGCTACCCGGTACCTACCCTGGAGCAGCTACCCTGTAGCTACCCTGGAACGGCCTACCCTGTAGCGCATCCTGCCGGTGGACCTTTAAACTCTTGTTATTTTAAAGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_12\n+GGCTCTTCGGGGCATGTGCTCGCCTGTCACCTTTATCTTTCCACCTGTGCACACACTGTAGTCCTGGATACCTCTCGCCGCAAGGCGGATGCAGAGACTGCTGCTCAGCCTCCGAAAGGGGGAGGACGGCTATCTTTGAATTTCCAGGTCTACGATTATCACATACCCCAATTGAATGTTACAGAATGTTATCAAAGGGCCTTGTGCCTATAAACCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_13\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_14\n+GAACCAGCGGAGGGATCATTAACGAGTTTCGTACTCCAAACCCTTTGTGAACATACCTGTTTTCGTTGCTTCGGCAGGTGAAGGCGGAGGGCCTCCGGGCCTGAAGCCGCCGCCGGGCGGACCCCTCGCGGGGCGCTGCCGGGTGGGCCTGCCGGAGGGCACAGACTCTGTATTACAACGTACCTCTCTGAGTTATATTTTACAAACAAGTAAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_15\n+AACTTCTTTGGAGATAGTACTGTTGCTGGCCTTGTAATGAGGTATGTGCACGTTCTATTGCCAATTTATTCATCCACCTGTGCACTTTTTGTAGGAGTTCTTTGGGGTTATTTTGTACTTGGTGCAATTTGGCTTTGAAAGGCTTCTATGTCTTATAAACCATTAGTATGTCTCTGAATGTTTTTTATTGGGACTTG'..b'CGTGGGTCGGACGGTGGTCGAAAGGAATTAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_40\n+CTGCGGAAGGATCATTATTGAAATAAATCTGATGAGTTGCTGCTGGTTCTCTTAGGGAGCATGTGCACACTTGTCATCTTTATATTCTCCACCTTGTGCACCTTTTGTAGACCTGGATATCTCTCTGAGTGCTTTTAGCACTCAGGTTTGGAGGATTGACTTTTCTGTCTTTCCTTACCTTTCCCGGCCTATGTTTCTTCAAATACCCAATGTGTATGTCATTAGAATGTAATAAATGGGCTTTTGTGCCTTATAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_41\n+GTGACTGCGGAGGATCATTATTGAAATAAAGCTTGGTTAGGTTGTTGCTGGCTCTTCGGGGCATGTGCACACCTGACACCAACTTTTCTTACCACCTGTGCACTTTTTGTAGACTTTGGAATACCTCTCGAGGAAACTCGGTTTTGAGGACTGCTGTGCGCAAGCCGGCTTTCCTTACATTTTCCGGTCTATGTTTTTCTATATACCCTATAGTATGTCACAGAATGTCATTTTAATGGGCTTAATTGCCTTTAAACCTATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_42\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_43\n+ATCCGGAGGGGAGATGAAGAGGGAATTTAGTAGGAACCGTAGGCATTGTCGCTGGCCTTTGGAAACAAACGCATGTGCACATCTCGAAAGTCTTACTTAGTACCTCGATCTCTTTCCTTTTGTGAACCCCTTTTCTTACACCTGTGCACCCATTGTAGGTCCCGCGAGGGATCCTATGTCTCTATCTACTCTTAAATGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTTGGTTGGCGGCAGTAAAGAACCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_44\n+ATCCGGAGGGGGGGAGACGAGAGAAATTTGGGGTAGGAACGGAAGGGACTGTCGCTGGCCTTTGGAAACGAAGGCATGTGCACGTCTCGAAGTCTTACTTTTTTAGTATCTCGATCTCTTTCCTTTCGTGAGACCCTTTTCTTACACCTGTGCACCTATTGTAGGTCCCGCGAGGGATCTATGTCTCTATCTACTCTAAAACGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTCGGTTGGCGGCAGTAAAGAACTTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_45\n+CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_46\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_47\n+GCGGAAGGATCATTACTGAATTGAAATGCGTTAGTTAGTTGAGCTGACCTTCTCCCTTTAATGGGGGGGGGAGTAGTATGTGCTCGCTATATCGCTTTTTCTAACTCCCCACTGTGCACCTCTATTGTAGGCTACGAGTGACTCTCAAGTAGACACACTCCCATAACACACCCTTTGTGCGCAGAAGGGGGGGGAAAAGGGTCTATTTGGGTTTAAGAAGGCTTATCGGGCATCCATTTTGCTTGCTTTCGACTTTGTAGCCTATGATCTTACAACAAACTACTTTGATAAAGTCTTGATGAATGATAGATTGGTCTTTTGAACCAATATAAAAGTTGTACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_48\n+TGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>Cluster_49\n+TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_50_FROGS_combined\n+GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/14-tsv2biom.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/14-tsv2biom.log Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,13 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/tsv_to_biom.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/tsv_to_biom.py --input-tsv res_3.2.2/12-biom2tsv.tsv --input-multi-affi res_3.2.2/12-biom2tsv-affiliation_multihit.tsv --output-biom res_3.2.2/14-tsv2biom.biom --output-fasta res_3.2.2/14-tsv2biom.fasta --log-file res_3.2.2/14-tsv2biom.log
+
+########################################################################################################
+# Converts a TSV file in Biom. (tsv2biom.py version : 1.2.0)
+Command:
+ tsv2biom.py --input-file res_3.2.2/12-biom2tsv.tsv --input-multihits res_3.2.2/12-biom2tsv-affiliation_multihit.tsv --output-file res_3.2.2/14-tsv2biom.biom --output-fasta res_3.2.2/14-tsv2biom.fasta --fields comment rdp_tax_and_bootstrap blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length seed_id seed_sequence observation_name --samples-names 01_subsample 02_subsample 03_subsample
+
+Execution:
+ start: 01 Apr 2021 16:02:54
+ end: 01 Apr 2021 16:02:54
+

diff -r 000000000000 -r 834843ebe569 test-data/references/15-tree-mafft.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/15-tree-mafft.html Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,530 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>FROGS Tree</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="3.2.2">\n+\t\t\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAF;\n+\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n+\t\t\t}\n+\t\t\ta {\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\ta:hover{\n+\t\t\t\tcolor:#648a89;\n+\t\t\t}\n+\t\t\t\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 35px;\n+\t\t\t\tmargin-bottom: 12px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 25px;\n+\t\t\t\twidth: 25px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue background */\n+\t\t\t.container input:checked ~ .checkmark {\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\topacity:1;\n+\t\t\t}\n+\n+\t\t\t/* Create the checkmark/indicator (hidden when not checked) */\n+\t\t\t.checkmark:after {\n+\t\t\t\tcontent: "";\n+\t\t\t\tposition: absolute;\n+\t\t\t\tdisplay: none;\n+\t\t\t}\n+\n+\t\t\t/* Show the checkmark when checked */\n+\t\t\t.container input:checked ~ .checkmark:after {\n+\t\t\t\tdisplay: block;\n+\t\t\t}\n+\n+\t\t\t/* Style the checkmark/indicator */\n+\t\t\t.container .checkmark:after {\n+\t\t\t\tleft: 9px;\n+\t\t\t\ttop: 5px;\n+\t\t\t\twidth: 5px;\n+\t\t\t\theight: 10px;\n+\t\t\t\tborder: solid white;\n+\t\t\t\tborder-width: 0 3px 3px 0;\n+\t\t\t\t-webkit-transform: rotate(45deg);\n+\t\t'..b'526618,Cluster_33 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Strophariaceae g__Pholiota s__Pholiota_highlandensis:0.092885557)0.814:0.049985863,(Cluster_10 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_cyathuliformis:0.006440785,(Cluster_22 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_semisanguifluus:0.131339581,Cluster_17 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_sp:0.007841356)0.558:0.00137664)1.000:0.407651791)0.576:0.050558999,Cluster_41 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Tricholomataceae g__Tricholoma s__Tricholoma_portentosum:0.109176272)0.923:0.055454674)0.500:0.029841001)0.272:0.021549163,Cluster_37 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Entolomataceae g__Entoloma s__Entoloma_sp:0.290557943)0.267:0.027757147,Cluster_42 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Inocybaceae g__Inocybe s__Inocybe_sindonia:0.38494924)0.656:0.010910853,Cluster_15 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Omphalotaceae g__Gymnopus s__Gymnopus_hybridus:0.337166819)0.426:0.012687292)0.772:0.054937667,Cluster_45 k__Fungi p__Basidiomycota c__Agaricomycetes o__Hymenochaetales f__Hymenochaetaceae g__Hymenochaete s__Hymenochaete_longispora:0.442699665)0.013:0.053773292,((Cluster_43 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Paxillaceae g__Alpova s__Alpova_alpestris:0.075270238,Cluster_44 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Paxillaceae g__Alpova s__Alpova_corsicus:0.015753579)0.999:0.235752147,(Cluster_8 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Suillaceae g__Truncocolumella s__Truncocolumella_rubra:0.103502103,Cluster_39 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Boletaceae g__Xerocomus s__Xerocomus_porophyllus:0.171013076)0.456:0.049114709)0.996:0.222741056)0.842:0.085484652,(Cluster_46 k__Fungi p__Basidiomycota c__Agaricomycetes o__Hymenochaetales f__Hymenochaetaceae g__Pseudochaete s__Pseudochaete_subrigidula:0.448203133,(Cluster_24 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Hydnellum s__Hydnellum_peckii:0.119517963,Cluster_34 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Hydnellum s__Hydnellum_suaveolens:0.261732512)0.883:0.120552873)0.704:0.070724767)0.582:0.0779813415)NA;\');\n+ tree.backColour = true;\n+ tree.draw();\n+\t\t\t});\n+\t\t</script>\n+ <script>\n+ $(document).ready(function() { $(\'div:empty\').remove(); });\n+ </script>\n+\t</head>\n+\t<body>\n+\t\t\n+\t\t<p id="js-alert" class="alert alert-warning">\n+\t\t\tjavascript is needed to display data.<br />\n+\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+\t\t\n+\t\t<div id="content" class="hidden">\n+ <h2 class="pb-2 mt-4 mb-2 border-bottom">Summary</h2>\n+ <div class="row">\n+ <div id="nb-otu" class="col-md-6"></div>\n+ <div id="nb-abundance" class="col-md-6"></div>\n+ </div>\n+ <div id="OTUs-fail" style="display:none;">\n+ \t<h2 class="pb-2 mt-4 mb-2 border-bottom">Table of failed OTUs</h2>\n+ </div>\n+ <h1 class="page-header">Tree View\n+ <h5>Enabling zoom:</h5>\n+ </h1>\n+ <div class="onoffswitch">\n+\t <input type="checkbox" name="onoffswitch" class="onoffswitch-checkbox" id="myonoffswitch">\n+\t <label class="onoffswitch-label" for="myonoffswitch">\n+\t <span class="onoffswitch-inner"></span>\n+\t <span class="onoffswitch-switch"></span>\n+\t </label>\n+ \t</div>\n+ <div id="phylocanvas"></div>\n+ </div>\n+ </body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/15-tree-mafft.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/15-tree-mafft.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,33 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/tree.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/tree.py --nb-cpus 2 --input-sequences res_3.2.2/09-normalisation.fasta --biom-file res_3.2.2/09-normalisation.biom --out-tree res_3.2.2/15-tree-mafft.nwk --html res_3.2.2/15-tree-mafft.html --log-file res_3.2.2/15-tree-mafft.log
+
+Number of input OTUs sequences: 50
+
+########################################################################################################
+# Mafft multiple alignment. (mafft version : v7.407)
+Command:
+ mafft --maxiterate 1000 --globalpair --thread 2 res_3.2.2/09-normalisation.fasta > res_3.2.2/1617285775.168374_17456_mafft_aligned.fasta 2> res_3.2.2/1617285775.168374_17456_mafft.stderr
+
+Execution:
+ start: 01 Apr 2021 16:02:55
+ end:   01 Apr 2021 16:02:59
+
+########################################################################################################
+# reconstruction a phylogenetic tree (FastTree version : 2.1.9)
+Command:
+ FastTree -nt -gtr res_3.2.2/1617285775.168374_17456_mafft_aligned.fasta > res_3.2.2/1617285775.168374_17456_fasttree.nwk 2> res_3.2.2/1617285775.168374_17456_fasttree.stderr
+
+Execution:
+ start: 01 Apr 2021 16:02:59
+ end:   01 Apr 2021 16:03:01
+
+########################################################################################################
+# root newick tree with phangorn R package midpoint function. (root_tree.R version : 1.1.0 [R : 3.6.3; phangorn : 2.5.5])
+Command:
+ root_tree.R res_3.2.2/1617285775.168374_17456_fasttree.nwk res_3.2.2/15-tree-mafft.nwk
+
+Execution:
+ start: 01 Apr 2021 16:03:04
+ end:   01 Apr 2021 16:03:06
+

