Repository 'frogs_2_0_0'
hg clone https://toolshed.g2.bx.psu.edu/repos/frogs/frogs_2_0_0

Changeset 0:76c750c5f0d1 (2018-10-25)
Commit message:
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
added:
README.md
affiliation_OTU.xml
affiliations_stat.xml
biom_to_stdBiom.xml
biom_to_tsv.xml
clustering.xml
clusters_stat.xml
demultiplex.xml
filters.xml
normalisation.xml
preprocess.xml
r_alpha_diversity.xml
r_beta_diversity.xml
r_clustering.xml
r_composition.xml
r_import_data.xml
r_manova.xml
r_structure.xml
remove_chimera.xml
static/images/FROGS_affiliation_combined_percent_id.png
static/images/FROGS_affiliation_overlapped_percent_id.png
static/images/FROGS_affiliation_percent_id_formula.png
static/images/FROGS_affiliation_stat_alignment.png
static/images/FROGS_affiliation_stat_bootstrap.png
static/images/FROGS_affiliation_stat_rarefaction.png
static/images/FROGS_affiliation_stat_sunburst.png
static/images/FROGS_affiliation_stat_taxonomies.png
static/images/FROGS_affiliation_summary.png
static/images/FROGS_affiliation_summary_v3.png
static/images/FROGS_cluster_stat_clusterDistrib1.png
static/images/FROGS_cluster_stat_clusterDistrib2.png
static/images/FROGS_cluster_stat_rarefaction.png
static/images/FROGS_cluster_stat_sample_dist1.png
static/images/FROGS_cluster_stat_sample_dist2.png
static/images/FROGS_cluster_stat_seq_dist.png
static/images/FROGS_cluster_swarm.png
static/images/FROGS_logo.png
static/images/FROGS_preprocess_ampliconSize_multimodal.png
static/images/FROGS_preprocess_ampliconSize_multimodal_v3.png
static/images/FROGS_preprocess_ampliconSize_unimodal.png
static/images/FROGS_preprocess_ampliconSize_unimodal_v3.png
static/images/FROGS_preprocess_combined_sequence1.png
static/images/FROGS_preprocess_combined_sequence2.png
static/images/FROGS_preprocess_lengthsSamples.png
static/images/FROGS_preprocess_lengthsSamples_v3.png
static/images/FROGS_preprocess_overlapped_sequence.png
static/images/FROGS_preprocess_summary.png
static/images/FROGS_preprocess_summary_v3.png
static/images/biomfile.png
static/images/demultiplex_barcode.png
static/images/demultiplex_fastq_ex.png
static/images/fasta_ex.png
static/images/frogs_tree_otufile.png
static/images/frogs_tree_summary.png
static/images/frogs_tree_templatefile.png
static/images/nwk_treefile.png
static/images/phyloseq_alpha_diversity_table.png
static/images/phyloseq_bar_plot.png
static/images/phyloseq_beta_diversity.png
static/images/phyloseq_beta_diversity_matrix.png
static/images/phyloseq_clustering_ward.png
static/images/phyloseq_composition_plot.png
static/images/phyloseq_import_data_html.png
static/images/phyloseq_manova.png
static/images/phyloseq_plot_heatmap_red.png
static/images/phyloseq_plot_richness.png
static/images/phyloseq_plot_richness_box.png
static/images/phyloseq_plot_sample_ellipse.png
static/images/phyloseq_rarefaction_curves.png
static/images/phyloseq_samplefile.png
test-data/bergeyTrainingTree.xml
test-data/db.fasta
test-data/db.fasta.nhr
test-data/db.fasta.nin
test-data/db.fasta.nsq
test-data/db.fasta.properties
test-data/db.tax
test-data/frogs_db.loc
test-data/genus_wordConditionalProbList.txt
test-data/logWordPrior.txt
test-data/otus_pynast.fasta
test-data/references/01-prepro.fasta
test-data/references/01-prepro.html
test-data/references/01-prepro.tsv
test-data/references/02-clustering.biom
test-data/references/02-clustering.fasta
test-data/references/02-clustering_compo.tsv
test-data/references/03-chimera.biom
test-data/references/03-chimera.fasta
test-data/references/04-affiliation.biom
test-data/references/04-filters.biom
test-data/references/04-filters.excluded
test-data/references/04-filters.fasta
test-data/references/05-clustersStat.html
test-data/references/06-affiliationsStat.html
test-data/references/07-biom2tsv.multi
test-data/references/07-biom2tsv.tsv
test-data/references/08-affiliation_multihit.tsv
test-data/references/08-affiliation_std.biom
test-data/references/09-tsv2biom.biom
test-data/references/09-tsv2biom.fasta
test-data/references/10b-tree.nwk
test-data/references/11-phylo_import.Rdata
test-data/references/12-phylo_composition.html
test-data/references/13-phylo_alpha_div.tsv
test-data/references/14-phylo_beta_div.html
test-data/references/15-phylo_structure.html
test-data/references/16-phylo_structure.html
test-data/references/17-phylo_structure.html
test-data/references/Blast_affiliation.biom
test-data/references/Blast_affiliation.html
test-data/references/Unifrac.tsv
test-data/references/chaillou.biom
test-data/references/demultiplex_barcode.txt
test-data/references/demultiplex_log.txt
test-data/references/demultiplex_test2_R1.fq
test-data/references/demultiplex_test2_R2.fq
test-data/references/normalisation_report.html
test-data/references/sample_metadata.tsv
test-data/references/tree.nwk
test-data/swarm.biom
test-data/swarm.fasta
test-data/test_dataset.tar.gz
test-data/wordConditionalProbIndexArr.txt
tool-data/frogs_db.loc.sample
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test
tree.xml
tsv_to_biom.xml
b
diff -r 000000000000 -r 76c750c5f0d1 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Thu Oct 25 05:01:13 2018 -0400
[
@@ -0,0 +1,28 @@
+# FROGS-wrappers 2.0.0
+
+FROGS Galaxy Wrappers (for the Toolshed) for FROGS version 2.0.0
+
+## Description
+
+    FROGS is a galaxy/CLI workflow designed to produce an OTU count matrix from high depth sequencing amplicon data.