diff -r 000000000000 -r 834843ebe569 test-data/references/15-tree-mafft.nwk
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/15-tree-mafft.nwk Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,1 @@
+(((((((((Cluster_16:0.294637021,(Cluster_5:0.058546996,Cluster_11:0.016025716)0.968:0.158266053)0.936:0.131162271,Cluster_14:0.235307367)0.754:0.054791963,Cluster_2:0.474480884)0.691:0.049780986,(Cluster_1:0.213943848,(Cluster_3:0.187178327,(Cluster_7:0.071227926,Cluster_48:0.177457902)0.791:0.044816189)0.990:0.149578112)0.571:0.060098474)0.878:0.1145429,(Cluster_18:0.018225688,(Cluster_9:0.041431417,(Cluster_4:0.037275191,Cluster_21:0.077364146)0.139:0.011858572)0.788:0.03914001)0.998:0.237984437)0.615:0.089509622,Cluster_50_FROGS_combined:0.447067258)0.631:0.098224826,Cluster_20:0.380823886)0.937:0.185254213,Cluster_6:0.433076597)0.582:0.0034002915,(((((Cluster_23:0.156578999,Cluster_47:0.389321876)0.726:0.045755266,(((((((((Cluster_29:0.046482454,(Cluster_49:0.088673283,(Cluster_40:0.06738745,(Cluster_31:0.023816152,Cluster_32:0.033996038)0.959:0.025473747)0.183:0.005896439)0.731:0.004204585)0.719:0.010771056,Cluster_27:0.062029078)0.778:0.006259972,Cluster_35:0.025392868)0.646:8e-09,Cluster_38:0.071799589)1.000:0.100797162,(Cluster_13:0.142777829,Cluster_36:0.261025139)0.732:0.042606501)0.692:0.018870899,((Cluster_26:0.222535801,((Cluster_25:0.033254493,Cluster_30:0.052359157)0.995:0.115222977,(Cluster_12:0.044056603,Cluster_19:0.103806741)0.870:0.044198623)0.973:0.105117908)0.540:0.022692709,(((Cluster_28:0.110526618,Cluster_33:0.092885557)0.814:0.049985863,(Cluster_10:0.006440785,(Cluster_22:0.131339581,Cluster_17:0.007841356)0.558:0.00137664)1.000:0.407651791)0.576:0.050558999,Cluster_41:0.109176272)0.923:0.055454674)0.500:0.029841001)0.272:0.021549163,Cluster_37:0.290557943)0.267:0.027757147,Cluster_42:0.38494924)0.656:0.010910853,Cluster_15:0.337166819)0.426:0.012687292)0.772:0.054937667,Cluster_45:0.442699665)0.013:0.053773292,((Cluster_43:0.075270238,Cluster_44:0.015753579)0.999:0.235752147,(Cluster_8:0.103502103,Cluster_39:0.171013076)0.456:0.049114709)0.996:0.222741056)0.842:0.085484652,(Cluster_46:0.448203133,(Cluster_24:0.119517963,Cluster_34:0.261732512)0.883:0.120552873)0.704:0.070724767)0.582:0.0779813415)NA;

diff -r 000000000000 -r 834843ebe569 test-data/references/16-phylo_import.Rdata

Binary file test-data/references/16-phylo_import.Rdata has changed

diff -r 000000000000 -r 834843ebe569 test-data/references/16-phylo_import.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/16-phylo_import.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,15 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_import_data.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_import_data.py --biomfile data/chaillou.biom --samplefile data/sample_metadata.tsv --treefile data/tree.nwk --rdata res_3.2.2/16-phylo_import.Rdata --html res_3.2.2/16-phylo_import.nb.html --log-file res_3.2.2/16-phylo_import.log
+
+########################################################################################################
+# Run r_import_data.Rmd (Rscript version : [1] "R version 3.6.3 (2020-02-29)"
+[1] "Rmarkdown version:  2.7"
+[1] "Phyloseq version:  1.30.0")
+Command:
+ Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_import_data.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.nb.html', params=list(biomfile='/home/maria/workspace/FROGS_dev/test/data/chaillou.biom', samplefile='/home/maria/workspace/FROGS_dev/test/data/sample_metadata.tsv', treefile='/home/maria/workspace/FROGS_dev/test/data/tree.nwk', normalisation=FALSE, outputRdata='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', ranks='Kingdom Phylum Class Order Family Genus Species', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285786.8105457_17665_rmarkdown.stderr
+
+Execution:
+ start: 01 Apr 2021 16:03:17
+ end:   01 Apr 2021 16:04:10
+

diff -r 000000000000 -r 834843ebe569 test-data/references/17-phylo_composition.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/17-phylo_composition.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,15 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_composition.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_composition.py --varExp EnvType --taxaRank1 Kingdom --taxaSet1 Bacteria --taxaRank2 Phylum --numberOfTaxa 9 --rdata res_3.2.2/16-phylo_import.Rdata --html res_3.2.2/17-phylo_composition.nb.html --log-file res_3.2.2/17-phylo_composition.log
+
+########################################################################################################
+# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)"
+[1] "Rmarkdown version:  2.7"
+[1] "Phyloseq version:  1.30.0")
+Command:
+ Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_composition.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/17-phylo_composition.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType',taxaRank1='Kingdom',taxaSet1='Bacteria',taxaRank2='Phylum',numberOfTaxa=9, libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285850.7980647_17725_rmarkdown.stderr
+
+Execution:
+ start: 01 Apr 2021 16:04:18
+ end:   01 Apr 2021 16:05:08
+

diff -r 000000000000 -r 834843ebe569 test-data/references/18-phylo_alpha_div.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/18-phylo_alpha_div.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,15 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_alpha_diversity.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_alpha_diversity.py --varExp EnvType --rdata res_3.2.2/16-phylo_import.Rdata --alpha-measures Observed Chao1 Shannon --alpha-out res_3.2.2/18-phylo_alpha_div.tsv --html res_3.2.2/18-phylo_alpha_div.nb.html --log-file res_3.2.2/18-phylo_alpha_div.log
+
+########################################################################################################
+# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)"
+[1] "Rmarkdown version:  2.7"
+[1] "Phyloseq version:  1.30.0")
+Command:
+ Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_alpha_diversity.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/18-phylo_alpha_div.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', measures='Observed,Chao1,Shannon', varExp='EnvType',fileAlpha='/home/maria/workspace/FROGS_dev/test/res_3.2.2/18-phylo_alpha_div.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285909.0499587_17788_rmarkdown.stderr
+
+Execution:
+ start: 01 Apr 2021 16:05:16
+ end:   01 Apr 2021 16:05:48
+

diff -r 000000000000 -r 834843ebe569 test-data/references/18-phylo_alpha_div.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/18-phylo_alpha_div.tsv Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,65 @@
+ Observed Chao1 se.chao1 Shannon
+DLT0.LOT08 210 210 0 2.01603767724795
+DLT0.LOT05 221 254.785714285714 13.3895041926063 1.79800937304124
+DLT0.LOT03 226 226 0 3.45528429286049
+DLT0.LOT07 221 221 0 2.98216090690738
+DLT0.LOT06 278 278 0 3.20952140178085
+DLT0.LOT01 281 281 0 4.10685205650844
+DLT0.LOT04 247 247 0 2.47304361554073
+DLT0.LOT10 236 236 0 3.55173827807196
+MVT0.LOT05 158 158 0 2.34503849832531
+MVT0.LOT01 128 128 0 2.28541492757583
+MVT0.LOT06 157 157 0 3.92479836105885
+MVT0.LOT07 157 157 0 3.75898496293381
+MVT0.LOT03 160 160 0 3.34027078029461
+MVT0.LOT09 122 122 0 3.95221379962838
+MVT0.LOT08 124 124 0 2.30012425431142
+MVT0.LOT10 95 95 0 1.25959560361526
+BHT0.LOT01 103 103 0 2.53131370126125
+BHT0.LOT07 144 144 0 3.15166550279444
+BHT0.LOT06 155 155 0 2.92765820448176
+BHT0.LOT03 153 153 0 2.95001637842565
+BHT0.LOT10 159 159 0 2.7790079222459
+BHT0.LOT05 183 183 0 2.53671816912042
+BHT0.LOT04 209 209 0 3.47635995384084
+BHT0.LOT08 178 178 0 3.09192502544742
+VHT0.LOT02 132 132 0 1.4154609826759
+VHT0.LOT10 134 134 0 1.87555746873306
+VHT0.LOT03 206 206 0 3.51078572003616
+VHT0.LOT01 235 235 0 2.67402666784541
+VHT0.LOT08 157 157 0 3.31989163716182
+VHT0.LOT06 182 182 0 1.88583439498533
+VHT0.LOT07 156 156 0 1.41904291231118
+VHT0.LOT04 193 193 0 2.64373071960283
+SFT0.LOT08 111 165.473684210526 21.5900554349517 1.13874307530455
+SFT0.LOT07 110 110 0 2.96744303252776
+SFT0.LOT06 126 126 0 2.49355558700118
+SFT0.LOT03 119 119 0 2.92356922933234
+SFT0.LOT02 104 104 0 2.47818417340797
+SFT0.LOT05 75 210.125 60.9771168818602 1.33504649810823
+SFT0.LOT04 70 70 0 1.4778600596069
+SFT0.LOT01 117 117 0 1.98786858579725
+FST0.LOT07 150 150 0 2.99751683958306
+FST0.LOT08 152 152 0 3.4863921810005
+FST0.LOT05 156 156 0 3.37246744717753
+FST0.LOT06 165 165 0 3.40841441699795
+FST0.LOT01 149 149 0 2.43179269800015
+FST0.LOT03 168 168 0 2.92905427377967
+FST0.LOT10 186 186 0 3.03616027233611
+FST0.LOT02 179 179 0 3.18742279060019
+FCT0.LOT06 140 140 0 3.08227430433618
+FCT0.LOT10 172 172 0 3.89564247946871
+FCT0.LOT05 166 166 0 1.99860208269453
+FCT0.LOT03 197 197 0 2.70414675332528
+FCT0.LOT08 218 218 0 3.88853679266027
+FCT0.LOT02 195 195 0 2.55307056135657
+FCT0.LOT07 199 199 0 3.50534515553006
+FCT0.LOT01 200 200 0 3.88749477420522
+CDT0.LOT10 125 125 0 1.04948460066206
+CDT0.LOT08 175 175 0 3.25853898017873
+CDT0.LOT05 264 264 0 4.2074225334087
+CDT0.LOT04 269 269 0 4.45683686305649
+CDT0.LOT06 119 119 0 1.23721179294724
+CDT0.LOT09 177 177 0 1.91666097264414
+CDT0.LOT07 161 161 0 3.09013417675057
+CDT0.LOT02 174 174 0 2.42745280040353

diff -r 000000000000 -r 834843ebe569 test-data/references/19-phylo_beta_div.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/19-phylo_beta_div.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,15 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_beta_diversity.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_beta_diversity.py --varExp EnvType --distance-methods cc,unifrac --rdata res_3.2.2/16-phylo_import.Rdata --matrix-outdir res_3.2.2 --html res_3.2.2/19-phylo_beta_div.nb.html --log-file res_3.2.2/19-phylo_beta_div.log
+
+########################################################################################################
+# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)"
+[1] "Rmarkdown version:  2.7"
+[1] "Phyloseq version:  1.30.0")
+Command:
+ Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_beta_diversity.Rmd',knit_root_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/19-phylo_beta_div.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType', methods='cc,unifrac', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285948.7069905_17848_rmarkdown.stderr
+
+Execution:
+ start: 01 Apr 2021 16:05:56
+ end:   01 Apr 2021 16:06:07
+

diff -r 000000000000 -r 834843ebe569 test-data/references/19-phylo_beta_div.nb.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/19-phylo_beta_div.nb.html Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,381 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\n+<head>\n+\n+<meta charset="utf-8" />\n+<meta name="generator" content="pandoc" />\n+<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />\n+\n+\n+\n+\n+<title>FROGS Phyloseq: Beta Diversity Visualisation (version 3.2.2)</title>\n+\n+<script 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window.initializeSourceEmbed("phyloseq_beta_diversity.Rmd");\n+ window.initializeCodeFolding("hide" === "show");\n+});\n+</script>\n+\n+\n+\n+<script>\n+ (function () {\n+ var script = document.createElement("script");\n+ script.type = "text/javascript";\n+ script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";\n+ document.getElementsByTagName("head")[0].appendChild(script);\n+ })();\n+</script>\n+\n+</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/20-phylo_structure.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/20-phylo_structure.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,15 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_structure.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_structure.py --varExp EnvType --ordination-method MDS --rdata res_3.2.2/16-phylo_import.Rdata --distance-matrix res_3.2.2/unifrac.tsv --html res_3.2.2/20-phylo_structure.nb.html --log-file res_3.2.2/20-phylo_structure.log
+
+########################################################################################################
+# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)"
+[1] "Rmarkdown version:  2.7"
+[1] "Phyloseq version:  1.30.0")
+Command:
+ Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_structure.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/20-phylo_structure.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType',method='MDS',distance='/home/maria/workspace/FROGS_dev/test/res_3.2.2/unifrac.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285967.7486155_17907_rmarkdown.stderr
+
+Execution:
+ start: 01 Apr 2021 16:06:15
+ end:   01 Apr 2021 16:07:04
+

diff -r 000000000000 -r 834843ebe569 test-data/references/21-phylo_clustering.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/21-phylo_clustering.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,15 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_clustering.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_clustering.py --varExp EnvType --rdata res_3.2.2/16-phylo_import.Rdata --distance-matrix res_3.2.2/unifrac.tsv --html res_3.2.2/21-phylo_clutering.nb.html --log-file res_3.2.2/21-phylo_clustering.log
+
+########################################################################################################
+# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)"
+[1] "Rmarkdown version:  2.7"
+[1] "Phyloseq version:  1.30.0")
+Command:
+ Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_clustering.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/21-phylo_clutering.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/FROGS_dev/test/res_3.2.2/unifrac.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617286024.6000283_17972_rmarkdown.stderr
+
+Execution:
+ start: 01 Apr 2021 16:07:11
+ end:   01 Apr 2021 16:07:22
+

diff -r 000000000000 -r 834843ebe569 test-data/references/21-phylo_clustering.nb.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/21-phylo_clustering.nb.html Thu Apr 08 14:30:48 2021 +0000

[

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add bootstrap table styles to pandoc tables\n+function bootstrapStylePandocTables() {\n+ $(\'tr.odd\').parent(\'tbody\').parent(\'table\').addClass(\'table table-condensed\');\n+}\n+$(document).ready(function () {\n+ bootstrapStylePandocTables();\n+});\n+\n+$(document).ready(function () {\n+ $(\'.knitsql-table\').addClass(\'kable-table\');\n+ var container = $(\'.kable-table\');\n+ container.each(function() {\n+\n+ // move the caption out of the table\n+ var table = $(this).children(\'table\');\n+ var caption = table.children(\'caption\').detach();\n+ caption.insertBefore($(this)).css(\'display\', \'inherit\');\n+ });\n+});\n+\n+</script>\n+\n+\n+\n+<script>\n+$(document).ready(function () {\n+ window.buildTabsets("TOC");\n+});\n+\n+$(document).ready(function () {\n+ $(\'.tabset-dropdown > .nav-tabs > li\').click(function () {\n+ $(this).parent().toggleClass(\'nav-tabs-open\');\n+ });\n+});\n+</script>\n+\n+\n+<script>\n+$(document).ready(function () {\n+ window.initializeSourceEmbed("phyloseq_clustering.Rmd");\n+ window.initializeCodeFolding("hide" === "show");\n+});\n+</script>\n+\n+\n+\n+<script>\n+ (function () {\n+ var script = document.createElement("script");\n+ script.type = "text/javascript";\n+ script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";\n+ document.getElementsByTagName("head")[0].appendChild(script);\n+ })();\n+</script>\n+\n+</body>\n+</html>\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/22-phylo_manova.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/22-phylo_manova.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,15 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_manova.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_manova.py --varExp "EnvType" --rdata res_3.2.2/16-phylo_import.Rdata --distance-matrix res_3.2.2/unifrac.tsv --html res_3.2.2/22-phylo_manova.nb.html --log-file res_3.2.2/22-phylo_manova.log
+
+########################################################################################################
+# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)"
+[1] "Rmarkdown version:  2.7"
+[1] "Phyloseq version:  1.30.0")
+Command:
+ Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_manova.Rmd', output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/22-phylo_manova.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/FROGS_dev/test/res_3.2.2/unifrac.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617286042.4697833_18033_rmarkdown.stderr
+
+Execution:
+ start: 01 Apr 2021 16:07:29
+ end:   01 Apr 2021 16:07:39
+

diff -r 000000000000 -r 834843ebe569 test-data/references/23-deseq2_preprocess.Rdata

Binary file test-data/references/23-deseq2_preprocess.Rdata has changed

diff -r 000000000000 -r 834843ebe569 test-data/references/23-deseq2_preprocess.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/23-deseq2_preprocess.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,13 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_preprocess.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_preprocess.py --data res_3.2.2/16-phylo_import.Rdata --log-file res_3.2.2/23-deseq2_preprocess.log --out-Rdata res_3.2.2/23-deseq2_preprocess.Rdata --var EnvType
+
+########################################################################################################
+# Construc DESeq2 object from a Phyloseq one. (deseq2_preprocess.R version : 1.1.0 [R : 3.6.3; DESeq2 : 1.26.0; Phyloseq : 1.30.0])
+Command:
+ deseq2_preprocess.R --inRdata /home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata --var EnvType --outRdata /home/maria/workspace/FROGS_dev/test/res_3.2.2/23-deseq2_preprocess.Rdata 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617286059.6610422_18092_R.stderr
+
+Execution:
+ start: 01 Apr 2021 16:07:54
+ end: 01 Apr 2021 16:08:17
+

diff -r 000000000000 -r 834843ebe569 test-data/references/24-deseq2_visualisation.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/24-deseq2_visualisation.log Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,14 @@
+## Application
+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_visualisation.py (version : 3.2.2)
+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_visualisation.py --phyloseqData res_3.2.2/16-phylo_import.Rdata --dds res_3.2.2/23-deseq2_preprocess.Rdata --log-file res_3.2.2/24-deseq2_visualisation.log --html res_3.2.2/24-deseq2_visualisation.nb.html --var EnvType --mod1 BoeufHache --mod2 SaumonFume
+
+########################################################################################################
+# Run deseq2_visualisation.Rmd (Rscript version : [1] "R version 3.6.3 (2020-02-29)"
+[1] "DESeq2 version: 1.26.0")
+Command:
+ Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_visualisation.Rmd', output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/24-deseq2_visualisation.nb.html', params=list(phyloseq_data='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', dds='/home/maria/workspace/FROGS_dev/test/res_3.2.2/23-deseq2_preprocess.Rdata', var='EnvType', mod1='BoeufHache', mod2='SaumonFume', padj=0.05), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617286097.1064806_18132_R.stderr
+
+Execution:
+ start: 01 Apr 2021 16:08:27
+ end: 01 Apr 2021 16:09:29
+

diff -r 000000000000 -r 834843ebe569 test-data/references/24-deseq2_visualisation.nb.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/24-deseq2_visualisation.nb.html Thu Apr 08 14:30:48 2021 +0000

[

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diff -r 000000000000 -r 834843ebe569 test-data/references/demultiplex.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/demultiplex.log Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,473 @@\n+## Application\n+Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/demultiplex.py (version : 3.2.2)\n+Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/demultiplex.py --input-R1 data/demultiplex.fastq.gz --input-barcode data/demultiplex.barcode.txt --mismatches 1 --end both --output-demultiplexed res_3.2.2//demultiplexed.tar.gz --output-excluded res_3.2.2//undemultiplexed.tar.gz --log-file res_3.2.2//demultiplex.log --summary res_3.2.2//demultiplex_summary.txt\n+\n+\n+#Demultiplexing demultiplex.fastq.gz with forward_bc in bol strand\n+########################################################################################################\n+# Demultiplex reads. (splitbc.pl version : unknown)\n+Command:\n+\tsplitbc.pl data/demultiplex.fastq.gz --bol --bcfile res_3.2.2/forward_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Demult.log\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:55:53\n+\tend: 01 Apr 2021 15:55:54\n+\n+Results :\n+\tnb seq before demultiplexing : 4513.0\n+\tnb seq after process matched : 4271.0\n+\tnb seq after process non-ambiguous : 4271.0\n+\n+#Demultiplexing ACAGCGT_R1.fastq with ACAGCGT_reverse_bc in eol strand\n+########################################################################################################\n+# Demultiplex reads. (splitbc.pl version : unknown)\n+Command:\n+\tsplitbc.pl res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/ACAGCGT_R1.fastq --eol --bcfile res_3.2.2/ACAGCGT_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285354.2635067_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Demult.log\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:55:54\n+\tend: 01 Apr 2021 15:55:54\n+\n+Results :\n+\tnb seq before demultiplexing : 119.0\n+\tnb seq after process matched : 85.0\n+\tnb seq after process non-ambiguous : 85.0\n+\n+#Demultiplexing ACAGTAG_R1.fastq with ACAGTAG_reverse_bc in eol strand\n+########################################################################################################\n+# Demultiplex reads. (splitbc.pl version : unknown)\n+Command:\n+\tsplitbc.pl res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/ACAGTAG_R1.fastq --eol --bcfile res_3.2.2/ACAGTAG_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285354.3785884_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Demult.log\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:55:54\n+\tend: 01 Apr 2021 15:55:54\n+\n+Results :\n+\tnb seq before demultiplexing : 91.0\n+\tnb seq after process matched : 65.0\n+\tnb seq after process non-ambiguous : 65.0\n+\n+#Demultiplexing ACGTCAG_R1.fastq with ACGTCAG_reverse_bc in eol strand\n+########################################################################################################\n+# Demultiplex reads. (splitbc.pl version : unknown)\n+Command:\n+\tsplitbc.pl res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/ACGTCAG_R1.fastq --eol --bcfile res_3.2.2/ACGTCAG_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285354.483847_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Demult.log\n+\n+Execution:\n+\tstart: 01 Apr 2021 15:55:54\n+\tend: 01 Apr 2021 15:55:54\n+\n+Results :\n+\tnb seq before demultiplexing : 166.0\n+\tnb seq after process matched : 152.0\n+\tnb seq after process non-ambiguous : 152.0\n+\n+#Demultiplexing ACTCAGT_R1.fastq with ACTCAGT_reverse_bc in eol strand\n+########################################################################################################\n+# Demultiplex reads. (splitbc.pl version : unknown)\n+Command:\n+\tsplitbc.pl res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/ACTCAGT_R1.fastq --eol --bcfile res_3.2.2/ACTCAGT_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285354.5917869_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Dem'..b'ary.txt\n+\n+\n+#Demultiplexing demultiplex_test2_R1.fq.gz and demultiplex_test2_R2.fq.gz with forward_bc in bol strand\n+########################################################################################################\n+# Demultiplex reads. (splitbc.pl version : unknown)\n+Command:\n+\tsplitbc.pl data/demultiplex_test2_R1.fq.gz data/demultiplex_test2_R2.fq.gz --bol --bcfile res_3.2.2/forward_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/%_R1.fastq --prefix-r2 res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/%_R2.fastq >> res_3.2.2/1617717494.3218324_20409_Demult.log\n+\n+Execution:\n+\tstart: 06 Apr 2021 15:58:14\n+\tend: 06 Apr 2021 15:58:15\n+\n+Results :\n+\tnb seq before demultiplexing : 10.0\n+\tnb seq after process matched : 9.0\n+\tnb seq after process non-ambiguous : 8.0\n+\n+#Demultiplexing ACAGCGT_R1.fastq and ACAGCGT_R2.fastq with ACAGCGT_reverse_bc in eol strand\n+########################################################################################################\n+# Demultiplex reads. (splitbc.pl version : unknown)\n+Command:\n+\tsplitbc.pl res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/ACAGCGT_R1.fastq res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/ACAGCGT_R2.fastq --eol --bcfile res_3.2.2/ACAGCGT_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617717494.3218324_20409_tmp/1617717495.3003461_20409/%_R1.fastq --prefix-r2 res_3.2.2/1617717494.3218324_20409_tmp/1617717495.3003461_20409/%_R2.fastq >> res_3.2.2/1617717494.3218324_20409_Demult.log\n+\n+Execution:\n+\tstart: 06 Apr 2021 15:58:15\n+\tend: 06 Apr 2021 15:58:15\n+\n+Results :\n+\tnb seq before demultiplexing : 4.0\n+\tnb seq after process matched : 0.0\n+\tnb seq after process non-ambiguous : 0.0\n+\n+#Demultiplexing ACAGTAG_R1.fastq and ACAGTAG_R2.fastq with ACAGTAG_reverse_bc in eol strand\n+########################################################################################################\n+# Demultiplex reads. (splitbc.pl version : unknown)\n+Command:\n+\tsplitbc.pl res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/ACAGTAG_R1.fastq res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/ACAGTAG_R2.fastq --eol --bcfile res_3.2.2/ACAGTAG_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617717494.3218324_20409_tmp/1617717495.4231894_20409/%_R1.fastq --prefix-r2 res_3.2.2/1617717494.3218324_20409_tmp/1617717495.4231894_20409/%_R2.fastq >> res_3.2.2/1617717494.3218324_20409_Demult.log\n+\n+Execution:\n+\tstart: 06 Apr 2021 15:58:15\n+\tend: 06 Apr 2021 15:58:15\n+\n+Results :\n+\tnb seq before demultiplexing : 4.0\n+\tnb seq after process matched : 0.0\n+\tnb seq after process non-ambiguous : 0.0\n+\n+#Summarising result\n+\n+#Concatenation of undemultiplexed files 1\n+\n+#Concatenation of undemultiplexed files 2\n+\n+#Archive demultiplexed R1 and R2 files\n+########################################################################################################\n+# Archives files. (tar version : unknown)\n+Command:\n+\ttar -zcf res_3.2.2/demultiplexed.tar.gz -C res_3.2.2/1617717495.5449557_20409 MgArd0001_A_R1.fastq MgArd0002_R1.fastq MgArd0003_R1.fastq MgArd0004_R1.fastq MgArd0009_R1.fastq MgArd0010_R1.fastq MgArd0011_R1.fastq MgArd0012_R1.fastq MgArd0001_A_R2.fastq MgArd0002_R2.fastq MgArd0003_R2.fastq MgArd0004_R2.fastq MgArd0009_R2.fastq MgArd0010_R2.fastq MgArd0011_R2.fastq MgArd0012_R2.fastq\n+\n+Execution:\n+\tstart: 06 Apr 2021 15:58:15\n+\tend: 06 Apr 2021 15:58:15\n+\n+\n+#Archive undemultiplexed R1 and R2 files\n+########################################################################################################\n+# Archives files. (tar version : unknown)\n+Command:\n+\ttar -zcf res_3.2.2/undemultiplexed.tar.gz -C res_3.2.2/1617717495.557461_20409 demultiplex_test2_R1.fq.gz_excluded_demult demultiplex_test2_R2.fq.gz_excluded_demult\n+\n+Execution:\n+\tstart: 06 Apr 2021 15:58:15\n+\tend: 06 Apr 2021 15:58:15\n+\n+\n+#Removing temporary files\n'