+
+    
+## Sources
+
+FROGS 2.0.0 sources are here => [https://github.com/geraldinepascal/FROGS](https://github.com/geraldinepascal/FROGS)
+
+These wrappers use the FROGS Conda dependency => [https://bioconda.github.io/recipes/frogs/README.html](https://bioconda.github.io/recipes/frogs/README.html)
+
+
+## License
+    GNU GPL v3
+
+## Copyright
+    2015 INRA
+
+## Citation
+    Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
+
+## Contact
+    frogs@inra.fr
+
b
diff -r 000000000000 -r 76c750c5f0d1 affiliation_OTU.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/affiliation_OTU.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,169 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="0.8.0">
+ <description>Step 4 in metagenomics analysis : Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</description>
+  <requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+      <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>
+ #set $reference_fasta_filename = str( $ref_file.fields.path )
+ affiliation_OTU.py 
+                        --reference "${reference_fasta_filename}"
+ --input-biom $biom_abundance 
+ --input-fasta $fasta_sequences
+ --output-biom $biom_affiliation 
+ --summary $summary 
+ --nb-cpus $nb_cpu
+ --java-mem $mem 
+ #if $rdp
+                         --rdp
+                         #end if
+ </command>
+ <inputs>
+ <!-- JOB Parameter -->
+ <param name="nb_cpu" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1"></param>
+ <param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param>
+ <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list">
+         <options from_data_table="frogs_db"></options>
+ <validator type="no_options" message="A built-in database is not available" />
+ </param> 
+    <param name="rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allow you to perform it also with RDP classifier (default No)" />
+         <!-- Files -->
+         <param format="fasta" name="fasta_sequences" type="data" label="OTU seed sequence" help="OTU sequences (format: fasta)."/>
+         <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="OTU abundances (format: BIOM)."/>
+ </inputs>
+ <outputs>
+ <data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation.biom" from_work_dir="affiliation.biom" />
+ <data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/>
+ </outputs>
+        <tests>
+                <test>
+                        <param name="ref_file" value="db"/>
+                        <param name="fasta_sequences" value="swarm.fasta"/>
+                        <param name="biom_abundance" value="swarm.biom"/>
+                        <output name="biom_affiliation" file="references/Blast_affiliation.biom"/>
+                        <output name="summary" file="references/Blast_affiliation.html" 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
+
+Add taxonomic affiliation in abundance file.
+
+
+.. class:: infomark page-header h2
+
+Inputs/outputs
+
+.. class:: h3
+
+Inputs
+
+**Sequence file**:
+
+The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+**Abundance file**:

+The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+.. class:: h3
+
+Outputs
+
+**Abundance file** (tax_affiliation.biom):
+
+ The abundance file with affiliation (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+**Summary file** (report.html):
+
+ This file presents the number of sequences affiliated by blast, and the number of multi-affiliation (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).

+ .. image:: static/images/FROGS_affiliation_summary.png 
+    :height: 800
+    :width: 600
+
+
+.. class:: infomark page-header h2
+
+Reference database
+
+The databases come from `SILVA &lt;http://www.arb-silva.de/&gt;`_ a comprehensive and quality checked rRNA database.
+
+FROGS database(s) pre-process:
+
+1. The non-redondant small sub-unit database is retrieved from SILVA.
+
+2. This database is processed to keep only the taxonomy level: Domain - Phylum - Class - Order - Family - Genus - Species
+
+3. The database is splitted in two databses: prokaryote and eukaryote.
+
+
+.. class:: infomark page-header h2
+
+How it works
+
+.. csv-table:: 
+   :header: "Steps", "Description"
+   :widths: 5, 150
+   :class: table table-striped
+
+   "1", "`RDPClassifier &lt;https://rdp.cme.msu.edu/tutorials/classifier/RDPtutorial_RDP_classifier.html&gt;`_ is 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);*)."
+   "2", "`blastn+ &lt;http://blast.ncbi.nlm.nih.gov/&gt;`_ is used to find alignment between each OTU and the database. Only the bests hits with the same score has reported."
+   "3", "For each OTU with several blastn+ results a consensus is determined on each taxonomic level. If all the taxa in a taxonomic rank are identical the taxon name is reported otherwise *Multi-affiliation* is reported. By example, if you have an OTU with two corresponding sequences, the first is a *Bacteria;Proteobacteria;Gamma Proteobacteria;Enterobacteriales*, the second is a *Bacteria;Proteobacteria;Beta Proteobacteria;Methylophilales*, the consensus will be *Bacteria;Proteobacteria;Multi-affiliation;Multi-affiliation*."
+
+
+.. class:: infomark page-header h2
+
+Advices
+
+This tool can take large time. It is recommended to filter your abundance and your sequence file before this tool (see **FROGS Filters**).
+
+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.
+
+
+----
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+ </help>
+ <citations>
+ <citation type="doi">10.1186/1471-2105-10-421</citation>
+ <citation type="doi">10.1128/AEM.00062-07</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 affiliations_stat.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/affiliations_stat.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,178 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="1.1.0">
+ <description>Process some metrics on taxonomies.</description>
+        <requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+        <stdio> 
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>
+ affiliations_stat.py 
+     --input-biom $biom
+     --output-file $summary_file
+     --rarefaction-ranks $rarefaction_ranks
+     #if $affiliation.affiliation_type == "FROGS_blast"
+         --taxonomic-ranks Domain Phylum Class Order Family Genus Species
+      --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"
+     --taxonomic-ranks Domain Phylum Class Order Family Genus Species
+ --taxonomy-tag "rdp_taxonomy"
+ --bootstrap-tag "rdp_bootstrap"
+ #else
+ --taxonomic-ranks $affiliation.taxonomic_ranks
+ --taxonomy-tag "$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 "$affiliation.coverage_tag"
+ #end if
+ #end if
+ </command>
+ <inputs>
+ <!-- Files -->
+ <param format="biom1" name="biom" type="data" label="Abundance file" help="OTUs abundances and affiliations (format: BIOM)." optional="false" />
+ <!-- Parameters -->
+ <param name="rarefaction_ranks" type="text" label="Rarefaction ranks" help="The ranks that will be evaluated in rarefaction. Each rank is separated by one space." optional="false" value="Class Order Family Genus Species" size="80" />
+ <conditional name="affiliation">
+ <param name="affiliation_type" type="select" label="Affiliation processed" help="Select the type of affiliation processed. If your affiliation has been processed with an external tool: use 'Custom'.">
+ <option value="FROGS_blast" selected="true">FROGS blast</option>
+ <option value="FROGS_rdp">FROGS rdp</option>
+ <option value="custom">Custom</option>
+ </param>
+ <when value="FROGS_blast"></when>
+ <when value="FROGS_rdp"></when>
+ <when value="custom">
+ <param name="taxonomic_ranks" type="text" label="Taxonomic ranks" help="The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space." optional="false" value="Domain Phylum Class Order Family Genus Species" size="80" />
+ <param name="taxonomy_tag" type="text" label="Taxonomy tag" help="The metadata title in BIOM for the taxonomy." optional="false" value="taxonomy" size="20" />
+ <param name="bootstrap_tag" type="text" label="Bootstrap tag" help="The metadata title in BIOM for the taxonomy bootstrap." value="" size="20" />
+ <param name="identity_tag" type="text" label="Identity tag" help="The metadata tag used in BIOM file to store the alignment identity." value="" size="20" />
+ <param name="coverage_tag" type="text" label="Coverage tag" help="The metadata tag used in BIOM file to store the alignment OTUs coverage." value="" size="20" />
+ </when>
+ </conditional>
+ </inputs>
+ <outputs>
+ <data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="biom" value="references/04-affiliation.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" />
+ <!-- pas de parametre dans le formulaire pour multiple-tag, uniquement une option dans la ligne de commande -->
+ </conditional>
+ <output name="summary_file" file="references/06-affiliationsStat.html" compare="sim_size" delta="0" />
+ <!-- log-file option presente dans la ligne de commande dans le test.sh n'apparait pas du tout ici -->
+ </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 the quality of the affiliations.