diff -r 000000000000 -r 834843ebe569 test-data/references/demultiplex_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/demultiplex_summary.txt Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,12 @@
+#sample count
+MgArd0001_A 0
+MgArd0002 0
+MgArd0003 0
+MgArd0004 0
+MgArd0009 0
+MgArd0010 0
+MgArd0011 0
+MgArd0012 0
+MgArd0001_B 0
+unmatched 9
+ambiguous 1

diff -r 000000000000 -r 834843ebe569 test-data/references/unifrac.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/unifrac.tsv Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,65 @@\n+\tDLT0.LOT08\tDLT0.LOT05\tDLT0.LOT03\tDLT0.LOT07\tDLT0.LOT06\tDLT0.LOT01\tDLT0.LOT04\tDLT0.LOT10\tMVT0.LOT05\tMVT0.LOT01\tMVT0.LOT06\tMVT0.LOT07\tMVT0.LOT03\tMVT0.LOT09\tMVT0.LOT08\tMVT0.LOT10\tBHT0.LOT01\tBHT0.LOT07\tBHT0.LOT06\tBHT0.LOT03\tBHT0.LOT10\tBHT0.LOT05\tBHT0.LOT04\tBHT0.LOT08\tVHT0.LOT02\tVHT0.LOT10\tVHT0.LOT03\tVHT0.LOT01\tVHT0.LOT08\tVHT0.LOT06\tVHT0.LOT07\tVHT0.LOT04\tSFT0.LOT08\tSFT0.LOT07\tSFT0.LOT06\tSFT0.LOT03\tSFT0.LOT02\tSFT0.LOT05\tSFT0.LOT04\tSFT0.LOT01\tFST0.LOT07\tFST0.LOT08\tFST0.LOT05\tFST0.LOT06\tFST0.LOT01\tFST0.LOT03\tFST0.LOT10\tFST0.LOT02\tFCT0.LOT06\tFCT0.LOT10\tFCT0.LOT05\tFCT0.LOT03\tFCT0.LOT08\tFCT0.LOT02\tFCT0.LOT07\tFCT0.LOT01\tCDT0.LOT10\tCDT0.LOT08\tCDT0.LOT05\tCDT0.LOT04\tCDT0.LOT06\tCDT0.LOT09\tCDT0.LOT07\tCDT0.LOT02\n+DLT0.LOT08\t0\t0.392719389374763\t0.294382689116989\t0.390894424113643\t0.328770053910381\t0.389411250802876\t0.346311420062406\t0.389241305604783\t0.558647350042396\t0.634069916291667\t0.586977876499085\t0.618364439168374\t0.59310690982098\t0.644425105557425\t0.633386627311114\t0.676093271776652\t0.668166275142653\t0.647255138049382\t0.634194437155602\t0.629580000445943\t0.576755603792125\t0.588626884110114\t0.567337706288072\t0.627737130863146\t0.630979925473805\t0.662585829091919\t0.548077006064955\t0.565292617093312\t0.583061634989672\t0.559960446409113\t0.561005582218959\t0.555410973214134\t0.686198206609958\t0.704398980872343\t0.675272727535421\t0.711657734556618\t0.715799775906816\t0.768785445356757\t0.785667248244791\t0.696459130925707\t0.606145374094578\t0.651568775909291\t0.636874887259531\t0.65198384887721\t0.648424320754247\t0.572507853619064\t0.533534738606473\t0.612417013174867\t0.6538120765306\t0.591881312389585\t0.619093998659405\t0.585895717589353\t0.548200617493159\t0.594002797632857\t0.586013673904125\t0.585980145595343\t0.651109623648418\t0.62720674623346\t0.532414786060701\t0.547377296717564\t0.695399519089384\t0.602389412681498\t0.651285257071645\t0.625692860559332\n+DLT0.LOT05\t0.392719389374763\t0\t0.334665743823981\t0.352189924174674\t0.342174777989704\t0.389749555645828\t0.290240347963101\t0.390007860403765\t0.533242142441534\t0.598457283793849\t0.534095626389918\t0.595630244132359\t0.563155315513785\t0.627301946703866\t0.62362079028169\t0.676679178026565\t0.661442446324936\t0.607174222014807\t0.627098405326444\t0.611311880024972\t0.595770697120776\t0.579339730768954\t0.553223124743228\t0.610516542648508\t0.666088798070038\t0.657587079833307\t0.576069019426189\t0.556446826887928\t0.600775747996288\t0.5911490693311\t0.616992581263469\t0.601616192130504\t0.651100765662097\t0.681452439239435\t0.635746166689655\t0.656251161738522\t0.660748149236051\t0.718117436370543\t0.745868841494258\t0.651811755169484\t0.583079458698659\t0.611335962879801\t0.60471232308416\t0.626317689189847\t0.620601501298686\t0.555908156452842\t0.533249165381552\t0.574427223549588\t0.609466674526089\t0.554013286087225\t0.591520342983099\t0.578096390189169\t0.520647115926058\t0.532256954612006\t0.559759285330547\t0.567759482939216\t0.594543966139689\t0.566565902699841\t0.553655484607033\t0.540051048491254\t0.650961029981557\t0.575509994600553\t0.624808022531917\t0.595884187417361\n+DLT0.LOT03\t0.294382689116989\t0.334665743823981\t0\t0.372786534310374\t0.327187118252722\t0.359513238833913\t0.339907385955891\t0.38492662266766\t0.552498990377251\t0.589114989880665\t0.542041154505155\t0.59613025240974\t0.552461963400675\t0.617844578077283\t0.604774998121854\t0.664017875696736\t0.648793735381351\t0.622368182568259\t0.620604700459984\t0.591910414837232\t0.566744912701015\t0.561672474315041\t0.556623781014959\t0.59265696724107\t0.632841968867748\t0.66421462312413\t0.569031394968335\t0.538210280024464\t0.583964660155039\t0.555481448289844\t0.59213139931072\t0.579064617903163\t0.677073030113301\t0.679856615483388\t0.659776066311386\t0.671077096490443\t0.673953708382158\t0.753757865966224\t0.744905299647077\t0.669777464567699\t0.594953408905372\t0.594885764729724\t0.591809685788661\t0.623526170876335\t0.633556125967904\t0.563161599049313\t0.558391672795279\t0.58499884389222\t0.658968009415742\t0.598607385198043\t0.618132787151034\t0.591293863217907\t0.548709240291208\t0.589473963654829\t0.562723847684429\t0.5904743'..b'\t0.722926571406701\t0.688716587074794\t0.685695663618906\t0.662023385683372\t0.67171887301095\t0.661637888388034\t0.675884693159838\t0.718056925126289\t0.654689380709201\t0.68223217716672\t0.653431565041232\t0.668030013340577\t0.685721750598227\t0.664857249588266\t0.689007839280897\t0.657620741452954\t0.653159907372082\t0.6911709832662\t0.683048323863822\t0.62760665087889\t0.668064647721933\t0.657719412509422\t0.65224952356914\t0.668623077011986\t0.628907107332197\t0.39806333112609\t0.418710436434128\t0.493956484929211\t0.481853960906529\t0\t0.366581982149745\t0.33459366247948\t0.385617526833289\n+CDT0.LOT09\t0.602389412681498\t0.575509994600553\t0.603788346166801\t0.591747048678134\t0.590911650223996\t0.591128709519011\t0.596211588106372\t0.571045257287861\t0.676959809606389\t0.695735448994625\t0.656302270812522\t0.718752074389469\t0.677910104843752\t0.712925624298988\t0.688940943717879\t0.724298427985636\t0.691658377079775\t0.692390299429853\t0.738043468953429\t0.698843657322755\t0.710595249091952\t0.710704480082304\t0.680103050247559\t0.734034585210984\t0.735983991853843\t0.734177715029144\t0.710894437063629\t0.678216626620196\t0.726611832944889\t0.68943400429384\t0.726538682991375\t0.703934735934003\t0.685021220235917\t0.694000485914428\t0.65847379840122\t0.668428593392817\t0.684417168462003\t0.701730201468984\t0.747228196855636\t0.685789892025029\t0.661402723611022\t0.669569418359917\t0.666749198532296\t0.680906962176351\t0.639286727253157\t0.666965162172101\t0.625656721623157\t0.64187240650603\t0.624895467913965\t0.615367035307661\t0.592952488148562\t0.607656887251677\t0.596224675154877\t0.610325581395349\t0.606465036621361\t0.598082298898376\t0.373109422536506\t0.390635397515807\t0.399525443339596\t0.392890893785356\t0.366581982149745\t0\t0.276031056490361\t0.356132329302629\n+CDT0.LOT07\t0.651285257071645\t0.624808022531917\t0.64913139107594\t0.642435840637848\t0.635432939007904\t0.625734745112974\t0.661854102370782\t0.615716788093734\t0.713057822477221\t0.70725319961728\t0.695030292220513\t0.75388188880514\t0.715425373666082\t0.733377455922303\t0.726587115291575\t0.761600228513393\t0.746780765163785\t0.744787543632806\t0.776469707201759\t0.740662207095485\t0.742275725228979\t0.758118866017391\t0.723930347177148\t0.772206218845125\t0.772331986892959\t0.783036191562965\t0.732774666877935\t0.723812942859527\t0.749253135300688\t0.750838935182349\t0.765732188192081\t0.745824179825466\t0.682783418993296\t0.689407299921866\t0.664812264787866\t0.675686675415935\t0.657749916299696\t0.699231939335925\t0.743182582673147\t0.682473288565758\t0.659662717671486\t0.649555080406131\t0.657485049905096\t0.673519302214655\t0.639705749970948\t0.677946043152047\t0.641191867652921\t0.6338607965616\t0.616537536660449\t0.624473956262426\t0.598369113474161\t0.608336922498302\t0.602508666027023\t0.599687899540733\t0.612156751972582\t0.589737494611394\t0.392692065340501\t0.395944406470722\t0.421445278873761\t0.403327762530912\t0.33459366247948\t0.276031056490361\t0\t0.262604627863368\n+CDT0.LOT02\t0.625692860559332\t0.595884187417361\t0.634885811126848\t0.630280901585683\t0.61954988437347\t0.598340604510949\t0.640400830079576\t0.587237310711496\t0.675724750008455\t0.683410925286943\t0.683005264844442\t0.733863328731698\t0.685326629294412\t0.717368667575385\t0.700338598239352\t0.757303323727124\t0.744709272880933\t0.742947967230519\t0.755202079068598\t0.71824909257714\t0.733357829872864\t0.738829625170803\t0.705643199092123\t0.75184527156467\t0.743889397202228\t0.742393370191739\t0.712447865590699\t0.705301737592034\t0.729768073962883\t0.728603522808165\t0.74423504571082\t0.723331902670937\t0.663192007703921\t0.682769097334482\t0.671805359299952\t0.66612489889745\t0.69817254539659\t0.685143179552477\t0.740007909758363\t0.679715940692331\t0.641964763504036\t0.622223781286026\t0.642501131705744\t0.642289648764428\t0.645156215339451\t0.650958013541358\t0.609247236482718\t0.618787322862652\t0.623271100846613\t0.598866168952099\t0.594835464062659\t0.589729224189693\t0.56189574233229\t0.590985763748343\t0.603650051814384\t0.575990456814244\t0.439190482012837\t0.458652758468832\t0.396846421505181\t0.415427714008917\t0.385617526833289\t0.356132329302629\t0.262604627863368\t0\n'