+
+
+.. class:: infomark page-header h2
+
+Input/output
+
+.. class:: h3
+
+Input
+
+**Abundance file**:

+The abundance and affiliation of each OTUs in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_). 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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):

+  *-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: 650  
+
+  .. image:: static/images/FROGS_affiliation_stat_rarefaction.png
+    :height: 380
+    :width: 550
+
+  .. image:: static/images/FROGS_affiliation_stat_sunburst.png
+    :height: 380
+    :width: 430
+  
+  -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: 650
+
+  -Alignment distribution: display for affiliation methods with alignment the distribution of identity/covrage
+
+  .. image:: static/images/FROGS_affiliation_stat_alignment.png
+    :height: 380
+    :width: 650
+
+
+
+----
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+ </help>
+        <citations>
+                <citation type="doi">10.1093/bioinformatics/btx791</citation>
+                <citation type="doi">10.1128/AEM.01043-13</citation>
+                <citation type="doi">10.14806/ej.17.1.200</citation>
+                <citation type="doi">10.1093/bioinformatics/btr507</citation>
+        </citations>
+
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 biom_to_stdBiom.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_to_stdBiom.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,107 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="1.1.0">
+ <description>Converts a FROGS BIOM in fully compatible BIOM.</description>
+  <requirements>
+                <requirement type="package" version="2.0.1">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 $output_metadata 
+ </command>
+ <inputs>
+ <!-- Files -->
+ <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The FROGS BIOM file to convert (format: BIOM)." optional="false" />
+ </inputs>
+ <outputs>
+ <data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom"/>
+ <data format="tabular" name="output_metadata" label="${tool.name}: blast_metadata.tsv" from_work_dir="blast_metadata.tsv" />
+ </outputs>
+ <tests>
+ <test>
+ <param name="input_biom" value="references/04-affiliation.biom"/>
+ <output name="output_biom" value="references/08-affiliation_std.biom"/>
+ <output name="output_metadata" value="references/08-affiliation_multihit.tsv"/>
+ </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 problematic metadata 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 &lt;http://biom-format.org/&gt;`_).
+
+.. class:: h3
+
+Outputs
+
+**Abundance file**:
+
+ The abundance without the incompatible metadata (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+**Blast metadata file**:
+
+ The details for each alignment on clusters (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
+
+
+.. class:: infomark page-header h2
+
+How it works
+
+FROGS BIOM to std BIOM extracts the blast alignment metadata in a second file, write a BIOM usable in every tools using BIOM and defined the taxonomy provided by blast as main taxonomy.
+
+
+
+----
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 biom_to_tsv.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_to_tsv.xml Thu Oct 25 05:01:13 2018 -0400
[
@@ -0,0 +1,129 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_biom_to_tsv" name="FROGS BIOM to TSV" version="2.1.0">
+ <description>Converts a BIOM file in TSV file.</description>
+  <requirements>
+                <requirement type="package" version="2.0.1">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 $multi_affi_file
+               #end if   
+ </command>
+ <inputs>
+ <!-- Files -->
+ <param format="biom1" name="biom_file" type="data" label="Abundance file" help="The BIOM file to convert (format: BIOM)." optional="false" />
+ <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta). If you use this option the sequences will be add in TSV." optional="true" />
+ <!-- Parameters -->
+ <param name="extract_multi_align" type="boolean" label="Extract multi-alignments" help="If you have used FROGS affiliation on your data, you can extract information about multiple alignements in a second TSV." />
+ </inputs>
+ <outputs>
+ <data format="tabular" name="tsv_file" label="${tool.name}: abundance.tsv" from_work_dir="abundance.tsv"/>
+ <data format="tabular" name="multi_affi_file" label="${tool.name}: multi_hits.tsv" from_work_dir="multi_hits.tsv" >
+ <filter>extract_multi_align</filter>
+ </data>
+ </outputs>
+ <tests>
+ <test>
+ <param name="biom_file" value="references/04-affiliation.biom"/>
+ <param name="sequence_file" value="references/04-filters.fasta"/>
+ <param name="extract_multi_align" value="true"/>
+ <output name="tsv_file" value="references/07-biom2tsv.tsv"/>
+ <output name="multi_affi_file" value="references/07-biom2tsv.multi"/>
+ </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 &lt;http://biom-format.org/&gt;`_).