diff -r 000000000000 -r 834843ebe569 tool-data/Unite_s_7.1_20112016_ITS1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Unite_s_7.1_20112016_ITS1.fasta Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,108366 @@\n+>AF201716_SH204808.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Sordariomycetes [id: 3];o__Xylariales [id: 4];f__Xylariaceae [id: 5];g__Annulohypoxylon [id: 6];s__Annulohypoxylon_truncatum [id: 7]\n+CCGAGTTATCACAACTCCAACCCTTTGTGAACCTTACCGTCGTTTCCTCGGCGCACTGCTGTGGGAGGCTACCCTGTAGCGGTTGTTTACCCTACAGGACGCACCCTGCAGCGGCGCCGAAAGGACTACCAAAACTCTTTTATCCAAGTTACCTCGAACAATTTACTATACAATAGTTTA\n+>UDB004660_SH465869.07FU_reps_singleton Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Boletales [id: 10];f__unidentified [id: 11];g__unidentified [id: 12];s__Boletales_sp [id: 13]\n+GGAAGGACATTATCGAAACAAATGGGGGGAAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCGACCTCTTCATACACACACACCTGTGCACCTTTGGTAGGTCTTCGAAAGAGGATCTATGATTATCATCACACCCTGTCGTATGGCCAGAATGTCTATATCACATAATA\n+>FJ362054_SH204600.07FU_reps Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Marasmiaceae [id: 15];g__Moniliophthora [id: 16];s__Moniliophthora_sp [id: 17]\n+TTGAAAAAACATTGTGAAGGAGGTTGAGCTGGCTCTTCTAGGGCAATGTGCTCGCTGCCTTTCAATAATTTTCATCCACCTGTGCACTTTTTGTAGGGGATCTGGAATTTGGACGTGCGCAAGCTTTGTTCATTAGTACGGGTCTTCTATGTTTTTACACACTCTTTAAATGTATGTCTAGAATGTTTAACGTTTATTGGGACTTAGTTGGCCCTCTAAAGAAACTATA\n+>JX454898_SH207904.07FU_reps Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Entolomataceae [id: 18];g__Entoloma [id: 19];s__Entoloma_hebes [id: 20]\n+CATTAATGAATAAACTTGGTTAGGTTGTTGCTGGTTCTTAGGAACATGTGCACGCCGACTCCATCTTTAACCACCTGTGCACATTGCGTAGATCTGATATTCTCGAGGAAACTCGGTCTGAGAATTGCTGTGCACTTGCCAGCTCTTCTTGTAATCAGGTCTATGTTACTATATACTCCACATGAATGTAATCGAATGCTTAATTGGCCTTTGTGCCTTTAAAACAAATA\n+>KT328615_SH488012.07FU_reps_singleton Root;k__Fungi [id: 1];p__unidentified [id: 21];c__unidentified [id: 22];o__unidentified [id: 23];f__unidentified [id: 24];g__unidentified [id: 25];s__Fungi_sp [id: 26]\n+ACGTGTTTGGGTCCCCTCGGGGGCCCGACATCCCACCCTTTGTTGTCACTTCAATGCGTTGCTTCGGCGGGACGGACGCCCTGCGTCCGCCGGGCCCCAAAAAACGCCCGGAGAGCTCCCGCCGGGGTCATACAAACTCTAGCCTTTGAACGAGTCGTCAGAGTGGAATTTACAAATAATTCA\n+>U68322_SH012276.07FU_reps_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 27];o__Ascosphaerales [id: 28];f__Ascosphaeraceae [id: 29];g__Ascosphaera [id: 30];s__Ascosphaera_asterophora [id: 31]\n+ACGTGTGTCTGTACGGTCTGGTCAATCGCCGGCCGTGCACTCCCACCCTTGTCTATCTTACCTGTTGCTTTGGCGGACCTGCGGGTGCTTGCACCTGCTGCCGGGATGGCGTTTGCGTCTCCGGGCTCGCGTCCGCGAAGGTTATTGAACTCCGATCGAAGATTGAAGTCTGAAGAATAAAGATTAATAAATCA\n+>UDB013960_SH221606.07FU_reps Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Russulales [id: 32];f__Russulaceae [id: 33];g__Russula [id: 34];s__Russula_sp [id: 35]\n+GGAAGGATCATTATCGTAACAACGGGAGGCACCGAGGGCTGTCGCTGGCCTTTACAGGTTGTGCACGCCCAAAGTACTCTCTCACATCCATTTTTCACACCTTTGTGCATCTCCGCGTGGGGCCTCCTCTTACTGGGGAGGCTTCGCGTTTTTACAATACACCCATTCTTAATGCATGTATAGAATGACTTTGCGATGATACGCAATCAATA\n+>KR673632_SH492372.07FU_reps_singleton Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Mycenaceae [id: 36];g__Mycena [id: 37];s__Mycena_crocata [id: 38]\n+TATCTTCTCTTGTGCACATTTTGTAGTCTCCAAAGTCGAAAAGTGAACCCTCTCGCAGCAATGCGGTTTGGGGGACTAGAGCTAACACCTCTTTCCCCTGCCTTGCTTTTTCTTCTTTCGATGGCTATGTTTTCATATACACTATAAAGTTACAGAATGTCTATTAACGATCCTTAAAAACGATCATTAAACCTATA\n+>KJ950804_SH523811.07FU_reps Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Amanitaceae [id: 39];g__Amanita [id: 40];s__Amanita_sp [id: 41]\n+TTGAATAAAGTCTGGTGGAGGCTGTTGCTGGTCCAAAAACACACAGGGCATTTGTGCACGTCTCAATAAAAGCCAGTTTTCATATATATATTTTCCTGTGCATTTTTGTAGACACTTTTGGAATGAGGAACTTTTTATAAGTTTCTTGCTGTGAAACATCAAGGTGTCTATGGTTTTTAACGAACACAAGTGAATGTATAAGAAAGACAATTGTTAATGAACAATGTTAAATA\n+>DQ656654_SH492954.07FU_reps_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Orbiliomycetes [id: 42];o__Orbiliales [id: 43];f__Orbiliaceae [id: 44];g__Hyalorbilia [id: 45];s__Hyalorbilia_lunata [id: 46]\n+CATGAGCCTTGATCTCGCCGGTTAAGCAGAGGCCTCACGGTCCGCGGGTAATCTCGCCGGCCG'..b'iomycetes [id: 27];o__Eurotiales [id: 61];f__Trichocomaceae [id: 62];g__Aspergillus [id: 353];s__Aspergillus_salwaensis [id: 24150]\n+AAGGATCATTACTGAGTGAGGGTCCCTCGGGGCCCAACCTCCCACCCGTGTATACCGTACCTTGTTGCTTCGGCGGGCCCGCCGCGCAAGCGGCCGCCGGGGGGGCGTCAAACCCCCCTCCCTAGGCGAGCGCCCGCCGGAGACACCAACGTGAACACTGTCTGAAGTTTTGTTGTCTGAGTTCGATTGTATCGCAATCAGTTA\n+>KJ663853_SH614186.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Leotiomycetes [id: 80];o__Helotiales [id: 340];f__Phacidiaceae [id: 11582];g__Phacidium [id: 11583];s__Phacidium_pseudophacidioides [id: 24151]\n+ATGAGATCATGCCCTTCGGGGTAGACCTCCCACCCTCTGTATACAATACCTTTGTTGCTTTGGCGGCCCCGTCGCAAGACAACCGGCTCCGGCTGGTCAGTGGCCGCCAGAGGAATCAAAACTCTTATTATTATTGTCGTCTGAGTACTATATAATAGTTA\n+>KT290244_SH616293.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Dothideomycetes [id: 52];o__Botryosphaeriales [id: 152];f__Botryosphaeriaceae [id: 153];g__Diplodia [id: 3397];s__Diplodia_crataegicola [id: 24152]\n+GATCATTACCGAGTTCTCGGGCTTCGGCTCGAATCTCCCACCCCTTTGTGAACATACCTCTGTTGCTTTGGCGGCTCTTTGCCGCGAGGAGGCCCTCGCGGGCCCCCCCCGCGCGCTTTCCGCCAGAGGACCTTCAAACCCCAGTCAGTAAACGTCGACGTCTGATAAACAAGTTAATAAACTA\n+>KJ775685_SH618623.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 27];o__Eurotiales [id: 61];f__Trichocomaceae [id: 62];g__Penicillium [id: 63];s__Penicillium_mexicanum [id: 24153]\n+AAGGATCATTACTGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTGTACCTTGTTGCTTCGGCGGGCCCGCCTTTATGGCCGCCGGGGGGCTTACGCTCCCGGGCCCGCGCCCGCCGAAGACACCCTCGAACTCTGTCTGAAGATTGTAGTCTGAGTGGAATTGTAAATTATTTA\n+>KM189541_SH619611.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 27];o__Eurotiales [id: 61];f__Trichocomaceae [id: 62];g__Penicillium [id: 63];s__Penicillium_ranomafanaense [id: 24154]\n+AAGGATCATTACTGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTGTACCTTGTTGCTTCGGTGAGCCCGCCTCACGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCGCTCGCCGAAGACACCCTTGAACTCTGTCTGAAGTTTGCAGTCTGAGCGAAAACTAAATAAGTTA\n+>KJ718170_SH620157.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Dothideomycetes [id: 52];o__Pleosporales [id: 212];f__Pleosporaceae [id: 348];g__Alternaria [id: 1704];s__Alternaria_echinaceae [id: 24155]\n+ATCATTACACAAATATGAAGGCGGGCTGGCACCTCTCGGGGTGGCAGCCTTGCTGAATTATTCACCCGTGTCTTTTGCGTACTTCTTGTTTCCTTGGTGGGTTCGCCCACCACAAGGACCAATCCATAAACCTTTTTGTAATGGCAATCAGCGTCAGTAACAACATAATAATTA\n+>KT359601_SH620263.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 27];o__Eurotiales [id: 61];f__Trichocomaceae [id: 62];g__Aspergillus [id: 353];s__Aspergillus_sp [id: 1057]\n+CCGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTCTATCGTACCTTGTTGCTTCGGCGGGCCCGCCGTTTCGACGGCCGCCGGGGAGGCCTCGCGCCCCCGGGCCCGCGCCCGCCGAAGACCCCAACATGAACGCTGTTCTGAAAGTATGCAGTCTGAGTTGATTATCATAATCAGTTA\n+>KM390702_SH623220.07FU_refs_singleton Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Strophariaceae [id: 98];g__Hebeloma [id: 224];s__Hebeloma_pallidolabiatum [id: 24156]\n+TTGAATGAACTTGGTGTGGTTGTCGCTGGCCCTCTTGGGGGCATGTGCACACCTACCATCCTCATCTCTCCACCTGTGCACCTCTTGTAGATTTGGAATTGATTATCCGAGGCAACTCGGTCGTAAGGACTGCTAGCACTTAGCTGGCTTTCTTTGCAATTCCAGGTCTATGTTTTTCATATACCCCATTGTATGTAACAGAATGTATCATTGGGCCTTGTGCCTATAAACCTTATA\n+>KJ718230_SH625867.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Dothideomycetes [id: 52];o__Pleosporales [id: 212];f__Pleosporaceae [id: 348];g__Alternaria [id: 1704];s__Alternaria_sennae [id: 24157]\n+ATCATTACACAAATATGAAGGCGGGCTGGCACCTCTCGGGGTGGCCAGCCTTGCTGAATTATTCCACCCGTGTCTTTTGCGTACTTCTTGTTTCCTTGGTGGGCTCGCCCACCACAAGGACCAACCCATAAACCTTTTTGTAATGGCAATCAGCGTCAGTAACAATGTAATAATTA\n+>KR476718_SH627048.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Leotiomycetes [id: 80];o__Helotiales [id: 340];f__Phacidiaceae [id: 11582];g__Phacidium [id: 11583];s__Phacidium_grevilleae [id: 24158]\n+ATGAGATCATGCCCTTCGGGGTAGACCTCCCACCCTCTGTATACAATACCTTTGTTGCTTTGGCGGCCCCGTCGCAAGACAACCGGCTCCGGCTGGTCAGCGGCCGCCAGAGGAATCAAAACTCATATTATTATTGTCGTCTGAGTACTATATAATAGTTA\n'

diff -r 000000000000 -r 834843ebe569 tool-data/Unite_s_7.1_20112016_ITS2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Unite_s_7.1_20112016_ITS2.fasta Thu Apr 08 14:30:48 2021 +0000

[

b'@@ -0,0 +1,107760 @@\n+>AF201716_SH204808.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Sordariomycetes [id: 3];o__Xylariales [id: 4];f__Xylariaceae [id: 5];g__Annulohypoxylon [id: 6];s__Annulohypoxylon_truncatum [id: 7]\n+CAACCCTTAAGCCCTGTTGCTTAGCGTTGGGAATCTGCTAGCCTCGGCGCAGTTCCTTAAATTCATTGGCGGAGCTGTGGCACACTCTAGGCGTAGTAGTTTAACACCTCGCCTNCTAGAGTGGCCGCGGTTACTGGCCGTAAAACCCCCATATTTCTAGTG\n+>UDB004660_SH465869.07FU_reps_singleton Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Boletales [id: 10];f__unidentified [id: 11];g__unidentified [id: 12];s__Boletales_sp [id: 13]\n+AATTCTCAACCATGTCTTGATTGATTTCAAGGCATTGGCTTGGACTGTGGGGGTTGCTGGCTGCGAAAGCGGTCGGCTCTCCTGAAATGCATTAGCAAGTCTCTTTGGACGTGCACGGCCTTTCGACGTGATAATGATCGTCGTGGCTGGAGCGTACACATGCTTGCTTCGAAAACCCTCTTGAGCTTCGGCTCAAATTGACTTGGAACTCGACCTCAAATCAGG\n+>FJ362054_SH204600.07FU_reps Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Marasmiaceae [id: 15];g__Moniliophthora [id: 16];s__Moniliophthora_sp [id: 17]\n+AATTCTCAACCTCAAAAGCTTTTTTTGAGGATTGGATGTGAGGGCTTTGCTGGCTTTGAATAAGAGTCGGCTCCCTTGAAATACATTAGTGGAAACCGTTTGGTGGACCACATTGGTGTGATAATTATCTACGCCATGACTTTGTTGTCCACACTTCGAATGCTATAGTTTTTTAAACAAAAGCTATAACACTTCGGTTTGGAGGGTTGCAAGTTGTGTAACAATGACTTTTGCTCTCTCTGTTAAAAGGTATCTGCTTCAAACCGTCCTAAGTTATTGGACAATTAATTGATTTG\n+>JX454898_SH207904.07FU_reps Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Entolomataceae [id: 18];g__Entoloma [id: 19];s__Entoloma_hebes [id: 20]\n+AAATTCTCAACCTTTCTAGCTTTTATAGCTGGTCAGGCTTGGATTGTGGAAGTTGCTGGTTCAACAATCAGCTCTTCTTAAATGTATTAGCAGAAACCTTTGCTGACCATCTTTGGTATGATAATTATCTATATCATTGACAATCAGTGTCCTCTAGGGGAGAGGCTTCGCTTCTAATAGTCTTTTAGACAACTTGACAAC\n+>KT328615_SH488012.07FU_reps_singleton Root;k__Fungi [id: 1];p__unidentified [id: 21];c__unidentified [id: 22];o__unidentified [id: 23];f__unidentified [id: 24];g__unidentified [id: 25];s__Fungi_sp [id: 26]\n+CAACCATCAAGCACAGCTTGGCATTGGGCCCCGCCCGCGGCCCTCACCGGCCCCGGGCGCGCCCCAAAACCGTCGGCAGAGTCAGCGAACCGCCGGGCGTAGCAGAAAAGGAAGGCGAGAGCCGACCCCTCACGTCCGACGGCCGCGGTCCCGCGCCGTTAAACCCCCAGGGCGCGCCTCCGGCGCGTCCGACCTCTCAAG\n+>U68322_SH012276.07FU_reps_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 27];o__Ascosphaerales [id: 28];f__Ascosphaeraceae [id: 29];g__Ascosphaera [id: 30];s__Ascosphaera_asterophora [id: 31]\n+CAACCCTCAAGCACGGCTTGTGTGATGGGTGATCGTCCTGTCTTTGGAAGGACGCACCTGAAAAGCAGTGACGGCGTCGTGTTCCGGTGCCCGAGCGTATGGGGCTTTGTCTTCCGCTCTTGTGGCCTGGCCGACTTGTCCGGTCGATACCATCTTTTTCTCGTGG\n+>UDB013960_SH221606.07FU_reps Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Russulales [id: 32];f__Russulaceae [id: 33];g__Russula [id: 34];s__Russula_sp [id: 35]\n+ACACCCTCAACCTTCTTGGTTTCTTGACTGGGAAGGCTTGGACTTTGGAGGTTCTTGCCAGCTTTTCATTTAAGTTGGCTCCTCCTAAATGAATTAGTGGGATCCACCAATCCTTGACGTGATAAGTATGCTTTGTACGTCTTGGATTTTGCACTGTTGTGCTGGAACCTGCTTCTGAATGGTCTTCAAAGAAAGACAACGTTCGAGTTGCGTCGCGAGTCGTAACTTGGCCTCACTGAC\n+>KR673632_SH492372.07FU_reps_singleton Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Mycenaceae [id: 36];g__Mycena [id: 37];s__Mycena_crocata [id: 38]\n+AATTATCAACCTTTCTCTCGCTTGTTCGCAGGTTTGAGTTAGGCTTGGATGTGGGGGTTTATTGCTGGCTTCCTTCAGTGGATGGTCTGCTCCCCTGAAATGCATTAGCGGGATCTCTTGTGGACCGTCACTTGGTGTGATAATTATCTATGCCGTGTTGACTTTGAAGCAAAACT\n+>KJ950804_SH523811.07FU_reps Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Amanitaceae [id: 39];g__Amanita [id: 40];s__Amanita_sp [id: 41]\n+AATTCTCAAAAAGTCTTCTTCGTGACAAGGGGGGAGGAGTTTTGGACATTGGGGGTTGCAGGTTTATAAAGCCAGCTCTCCTGGAATGAATTAGCAGGGATATATGGCATTTTTCTCGGTTGGTGTGATAAAGTTTTACACCATGAAATAAGTGGCATATATAATTTCTGCTTTCTAAATGAATTTGTGTCGTTAAGACAGAAGTTTGACCGA\n+>DQ656654_SH492954.07FU_reps_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Orbiliomycetes [id: 42];o__Orbiliales [id: 43];f__Orbiliaceae [id: 44];g__Hyalorbilia [id: 45];s__Hyalorbilia_lunata [id: 46]\n+TAACCTCTCCGG'..b'AGACTCGCCTTAAAGTCATTGGCAGCCGGCCTACTGGTTTCGGAGCGCAGCACAAGTCGCGCTCTCTTCCAGCCCCAAGGTCTAGCATCCACCAAGCCTTTTTTTTCAACT\n+>KJ775447_SH614178.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 27];o__Eurotiales [id: 61];f__Trichocomaceae [id: 62];g__Aspergillus [id: 353];s__Aspergillus_salwaensis [id: 24150]\n+CTGCCCTCAAGCACGGCTTGTGTGTTGGGTCGTCGTCCCCCCCCCCCGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTTGTAGGCCCGGCCGGCGCTGGCCGACGCTGAAAAGCAACCAACTATTTCTCCAG\n+>KJ663853_SH614186.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Leotiomycetes [id: 80];o__Helotiales [id: 340];f__Phacidiaceae [id: 11582];g__Phacidium [id: 11583];s__Phacidium_pseudophacidioides [id: 24151]\n+CAACCCTCAAGCTCTGCTTGGTATTGGGCGTCACCCCCGGGTGCGCCTTAAAATCAGTGGCGGTGCCGTCTGGCTTCAAGCGTAGTAATACTTCTCGCTTTGGAGTCCGGGCGAGCGTCCTGCCAAAACCCCCATATTTTTTCAG\n+>KT290244_SH616293.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Dothideomycetes [id: 52];o__Botryosphaeriales [id: 152];f__Botryosphaeriaceae [id: 153];g__Diplodia [id: 3397];s__Diplodia_crataegicola [id: 24152]\n+CAACCCTCAAGCTCTGCTTGGTATTGGGCGCCGTCCTCTCTGCGGACGCGCCTTAAAGACCTCGGCGGTGGCTGTTCAGCCCTCAAGCGTAGTAGAATACACCTCGCTTTGGAGCGGTTGGCGTCGCCCGCCGGACGAACCTTCTGAACTTTCTCAAGGTGACCTCGAT\n+>KJ775685_SH618623.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 27];o__Eurotiales [id: 61];f__Trichocomaceae [id: 62];g__Penicillium [id: 63];s__Penicillium_mexicanum [id: 24153]\n+CTGCCCTCAAGCACGGCTTGTGTGTTGGGCCCCGTCCTCCGATCCCGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTGTAGGCCCGGCCGGCGCTTGCCGATCAACCACATTTTTTCCAG\n+>KM189541_SH619611.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 27];o__Eurotiales [id: 61];f__Trichocomaceae [id: 62];g__Penicillium [id: 63];s__Penicillium_ranomafanaense [id: 24154]\n+CTGCCCTCAAGCACGGCTTGTTGTTGGGCCCCGTCCCCCTCTCCGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGAGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTTCGTAGGCCCGGCCGGCGCCAGCCGACCACAAATCATCCTTTTTTTCAG\n+>KJ718170_SH620157.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Dothideomycetes [id: 52];o__Pleosporales [id: 212];f__Pleosporaceae [id: 348];g__Alternaria [id: 1704];s__Alternaria_echinaceae [id: 24155]\n+GTACCCTCAAGCTTTGCTTGGTGTTGGGCGTCTTTTTGTCTCCCCTTGCGGGAGACTCGCCTTAAAGTCATTGGCAGCCGGCCTACTGGTTTCGGAGCGCAGCACAAGTCGCGCTCTCTTCCAGCCCCAAGGTCTAGCATCCAACAAGCCTTTTTTTCAACT\n+>KT359601_SH620263.07FU_refs Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Eurotiomycetes [id: 27];o__Eurotiales [id: 61];f__Trichocomaceae [id: 62];g__Aspergillus [id: 353];s__Aspergillus_sp [id: 1057]\n+CTGCCCTCAAGCACGGCTTGTGTGTTGGGCCCCCGTCCCCCTCTCCCGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTGTAGGCCCGGCCGGCGCCAGCCGACACCCAACTTTATTTCTAAG\n+>KM390702_SH623220.07FU_refs_singleton Root;k__Fungi [id: 1];p__Basidiomycota [id: 8];c__Agaricomycetes [id: 9];o__Agaricales [id: 14];f__Strophariaceae [id: 98];g__Hebeloma [id: 224];s__Hebeloma_pallidolabiatum [id: 24156]\n+AATTCTCAACCATTATCAACTTTTGCTGGTAATGGCTTGGATGTGGGGGTCTATTTTGCTGGCTTCTCAGATAGTCAGCTCCCCTTAAATGCATTAGCCGGTGCCCCGCGTGGACTGTCTATTGGTGTGATAATTATCTACGCTATAGACATCTGCAATCATATGGGTTTGCGCTGCTTCTAACAGTCTGTTAATACATGACAA\n+>KJ718230_SH625867.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Dothideomycetes [id: 52];o__Pleosporales [id: 212];f__Pleosporaceae [id: 348];g__Alternaria [id: 1704];s__Alternaria_sennae [id: 24157]\n+GTACCCTCAAGCTTTGCTTGGTGTTGGGCGTCTTTTTGTCCCCCCCTTTGCGGGGAGACTCGCCTTAAAGTCATTGGCAGCCGGCCTACTGGTTTCGGAGCGCAGCACAAGTCGCGCTCTCTTCCAGCCCCAAGGTCTAGCATCCAACAAGCCTCTTTTTTTCAACT\n+>KR476718_SH627048.07FU_refs_singleton Root;k__Fungi [id: 1];p__Ascomycota [id: 2];c__Leotiomycetes [id: 80];o__Helotiales [id: 340];f__Phacidiaceae [id: 11582];g__Phacidium [id: 11583];s__Phacidium_grevilleae [id: 24158]\n+CAACCCTCAAGCTCTGCTTGGTATTGGGTGTCACCCCCGGGTGCGCCTTAAAATCAGTGGCGGTGCCGTCTGGCTTCAAGCGTAGTAATACTTCTCGCTTTGGAGTCCGGGCGAGCGTCTTGCCAAAACCCCCATATTTTTTCAG\n'

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_HVL_db.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/frogs_HVL_db.loc.sample Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,37 @@
+# Copyright (C) 2014 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/>.
+#
+#
+#This is a sample file that enables tools FROGS_affiliations_postprocess to solve
+#inclusive amplicon sequence by selecting the smallest reference among multihit
+#You will need to create or download exact amplicon sequence reference fasta file
+#
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL_reference
+#
+#Finally you will need to create HVL_db.loc file similar to this one in your galaxy
+#tool-data directory.The HVL_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<unique_database_name>    <name>    <file_path>
+#
+#First column will be the visible name in galaxy.
+#So, for example, if you have  UNITE 7.1 ITS1 (only!) stored
+#in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta
+#then the HVL_db.loc entry would look like this:
+#
+# EXAMPLE FOR TEST :
+#Unite_extract_ITS1_test Unite_extract_ITS1_test ${__HERE__}/HVL_db_data/Unite_extract_ITS1.fasta
+#UNITE_7.1_ITS1 UNITE 7.1 ITS1 <PATH_TO>/Unite_s_7.1_20112016_ITS1.fasta
+#UNITE_7.1_ITS2 UNITE 7.1 ITS2 <PATH_TO>/Unite_s_7.1_20112016_ITS2.fasta

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_contaminant_db.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/frogs_contaminant_db.loc.sample Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,46 @@
+# Copyright (C) 2014 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/>.
+#
+#
+#This is a sample file that enables tools FROGS_otu_filters to identify contaminant.
+#You will need to create or download Blast+ index.
+#
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants
+#
+#Finally you will need to create phiX_db.loc file similar to this one in your galaxy
+#tool-data directory.The phiX_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<contaminant_name> <name> <file_path>
+#
+#First column will be the visible name in galaxy.
+#So, for example, if you had phix indexed stored in
+#/galaxy_databanks/phiX/
+#then the phiX_db.loc entry would look like this:
+#
+#
+# EXAMPLE FOR TEST :
+#phiX_test phiX_test ${__HERE__}/contaminant_db/phi.fa
+#
+#and your /galaxy_databanks/contaminant_db/ directory
+#would contain index files:
+#
+#-rwxrwxr-x 1 gpascal FROGS 5535 16 sept.  2015 phi.fa
+#-rw-rwxr-- 1 gpascal FROGS  132 16 sept.  2015 phi.fa.nhr
+#-rw-rwxr-- 1 gpascal FROGS   88 16 sept.  2015 phi.fa.nin
+#-rw-rwxr-- 1 gpascal FROGS 1348 16 sept.  2015 phi.fa.nsq
+#
+#phiX phiX tool-data/contaminant_db/phi.fa
+#Arabido_TAIR10_Chl_Mito Arabidopsis TAIR10 Chloroplast and mitochondrie tool-data/contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/frogs_contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa Thu Apr 08 14:30:48 2021 +0000