+
+**Sequence file [optional]**:
+
+The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+.. class:: h3
+
+Outputs
+
+**Abundance file**:
+
+ The abundance of each cluster in each sample and theirs metadata (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
+
+ 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 &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
+
+
+.. 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 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@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clustering.xml Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,178 @@\n+<?xml version="1.0"?>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<tool id="FROGS_clustering" name="FROGS Clustering swarm" version="2.3.0">\n+\t<description>Step 2 in metagenomics analysis : clustering.</description>\n+ \t<requirements>\n+                <requirement type="package" version="2.0.1">frogs</requirement>\n+        </requirements>\n+        <stdio>\n+                <exit_code range="1:" />\n+                <exit_code range=":-1" />\n+        </stdio>\n+\t<command>\n+\t\tclustering.py \n+\t\t                --nb-cpus $nb_cpus\n+\t\t                --distance $maximal_distance\n+\t\t                --input-fasta $sequence_file\n+\t\t                --input-count $count_file\n+\t\t                --output-biom $abundance_biom\n+\t\t                --output-fasta $seed_file\n+\t\t                --output-compo $swarms_composition\n+\t\t                $denoising     \n+\t</command>\n+\t<inputs>\n+\t\t<!-- Files -->\n+\t\t<param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta)." optional="false" />\n+\t\t<param format="tabular" name="count_file" type="data" label="Count file" help="It contains the count by sample for each sequence (format: TSV)." optional="false" />\n+\t\t<!-- Parameters -->\n+\t\t<param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" />\n+\t\t<param name="maximal_distance" type="integer" label="Aggregation distance" help="Maximum number of differences between sequences in each aggregation step." value="3" min="1" max="15" optional="false" />\n+\t\t<param name="denoising" type="boolean" checked="true" truevalue="--denoising" falsevalue="" label="Performe denoising clustering step?" help="If checked, clustering will be perform in two steps, first with distance = 1 and then with your input distance"/>\n+\t</inputs>\n+\t<outputs>\n+\t\t<data format="fasta" name="seed_file" label="${tool.name}: seed_sequences.fasta" from_work_dir="seeds.fasta"/>\n+\t\t<data format="biom1" name="abundance_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" />\n+\t\t<data format="tabular" name="swarms_composition" label="${tool.name}: swarms_composition.tsv" from_work_dir="swarms.tsv"/>\n+\t</outputs>\n+\t<tests>\n+\t\t<test>\n+\t\t\t<param name="sequence_file" value="references/01-prepro.fasta"/>\n+\t\t\t<param name="count_file" value="references/01-prepro.tsv"/>\n+\t\t\t<param name="maximal_distance" value="3"/>\n+\t\t\t<param name="denoising" value="true"/>\n+\t\t\t<output name="seed_file" file="references/02-clustering.fasta" compare="sim_size" delta="0" />\n+                        <!-- output name="abundance_biom" file="references/02-clustering.biom"  -->\n+                        <!-- Voila deux autres facon de comparer: (Mais ca ne marche pas dans ce cas car les fichiers g\xc3\xa9n\xc3\xa9r\xc3\xa9s par planemo sont vraiments diff\xc3\xa9rents compar\xc3\xa9 \xc3\xa0 nos test manuels (cf. /tmp/frogs-test-result-olivier /tmp/frogs-test-result-olivier2) -->\n+                        <!-- cf. https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests-test-output -->\n+\t\t\t<!--output name="abundance_biom" file="references/02-clustering.biom" compare="sim_size" delta="10"/-->                    \n+\t\t\t<!--output name="abundance_biom" file="references/02-clustering.biom" compare="diff" lines_diff="1"/-->\n+\t\t\t<output name="swarms_composition" file="references/02-clustering_'..b'inkage clustering on sequences.\n+\n+\n+.. class:: infomark page-header h2\n+\n+Inputs/Outputs\n+\n+.. class:: h3\n+\n+Inputs\n+\n+**Sequences file**:\n+\n+The sequence file with all samples sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_). These sequences are dereplicated: strictly identical sequence are represented only one and the initial count is kept in count file.\n+\n+The sequence ID must be "sequenceID;size=X" with X equal to the total abundance among all samples.\n+\n+*It corresponds to one output of FROGS Pre-process tools.*\n+\n+**Count file**:\n+\n+This file contains the count of all uniq sequences in each sample (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).\n+ \n+Example::\n+\n+     #id\tsplA\tsplB\n+     seq1\t1289\t2901\n+     seq2\t3415\t0\t\n+ \n+\n+.. class:: h3\n+\n+Outputs\n+\n+**Abundance file** (abundance.biom):\n+\n+ The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_). This format is widely used in metagenomic softwares.\n+\n+\n+**Clusters seeds** (seed_sequences.fasta):\n+\n+ The clusters representative sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).\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", "With denoising", "Without denoising"\n+   :widths: 5, 150, 150\n+   :class: table table-striped\n+\n+   "1", "Sorting the reads by their abundance", "Sorting the reads by their abundance"\n+   "2", "Clusters the reads (`Swarm &lt;https://github.com/torognes/swarm&gt;`_). The distance parameter is 1", "/"\n+   "3", "Sorting the pre-clusters by their abundance", "/"\n+   "4", "Clusters the pre-clusters (`Swarm &lt;https://github.com/torognes/swarm&gt;`_) with the distance you specify", "Clusters the reads (`Swarm &lt;https://github.com/torognes/swarm&gt;`_) with the distance you specify"\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\t\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+\t\n+.. class:: infomark page-header h2\n+\n+Advices\n+\n+The denoising step allows to build very fine clusters with minimal differences. In this case, the number of differences is equal at 1 between sequences of each crowns. 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.\n+\t\t\n+To have some metrics on your clusters, you can use the tool **FROGS Clusters Stat**.\n+\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs@inra.fr\n+\n+Repository: https://github.com/geraldinepascal/FROGS\n+\n+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf\n+\n+Depending on the help provided you can cite us in acknowledgements, references or both.\n+\t</help>\n+\t<citations>\n+\t\t<citation type="doi">10.7287/peerj.preprints.386v1</citation>\n+\t</citations>\n+</tool>\n'
b
diff -r 000000000000 -r 76c750c5f0d1 clusters_stat.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clusters_stat.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,128 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_clusters_stat" name="FROGS Clusters stat" version="1.4.0">
+ <description>Process some metrics on clusters.</description>
+  <requirements>
+                <requirement type="package" version="2.0.1">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}: summary.html" from_work_dir="summary.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="biom" value="references/04-affiliation.biom"/>
+ <output name="summary_file" value="references/05-clustersStat.html" 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
+
+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 &lt;http://biom-format.org/&gt;`_).