b'@@ -0,0 +1,6603 @@\n+>ChrC CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2005-06-03\n+ATGGGCGAACGACGGGAATTGAACCCGCGATGGTGAATTCACAATCCACTGCCTTAATCCACTTGGCTACATCCGCCCC\n+TACGCTACTATCTATTCTTTTTTGTATTGTCTAAAAAAAAAAAAAAATACAAATTTCAATAAAAAATAAAAAAAGGTAG\n+CAAATTCCACCTTATTTTTTTTCTAATAAAAAATATATAGTAATTTTTTATTATTTATTATTATTATTTATTATTAATA\n+TAATAAATAAAGTAAAATATGATACTCTATAAAAATTTGCTCATTTTTATAGAAAAAAACGAGTAATATAAGCCCTCTT\n+TCTTATTTAAAGAAGGCTTATATTGCTCGTTTTTTACTAAACTAGATCTAGACTAACACTAACGAATTATCCATTTGTA\n+GATGGAGCCTCAACAGCAGCTAGGTCTAGAGGGAAGTTGTGAGCATTACGTTCATGCATAACTTCCATACCAAGGTTAG\n+CACGGTTAATAATATCAGCCCAAGTATTAATAACACGTCCTTGACTATCAACTACTGATTGGTTGAAATTGAAACCATT\n+TAGGTTGAAAGCCATAGTACTAATACCTAAAGCAGTAAACCAAATACCTACTACCGGCCAAGCCGCTAAGAAGAAATGT\n+AAAGAACGAGAATTGTTGAAACTAGCATATTGGAAAATCAATCGGCCAAAATAACCGTGAGCAGCTACAATGTTGTAAG\n+TTTCTTCTTCTTGCCCGAATCTGTAACCTTCATTAGCAGATTCATTTTCTGTGGTTTCCCTGATCAAACTAGAAGTTAC\n+CAAGGAACCATGCATAGCACTAAAAAGGGAGCCGCCGAATACACCAGCTACACCTAACATGTGAAATGGGTGCATAAGA\n+ATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTGAAAGTACCAGAGATTCCTAGAGGCATACCATCAGAAAAACTTC\n+CCTGACCAATTGGATAGATCAAGAAAACAGCAGTCGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGACG\n+CATACCCAGACGGAAACTAAGTTCCCACTCACGACCCATATAACAAGCTACACCAAGTAAAAAGTGTAGAACAATTAGT\n+TCATAAGGACCGCCGTTGTATAGCCATTCATCAACGGATGCAGCTTCCCAGATTGGGTAAAAATGCAATCCAATAGCTG\n+CAGAAGTAGGAATAATGGCACCGGAAATAATATTGTTTCCGTAAAGAAGAGATCCAGAAACAGGTTCACGAATACCATC\n+AATATCTACTGGAGGAGCAGCAATGAATGCGATAATAAAAACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACA\n+CCAAACCATCCAATGTAAAGACGGTTTTCAGTGCTAGTTATCCAGTTACAGAAGCGACCCCATAGGCTTTCGCTTTCGC\n+GTCTCTCTAAAATTGCAGTCATGGTAAAATCCTTGGTTTATTTAATAATCAGGGACTCCCAAGCGCACAAATTCTCTAA\n+GTAGATAATTGAGAGCTTGTTATGAAACAGTATAACATGACTTATATAGCCATGTCAACCAATGTAAAATGGATAAGAT\n+CCTTTTAGTTTAGATTCATAAAAAATTTTTTGTAATCGATGAAATAAATTAGAAGCGAATCCACATACATAGAAATAGA\n+ATTGCTCTAGGAATATTTTTTCCAAATCATATGAATACGATTGAATACGATCCGTAGTGGGTTGCCCGGGACTCGAACC\n+CGGAACTAGTCGGATGGAGTAGATAATCTCCTTGTTAAAATGAAAAAAAAAAGGTAAAAAACCCCTCCCCAAACCGTGC\n+TTGCATTTTTCATTGCACACAGCTTTCTCTATGTATACATAGAAAACTCAATTTCTTTGGTTCCTTATAAATAGGACTC\n+CAAATTCAATACTCAGTAAATTTAATCGTAGTCTTACTGTATGAACATTTAATAATAGAAATAAAGCACTTTTGATAAT\n+AAAAAATAATTGATTTTTTTTGTTATCTCTGCATAAATTTTAATAAATTTCGATTTCATTTATGGGGTCTCAGAACCCA\n+ATTATTCATGATTGACCAAATCATTAAGATAAAGAATATCCAAATACCAAATTCGCACTCGATATAATCTTTTAGAAGC\n+ATAATAACTTCTTGGGAAGATTAAAGAAAGAACTTGGTCTTCCCCCGTAAGGAATTCTTCCAATAAACCAGAGCCCAAC\n+CTTTTTAAAAAAGTGCGTACAGTACTTTTGTGTTTACGAGCCAAAGTTTTAACACAACAAAGACGAAGTATATATTTTA\n+TTCGATACAAATTCTTTTTTTTTGAAGATCCGCTGTAATAATGAGAAATATTTCTGCATATCCGCACAAATCGGTTGAG\n+AATATCAGAATCTGATGAATCCGTCCAGGTTGCTTTACTAATGGGATGCCCTAATACATTACAAAATTTATCTTTAGCC\n+AACGATCCAATAATAGAAGAAATTGGAATTTTGCTATCCAATTTGATTCTAACATTATCTATTAGAAATGAGTTTTCTA\n+GCATTTGACTACGTACCACTAAAGGGTTTAATCGCAAACTTGACAGATAACCCAGAAACTCTAAATTATCTTTAGATAA\n+TTGATTTATATTGACCTTTTGCGATTGAAACCATACCGAAAAATAACATTGCCATAAATTAACAAAATAATATTTCCAT\n+TTATTCATCAGAAGCGGCGTATCCTTTGTTGCCAGAATGCATCTTCCGTGATATCTAACATAATGTATGAAAGGATCCT\n+TGAGCAACCCTAGGATTGCCGGAAAATTATTAACAAAAACTTTGAAAAAATGGTGTATTTTTCCATAGAATACAATTCG\n+CTCAAAAAGGACTTCATAAGATGTCGATCGTAAATGCGAAGACCGCTTGCGTAGAAAAAAAAAGATGGATTCGTATTCA\n+CATACATGAGAATTATATAAGAACAAGAAAAATCTTGGATTCAAAATTGATTTTTTTTTAATATAAAAATTCTTCCAAT\n+TACAATACTCGTATAAACAGAACCGAAAAAAATGCAAAGAAGAGGCATCTTTTACCCGGTAACGTAGGGTTTGAACCAA\n+GATTTCTAGATGGATGGGGTAAGGTATTAGTACATCTAACACATAATTAAAATGTCCTAATTTGTCTTCTAAAAAGGGA\n+AATATTGAATGAATTGATTGTAAATTATAAGATTTTTTTAATTGTTTTCCTTGAAAAGAGGATCCTAATCTTAGGGAAA\n+ATGGAATTTCGACAATCACTGCAAATAAAACAGATATCATTTGATAATAGAAAAGACTGGTATGCCCCAAAAAGGAATT\n+TTGGTTCACATCCTTAGTGGGAATAATCAAACGATTCTGTTCATACATTCGCAAAATTAAGCGTTTCGTAATTAGTGAA\n+CTATATTTTTTGTCATAATCCGCATTTTCCAAGAAAATATAGCGATTTCTATTTAATCTATTTAAACCATGATCATAAG\n+CAAGTACATAAATATACTCCCGAAAAAAAAGTGGATATAGAAAACTCTGTTGCCGAGCCCCATCGAACTCTAAATATCC\n+TTGAAATTTATCCATTTGGATTGAAATTCGATTTGAACTGAAGGTAAAGTCTTTATTTTCTTGAGTTCTGAAATGACAC\n+ATAGTGCGATACAGTCAAAATAAGGTATTAGACTACGAAAGCTATAGATATAGATACCTCATAAACAGGTAGACTGCTA\n+ACCGGATTCTCTATCTTTAATAGGTTTCTGTTCGTTATATTATAGAATAACAAAACAAGATTATTAGAAATCCTTTATT\n+TTTTTAACCTAATC'..b'TAGCTTTCTTCAGGATTTGGCCCGAACTGTTC\n+GGCAGATTCCCACGCCTTACGCACCCGTTCGCCACTTTGTTCTCAACTCTTCCCGCCTCCTGGGCGAGACAAGCTACCT\n+TGAGCTAGGAGCCTCTTTTCCTTCTGCCTAGCTCCCCGAGAACAACGTTCGACTTGCATGTGTTAAGCATATAGCTAGC\n+GTTCCTTCTGAGCCAGGATCAAACTCTTCTTTTGACTATGATTGGGCCCTGCAGTGGTAGAACCTCGTGAACCGGGCGT\n+ACTACTTCCCAACCTTCTGTGGACCTTTCTTCTCTTATTCAATTCCACTTTGTTTAGTTTAGTGATAGTTAGAGGTTAG\n+AGAAGAGAGCTAGATCACTCCTCTAAGCAGCCTTCTGATTATATACGTATTATTCTATCAATCGATAAGCAAGGGTAGG\n+GTTCCTGGATCGGTCTCGACCAGAAGACCGAGAGGTACTTTTGTCACGAGCTGGCTTAACCCATTCCCTTAACACCAAG\n+CCTGGATAAGCAACTGAAAAGTCAAGTAGAATCCCTGGCTTGTGTAGGCGAGCTAAACACAAATCTTTCTTTTCATTTT\n+ATATAGATGGAAAAGTAAGAAATCCTATTTTCCTTCGTAAGAGCACATCTTACATCGCAAACTTTCTCTTTATATACCG\n+AGGATTTGATGAAATACCATTTTAGCTCTATGGAGCCGTGGTGGAAAAGAGAATTTTCATTTTGTATACCGGCGATTTA\n+TATCAAAATGGCATCAATCTCACTTTTTCAAAATAGTTGGCTGAAGATGAAACATCTCCCTAGTTGCCTATTCACCCAG\n+ACAACCAACACTTTAGGCATTTACAGGAAAAAAAAACCTAACCATAGTCGTGACAACCCTAGAATCAACTCAAACCTTT\n+CGACCAACTATGCCCAAGCTAAGTCAGTTGAGAGATCAAGATCCAATAGCCTCAACTCAGGCCCAAACCCATTAGAGAA\n+TGCCACGTAGAGAACCATCGGGCACATAAACTTCTATATTCCACCCGATGAGACTAATGCTGTCACTCGAAACCAAGCT\n+GCTCAAACTAATGCTAGCTAGGCTGTGAACTTTGAAGGGGTAGATAGCAATCCAAGTCTTATACCCGAAATGCTGCAAA\n+TAACTTGAGAAGTGCCTAGAGAGTTCCTACGAAAAGATACTACATCATCATCGATAAGCTGAGCTCCACCCGCATAAGC\n+ATTTCCATGTTAGAGCTGCTTAAAACTTTGCTTGTGCGTAGGGATGCTTTCGTGAGAGAAGTGCTACTCTCGGTTTGGA\n+TCAAAAGAATATACTGCTGAACCTATTGACTGACTACTTTATGCAACTACTCGCTATAAAGCCTTAAAGCTAGCTCTCA\n+CTAACAAAGCCAGTGAAATCTCTATTAGCCCATAGGGTATACTCTCAACCATTACTTGCCCTTTACTAGATTGTCTGAA\n+ACTTGTCTTATTGCTGCTTTGTCTTAGGATAACCACCCTGCAAAGGCATGGGGAAAGCTATAGGCATCAGCAGAAAGGC\n+AAGCAAAGGCGTAGGTAGCCAAATGGTCTAGTCCCTGCCAGAGAACAACTGCAGCTGAGACGAGAGCTGACAAGTATGT\n+AACACCTACTTCCACCCCATCGGGGAGTGAAATAGAACATGAAACCGTAAGCTCCCAAGCAGTGGGAGGAGCCCTGGGC\n+TCTGACCGCGTGCCTGTTGAAGAATGAGCCGGCGACTCATAGGCAGTGGCTTGGTTAAGGGAACCCACCGGAGCCGTAG\n+CGAAAGGCGAGTCTTCATAGGGCAATTGTCACTGCTTATGGACCCGAACCTGGGTGATCTATCTATGACCAGGATGAAG\n+CTTGGGTGAAACTAAGTGGAGGTCCGAACCGACTGATGTTGAAAAATCAGCGGATGAGTTGTGGTTAGGGGTGAAATGC\n+CACTCGAACCCAGAGCTAGCTGGTTCTCCCCGAAATGCGTTGAGGCGCAGCAGTTGACTGGACATCTAGGGGTAAAGCA\n+CTGTTTCGGTGCGGGCCGCGAGAGCGGTACCAAATCGAGGCAAACTCTGAATACTAGATATGACCTCAAAATAACAGGG\n+GTCAAGGTCGGCCAGTGAGACGGTGGGGGATAAGCTTCATCGTCGAGAGGTTGTTTACATACTCGACTAAAAGGAGAGG\n+TCCAAAATCGACTGATAAAGGAGAGGTCCGGAGGTATTAACTAGTTGATGAGGTCTCGACGAGCGACTGAAAGGTTCAC\n+CTAGTGCTCGAGAGAGAATTGGGTCGCGCACCTTCTGAACCCGACCACCACCTATAAGACGACGTCAAGAAAGCCAACT\n+CTCAGGCCAAGAGAACATACCTCGCCTAATAGACTGGAGGAGGTGTCCCGTACCCTTAGAATCGTCTAATAAAAAAAAT\n+GTGCTTACCTTCATGAGAGCTGACATTACTTCTTTTGATATCGATGCCTTAGTCAGGCTAACTATATGCGATGCGTCAA\n+ACATAAAATGAAATTCATCCTACCGAAACCAGACCAGAGAAAAGAGGATCTCCGGAGCTCAACCATCGAATCGGGAAAG\n+CACTCTTTCCAGCTTAAAACAGAGCACAGAAAGGACACTCAAAGCAGGTCCGTCTGTATTTCATTATAGTAGTGATCCC\n+CTTCTCTTGATCAATTAGACAAGAACTTTACTTTGTTAAAGACATAAAAGGAGGTCCCACTATGACTATTAGCGGTTCC\n+TAGCAGGCATGGGAGAAGAGCAGGAAGAGAAAGAAAAAAGAGACAAAGATAGACTAGCCACTTCCTTATTATACGAAAA\n+GTTTTTGATTGATGAGTTCTCACCTTCTCTCATGGAGTAGGTAGATGAGACAGAAGGGAAAAGGAGTGACCCCTACTAT\n+GACTCATCTCAGTTACTCTTCATCACAGGACAAGATACGAGCAGAATCAGAGGAAAATCGAACAACTACAAGCTAAGAT\n+GAAAAATCTAAGTGAAAGACTAACTGATAGGCCCTGGCTGGACCGATGGAATGTTTCAAGTAAAGGGCTAACTCTTAAC\n+TAGGCTAGCGAAGGAACTGACATTAGGGAAAGAACTCCTGACTCTCGGGGAAAGATCTCTCTCTTTAATACGAGATTCC\n+CTAACCCTGAAGCATTTAGCAAACTCAGCAAAACCTGAATGGGGATCAAGGACTTTTGATAACTTATTTTGACCCCCAA\n+TCCACCCAAAGCAGATTCATAGACTTTGGCGACTTCCTGATCGGCAATGACAACATCATCACCGAGTACCGCGTACGAT\n+GTAAAGCGTACACCAGGATGCACCTGTTTCGCACACCACCACACTAATATATGGTGTGATAGCGCGAAAGTAGGCCAAG\n+AACCGTGATATCCCAATGGCTGCCCTGCCACAAAGCATACTTGAGAGAACCTTCGTTTAAGTTTAACAAAAGGCACCTC\n+AAAGATATTGCATGCAAATGCAGAATTAACCACACTTGAGGCAAAGGAGCGGTCAAATAGGTACTGCACCACCTCAAAC\n+AGAAAGACTAAAGGCCAACGATCAGTGGCCGACTTTAAGTCAAAGGAGAAAGAGTGCCTACTGCCAACCAGTCGATCAA\n+AAGGCTGTGTTTGGTTAAAAGTCCCATCTTGGGGGAGACGTCTTCTCCGCCCCCCAAACATGGAAGGGGTGTAACAACC\n+TATTATTAACGTAGTTCCCAATGGCGAATAGAAGGCTTTTGCCACCTCCCTCAACAACCTGACCTAGTCGGCCCATCCT\n+CCGAGGTTTTTGTTCTGCTGATATGATAGCTCTTTTAAAGAAGAGGTCTCAACGAGCCTCCTGAATTTAATTTCATCCA\n+TACAGGAGAATGCATCATTCTTATCGCAGAATGGAAACAAACCGGATT\n\\ No newline at end of file\n'

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa.nhr

Binary file tool-data/frogs_contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa.nhr has changed

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa.nin

Binary file tool-data/frogs_contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa.nin has changed

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa.nsq

Binary file tool-data/frogs_contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa.nsq has changed

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_contaminant_db/phi.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/frogs_contaminant_db/phi.fa Thu Apr 08 14:30:48 2021 +0000

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_contaminant_db/phi.fa.nhr

Binary file tool-data/frogs_contaminant_db/phi.fa.nhr has changed

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_contaminant_db/phi.fa.nin

Binary file tool-data/frogs_contaminant_db/phi.fa.nin has changed

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_contaminant_db/phi.fa.nsq

Binary file tool-data/frogs_contaminant_db/phi.fa.nsq has changed

diff -r 000000000000 -r 834843ebe569 tool-data/frogs_db.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/frogs_db.loc.sample Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,54 @@
+# Copyright (C) 2014 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/>.
+#
+#
+#This is a sample file that enables tools FROGS_affiliations_OTU to use taxonomy database for
+#taxonomy affiliation. You will need to create or download Blast+ index and train your database
+#for RDP classifier these data files.
+#
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation
+#
+#Finally you will need to create frogs_db.loc file similar to this one.
+#The frogs_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<unique_database_name>   <printed_database_name>   <file_path>
+#
+#Second column will be the visible name in galaxy.
+#So, for example, if you had 16S silva 128 indexed stored in
+#/galaxy_databanks/16S/silva_128/
+#then the frogs_db.loc entry would look like this:
+#
+#silva_128_16S    silva 128 16S    /galaxy_databanks/16S/silva_128/silva_128_16S.fasta
+#
+#and your /galaxy_databanks/16S/silva_128/ directory
+#would contain index files:
+#
+#-rw-r--r-- 1 mbernard FROGS    8097966  5 déc.  16:56 bergeyTrainingTree.xml
+#-rw-r--r-- 1 mbernard FROGS 1572981589  5 déc.  16:56 genus_wordConditionalProbList.txt
+#-rw-r--r-- 1 mbernard FROGS       1654  5 déc.  16:56 LICENCE.txt
+#-rw-r--r-- 1 mbernard FROGS    1072228  5 déc.  16:56 logWordPrior.txt
+#-rw-r--r-- 1 mbernard FROGS  940834335  5 déc.  16:56 silva_128_16S.fasta
+#-rw-r--r-- 1 mbernard FROGS  152606489  5 déc.  16:56 silva_128_16S.fasta.nhr
+#-rw-r--r-- 1 mbernard FROGS    6918588  5 déc.  16:56 silva_128_16S.fasta.nin
+#-rw-r--r-- 1 mbernard FROGS  205320030  5 déc.  16:56 silva_128_16S.fasta.nsq
+#-rw-r--r-- 1 mbernard FROGS        281  5 déc.  16:56 silva_128_16S.fasta.properties
+#-rw-r--r-- 1 mbernard FROGS    3420464  5 déc.  16:56 silva_128_16S.tax
+#-rw-r--r-- 1 mbernard FROGS     964048  5 déc.  16:57 wordConditionalProbIndexArr.txt
+#
+#
+#<value>    <name>    <file_path>
+#
+#ITS_test ITS1 extract <FROGS-wrappers>/test-data/databases/frogs_db_data/ITS1.rdp.fasta

diff -r 000000000000 -r 834843ebe569 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,15 @@
+<tables>
+    
+    <table name="frogs_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/tool-data/frogs_db.loc" />
+    </table>
+    <table name="frogs_HVL_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/tool-data/frogs_HVL_db.loc" />
+    </table>
+    <table name="frogs_contaminant_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/tool-data/frogs_contaminant_db.loc" />
+    </table>
+</tables>

diff -r 000000000000 -r 834843ebe569 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,15 @@
+<tables>
+    
+    <table name="frogs_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/databases/frogs_db.loc" />
+    </table>
+    <table name="frogs_HVL_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/databases/frogs_HVL_db.loc" />
+    </table>
+    <table name="frogs_contaminant_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/databases/frogs_contaminant_db.loc" />
+    </table>
+</tables>

diff -r 000000000000 -r 834843ebe569 tree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tree.xml Thu Apr 08 14:30:48 2021 +0000

@@ -0,0 +1,129 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_Tree" name="FROGS Tree" version="3.2.2">
+    <description>Reconstruction of phylogenetic tree </description>
+    <requirements>
+        <requirement type="package" version="3.2.2">frogs</requirement>
+        <requirement type="package" version="7.407">mafft</requirement>
+        <requirement type="package" version="2.1.09">fasttree</requirement>
+        <requirement type="package" version="3.6.3">r-base</requirement>
+        <requirement type="package" version="2.5.5">r-phangorn</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <command>
+        tree.py
+            --input-sequences $input_otu
+            --biom-file $biomfile
+            --nb-cpus \${GALAXY_SLOTS:-1}
+            --out-tree $out_tree
+            --html $html
+    </command>
+    <inputs>
+    
+        <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+    </inputs>
+    <outputs>
+        <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/>
+        <data format="html" name="html" label="${tool.name}: report.html" from_work_dir="summary.html"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_otu" value="references/09-normalisation.fasta"/>
+            <param name="biomfile" value="references/09-normalisation.biom"/>
+            <output name="out_tree" value="references/15-tree-mafft.nwk" compare="sim_size" delta="30"/>
+            <output name="html" value="references/15-tree-mafft.html" compare="diff" lines_diff="2"/>
+            <output name="html" value="references/15-tree-mafft.html" compare="sim_size" delta="30"/>
+            <output name="html">
+                 <assert_contents>
+                    <has_text_matching expression="FROGS\sTree" />
+                    <has_text_matching expression="abundance_removed.*:\s0" />
+                    <has_text_matching expression="abundance_kept.*:\s300" />
+                    <has_text_matching expression="otu_removed.*:\s0" />
+                    <has_text_matching expression="otu_kept.*:\s50" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Creation of a multiple alignment of OTUs with `Mafft <http://mafft.cbrc.jp/alignment/software>`_.
+And creation of a rooted phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_ and `Phangorn R package <https://cran.r-project.org/web/packages/phangorn/index.html>`_.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**OTUs fasta file**:
+
+The OTUs sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
+Careful: FROGS Tree works only with less than 10 000 sequences!
+
+ .. image:: static/images/FROGS_tree_otufile.png
+
+**OTUs biom file**:
+
+The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_).
+This file can be obtained in particular with the FROGS pipeline.
+
+.. class:: h3
+
+Outputs
+
+**Newick file** (tree.nwk):
+
+The phylogenetic tree in Newick format (format `nwk or nhx <https://en.wikipedia.org/wiki/Newick_format>`_).
+
+ .. image:: static/images/FROGS_nwk_treefile.png
+
+**Html file** (summary.html):
+
+The summary file describing which OTUs are contained or not in the phylogenetic tree.
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+    </help>
+</tool>

diff -r 000000000000 -r 834843ebe569 tsv_to_biom.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tsv_to_biom.xml Thu Apr 08 14:30:48 2021 +0000

[

@@ -0,0 +1,139 @@
+<?xml version="1.0"?>
+
+<tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="3.2.2">
+ <description>Converts a TSV file in a BIOM file.</description>
+        <requirements>
+            <requirement type="package" version="3.2.2">frogs</requirement>
+        </requirements>
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+        </stdio>
+ <command>
+ tsv_to_biom.py
+                 --input-tsv $tsv_file
+                 --output-biom $biom_file
+               #if $multi_affi_file
+                 --input-multi-affi $multi_affi_file
+               #end if
+               #if $extract_fasta
+                 --output-fasta $sequence_file
+               #end if
+ </command>
+ <inputs>
+ 
+ <param format="tabular" name="tsv_file" type="data" label="Abundance TSV File" help="Your FROGS abundance TSV file. Take care to keep original column names." optional="false"/>
+ <param format="tabular" name="multi_affi_file" type="data" label="Multi_hits TSV File" help="TSV file describing multi_hit blast results." optional="true" />
+ 
+ <param name="extract_fasta" type="boolean" label="Extract seeds in FASTA file" help="If there is a 'seed_sequence' column in your TSV table, you can extract seed sequences in a separated FASTA file." />
+ </inputs>
+ <outputs>
+ <data format="biom1" name="biom_file" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" />
+ <data format="fasta" name="sequence_file" label="${tool.name}: sequences.fasta" from_work_dir="seed.fasta" >
+ <filter>extract_fasta</filter>
+ </data>
+ </outputs>
+ <tests>
+ <test>
+ <param name="tsv_file" value="references/12-biom2tsv.tsv" />
+ <param name="multi_affi_file" value="references/12-biom2tsv-affiliation_multihit.tsv" />
+ <param name="extract_fasta" value="true"/>
+ <output name="biom_file" file="references/14-tsv2biom.biom" compare="sim_size" delta="0"/>
+ <output name="sequence_file" file="references/14-tsv2biom.fasta" compare="diff" lines_diff="0"/>
+ </test>
+ </tests>
+ <help>
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+This tool converts a TSV file in a BIOM file.
+
+.. class:: h3
+
+Inputs
+
+**Abundance file**:
+
+The table with abundances each cluster in each sample and other details conerning the cluster (format TSV).
+
+Authorised column names :  rdp_tax_and_bootstrap, blast_taxonomy, blast_subject, blast_perc_identity, blast_perc_query_coverage, blast_evalue, blast_aln_length, seed_id, seed_sequence, observation_name, observation_sum
+
+**Multiple affiliation file**:
+
+The file that stores the multiple blast hits.
+
+.. class:: h3
+
+Outputs
+
+**Abundance file**:
+
+ The abundance of each cluster in each sample and their metadata (format `BIOM <http://biom-format.org/>`_).
+
+**Sequence file [optional]**:
+
+ By checking the "Extract seed FASTA file" option, the sequences will be extract from TSV to create a file in `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_ format.
+ For this option, be sure that your TSV file contains the seed_sequence column.
+
+
+.. class:: infomark page-header h2
+
+How it works
+
+FROGS TSV_to_BIOM detects any metadata (columns before "observation_name") and names of samples (columns after "observation_sum").
+
+Then it reconstructs the BIOM abundance file : for each "observation_name" it adds the associated metadata and the count of samples.
+
+If blast_taxonomy is included in metadata and if blast_subject is equal to "multi-subject", it parses multi_hit TSV file. Then it extracts the list of blast_affiliations that contains the non ambiguous blast_taxonomy.
+
+
+
+.. class:: infomark page-header h2
+
+Advices
+
+This tool is usefull if you have modified your abundance TSV file and  that you want to generate rarefaction curve or sunburst with the FROGS affiliation_stat tool.
+
+If you modify your abundance TSV file
+
+    * -do not modify column names
+    * -do not remove columns
+    * -take care to choose a taxonomy available in your multi_hit TSV file
+    * -if you delete lines of the multi_hit file, take care to not remove a complete cluster whithout removing all "multi tags" in you abundance TSV file.
+    * -if you want to rename a taxon level (ex : genus "Ruminiclostridium 5;" to genus "Ruminiclostridium;"), do not forget to modify also your multi_hit TSV file.
+
+----
+
+**Contact**
+
+Contacts: frogs-support@inrae.fr
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_
+
+ </help>
+</tool>