+
+The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format.
+
+.. class:: h3
+
+Output
+
+**Summary file** (summary.html):
+
+ Clusters metrics (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):

+ *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables
+
+ .. image:: static/images/FROGS_cluster_stat_clusterDistrib1.png
+    :height: 426
+    :width: 520
+
+ .. image:: static/images/FROGS_cluster_stat_clusterDistrib2.png
+    :height: 300
+    :width: 460
+   
+ *Sequences distributions* : describes the sequences distribution among clusters
+
+ .. image:: static/images/FROGS_cluster_stat_seq_dist.png
+    :height: 326
+    :width: 473
+
+ *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering &lt;http://en.wikipedia.org/wiki/Hierarchical_clustering&gt;`_ on samples abundance profile (distance method = `braycurtis &lt;http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis&gt;`_, 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@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 demultiplex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/demultiplex.xml Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,213 @@\n+<?xml version="1.0"?>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<tool id="FROGS_demultiplex" name="FROGS Demultiplex reads" version="2.0.0">\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="2.0.1">frogs</requirement>\n+                <requirement type="package" version="1.10">perl-io-zlib</requirement>\n+                <requirement type="package" version="0.20">perl-io-gzip</requirement>\n+                <requirement type="package">perl</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 $undemultiplexed_archive\n+\t</command>\n+\t<inputs>\n+\t\t<!-- Input file -->\n+\t\t<param format="tabular" name="barcode_file" type="data" label="Barcode file" help="This file describes barcodes and samples (one line by sample tabulated separated from barcode sequence(s)). See Help section" optional="false" />\n+\t\t\n+\t\t<conditional name="fastq_input">\n+\t      \t<param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single-end data">\n+\t      \t\t<option value="single">Single</option>\n+\t        \t<option value="paired">Paired</option>\n+\t        </param>\n+\t      \t<when value="paired">\n+\t        \t<param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" help="Specify dataset of your forward reads"/>\n+\t        \t<param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" help="Specify dataset of your reverse reads"/>\n+\t        </when>\n+\t        <when value="single">\n+\t        \t<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" help="Specify dataset of your single end reads"/>\n+\t      \t</when>\n+\t      \t</conditional>\n+\n+\t\t<!-- Option -->\n+\t\t<param name="mismatches" type="integer" label="Barcode mismatches" help="Number of mismatches allowed in barcode" value="0" optional="false" />\n+\t\t<param name="end" type="select" label="Barcode on which end ?" help="The barcode is placed either at the beginning of the forward end or of the reverse end or both?">\n+\t\t\t<option value="bol" selected="true">Forward</option>\n+\t\t\t<option value="eol">Reverse</option>\n+\t\t\t<option value="both">Both ends</option>\n+\t\t</param>\n+\t</inputs>\n+\t<outputs>\n+\t\t<data name="demultiplexed_archive" format="tar" label="${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+        <t'..b'idths: 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+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/demultiplex_barcode.png\n+   :height: 18\n+   :width: 286\n+\n+FASTQ : \n+ Text file describing biological sequences in a 4 line format: \n+\t\t\n+ -first line starts by "@" corresponds to the sequence identifier and optionally the sequence description\n+ \n+ -second line is the sequence itself\n+ \n+ -third line is a "+" following by the sequence identifier or not depending on the version\n+ \n+ -fourth line is the quality sequence, one code per base. The code depends on its version and the sequencer\n+ \n+`Click here for more details on the fastq format &lt;https://en.wikipedia.org/wiki/FASTQ_format&gt;`_\n+\n+Example of fastq read corresponding to the previous barcode file  \n+\n+.. image:: static/images/demultiplex_fastq_ex.png\n+   :height: 57\n+   :width: 420\n+\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 use the "unmatched" or "ambiguous" sequence file 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 &lt;https://github.com/indraniel/sff2fastq&gt;`_ or sff_to_fastq (installable in Galaxy)\n+\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs@inra.fr\n+\n+Repository: https://github.com/geraldinepascal/FROGS\n+\n+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf\n+\n+Depending on the help provided you can cite us in acknowledgements, references or both.\n+\t</help>\n+\t<citations>\n+\t\t<citation type="doi">10.7287/peerj.preprints.386v1</citation>\n+\t</citations>\n+</tool>\n'
b
diff -r 000000000000 -r 76c750c5f0d1 filters.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filters.xml Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,285 @@\n+<?xml version="1.0"?>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<tool id="FROGS_filters" name="FROGS Filters" version="1.3.0">\n+\t<description>Filters OTUs on several criteria.</description>\n+        <requirements>\n+                <requirement type="package" version="2.0.1">frogs</requirement>\n+        </requirements>\n+        <stdio> \n+                <exit_code range="1:" />\n+                <exit_code range=":-1" />\n+        </stdio>\n+\n+\t<command>\n+\t\tfilters.py\n+\t\t\t--nb-cpus $nb_cpu \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+\t\t\t#if $contaminations_filter.contaminations_filter_isApplied == "yes"\n+\t\t\t\t--contaminant $contaminations_filter.contaminants_db\n+\t\t\t#end if\t      \n+\t\t\t\n+\t\t\t#if $abundance_filters.abundance_filters_areApplied == "yes"\n+\t\t\t\t#if $abundance_filters.min_sample_presence\n+\t\t\t\t\t--min-sample-presence $abundance_filters.min_sample_presence\n+\t\t\t\t#end if\n+\t\t\t\t#if $abundance_filters.min_abundance\n+\t\t\t\t\t--min-abundance $abundance_filters.min_abundance\n+\t\t\t\t#end if\n+\t\t\t\t#if $abundance_filters.nb_biggest_otu\n+\t\t\t\t\t--nb-biggest-otu $abundance_filters.nb_biggest_otu\n+\t\t\t\t#end if\n+\t\t\t#end if\n+\n+\t\t\t#if $RDP_filters.RDP_filters_areApplied == "yes"\n+\t\t\t\t--min-rdp-bootstrap $RDP_filters.rdp_rank:$RDP_filters.rdp_bootstrap\n+\t\t\t#end if\n+\t\t\n+\t\t\t#if $blast_filters.blast_filters_areApplied == "yes"\n+\t\t\t\t#if $blast_filters.min_blast_length\n+\t\t\t\t\t--min-blast-length $blast_filters.min_blast_length\n+\t\t\t\t#end if\n+\t\t\t\t#if $blast_filters.max_blast_evalue\n+\t\t\t\t\t--max-blast-evalue $blast_filters.max_blast_evalue\n+\t\t\t\t#end if\n+\t\t\t\t#if $blast_filters.min_blast_identity\n+\t\t\t\t\t--min-blast-identity $blast_filters.min_blast_identity\n+\t\t\t\t#end if\n+\t\t\t\t#if $blast_filters.min_blast_coverage\n+\t\t\t\t\t--min-blast-coverage $blast_filters.min_blast_coverage\n+\t\t\t\t#end if\n+\t\t\t#end if\n+\t</command>\n+\t<inputs>\n+\t\t<!-- Files -->\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+\n+   \t\t<!-- Parameters -->\n+\t\t<param name="nb_cpu" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1"></param>\n+\t\t\n+\t\t<conditional name="abundance_filters">\n+\t\t\t<param name="abundance_filters_areApplied" type="select" label=" *** THE FILTERS ON OTUS IN SAMPLES, OTUS SIZE and SEQUENCE PERCENTAGE" help="If you want to filter OTUs on their abundance and occurrence." >\n+\t\t\t\t<option value="no">No filters</option>\n+\t\t\t\t<option value="yes">Apply filters</option>\n+\t\t\t</param>\n+\t\t\t<when value="no"></when>\n+\t\t\t<when value="yes">\n+\t\t\t\t<param name="min_sample_presence" type="integer" optional="true" label="Minimum number of samples" size="5" help="Fill the field only if you want this treatment. Keep OTU present in at least this number of samples." />\n+\t\t\t\t<param name="min_abundance" type="text" optional="true" label="Minimum proportion/number of sequences to keep OTU" size="5" help="Fill the field only if you want this treatment. Use decimal notation for proportion (example: 0.01 for keep OTU with at least 1% of all sequences) ; Use integer notation for nu'..b' file="references/04-filters.fasta" />\n+\t\t\t<output name="output_excluded" file="references/04-filters.excluded" />\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 :\n+\n+ -The abundance and the occurence of OTUs: presence in samples, OTU size and maximum number of OTUs.\n+\n+ -The taxonomic affiliation produced by RDP: rank and bootstrap.\n+\n+ -The taxonomic affiliation produced by Blast: e-value, percentage of identity, percentage of coverage and alignment length.\n+ \n+ -Contamination: phiX a control added in Illumina sequencing technologies.\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 &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).\n+\n+**Abundance file**:\n+\n+The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).\n+\n+\n+.. class:: h3\n+\n+Outputs\n+\n+**Sequence file** (sequences.fasta):\n+\n+ The sequences after filtering (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).\n+\n+**Abundance file** (abundance.biom):\n+\n+ The abundance after filtering (format `BIOM &lt;http://biom-format.org/&gt;`_).\n+\n+**Excluded file** (excluded.txt):\n+\n+ The list of the OTUs deleted by filters (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).\n+\n+**Summary file** (report.html):\n+\n+ The filters and the number of removed sequences (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).\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 an list of the OTUs to remove is generated."\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 &lt;http://www.nature.com/nmeth/journal/v10/n1/abs/nmeth.2276.html&gt;`_ ).\n+\n+If you use "FROGS Filters" before "FROGS Affiliation", the filters on RDP and Blast are useless.\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs@inra.fr\n+\n+Repository: https://github.com/geraldinepascal/FROGS\n+\n+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf\n+\n+Depending on the help provided you can cite us in acknowledgements, references or both.\n+\t</help> \n+        <citations>\n+                <citation type="doi">10.1093/bioinformatics/btx791</citation>\n+                <citation type="doi">10.1128/AEM.01043-13</citation>\n+                <citation type="doi">10.14806/ej.17.1.200</citation>\n+                <citation type="doi">10.1093/bioinformatics/btr507</citation>\n+        </citations>\n+\n+</tool>\n'
b
diff -r 000000000000 -r 76c750c5f0d1 normalisation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/normalisation.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,122 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="2.0.0">
+        <description>Normalize OTUs abundance.</description>
+        <requirements>
+                <requirement type="package" version="2.0.1">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 $summary_file 
+ </command>
+ <inputs>
+ <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalize (format: fasta)." />
+ <param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalize (format: BIOM)." />
+ <param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
+ </inputs>
+ <outputs>
+ <data format="fasta" name="output_fasta" label="${tool.name}: normalized.fasta" from_work_dir="normalized.fasta" />
+ <data format="biom1" name="output_biom" label="${tool.name}: normalized.biom" from_work_dir="normalized.biom" />
+ <data format="html" name="summary_file" label="${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-affiliation.biom"/>
+                 <param name="num_reads" value="100"/>
+                 <output name="summary_file" file="references/normalisation_report.html" 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
+
+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 &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+**Abundance file**:

+The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+.. class:: h3
+
+Outputs
+
+**Sequence file** (normalised_seed.fasta):
+
+ The normalised sequences file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+**Abundance file** (normalised_abundance.biom):
+
+ The normalised abundance file (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+**Summary file** (report.html):
+
+ Information about discarded data (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
+
+
+.. 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@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations> 
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 preprocess.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess.xml Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,389 @@\n+<?xml version="1.0"?>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<tool id="FROGS_preprocess" name="FROGS Pre-process" version="2.0.1">\n+        <description>Step 1 in metagenomics analysis: denoising and dereplication.</description>\n+ \t<requirements>\n+                <requirement type="package" version="2.0.1">frogs</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 $nb_cpus\n+\t\t#if $sequencer_type.sequencer_selected == "illumina"\n+\t\t    --min-amplicon-size $sequencer_type.min_amplicon_size --max-amplicon-size $sequencer_type.max_amplicon_size \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    --min-amplicon-size $sequencer_type.min_amplicon_size --max-amplicon-size $sequencer_type.max_amplicon_size \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_contiged"\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            --expected-amplicon-size $sequencer_type.input_type.archive_type.expected_amplicon_size \n+\t            --mismatch-rate $sequencer_type.input_type.archive_type.mm_rate\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_contiged"\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}\n+\t\t            #end for\n+\t\t            --R1-size $sequencer_type.input_type.files_by_samples_type.R1_size --R2-size $sequencer_type.input_type.files_by_samples_type.R2_size \n+\t\t            --expected-amplicon-size $sequencer_type.input_type.files_by_samples_type.expected_amplicon_size \n+\t\t            --mismatch-rate $sequencer_type.input_type.files_by_samples_type.mm_rate\n+\t\t        #end if\n+\t\t    #else\n+\t\t        --input-R1 \n+\t\t        #for $current in $sequencer_typ'..b'hsSamples.png \n+     :height: 350\n+     :width: 676 \n+\n+.. class:: infomark page-header h2\n+\n+How it works\n+\n+.. csv-table:: \n+   :header: "Steps", "Illumina", "454"\n+   :widths: 5, 150, 150\n+   :class: table table-striped\n+\n+   "1", "For un-merged data: merges R1 and R2 with a maximum of M% mismatch in the overlaped region (`FLASh &lt;http://ccb.jhu.edu/software/FLASH/&gt;`_). By default M is set to 10%", "/"\n+   "2", "Filters merged sequences on their length which must be range between \'Minimum amplicon size\' and \'Maximum amplicon size\'", "/"\n+   "3", "If sequencing protocol is the illumina standard protocol : Removes sequences where the two primers are not present and then remove primers in the remaining sequence (`cutadapt &lt;http://cutadapt.readthedocs.org/en/latest/guide.html&gt;`_). The primer search accepts 10% of differences", "Removes sequences where the two primers are not present, removes primers sequence and reverse complement the sequences on strand -  (`cutadapt &lt;http://cutadapt.readthedocs.org/en/latest/guide.html&gt;`_). The primer search accepts 10% of differences"\n+   "4", "Filters sequences on their length and with ambiguous nucleotides", "the tool removes sequences with at least one homopolymer with more than seven nucleotides and with a distance of less than or equal to 10 nucleo-tides between two poor quality positions, i.e. with a Phred quality score lesser than 10" \n+   "5", "Dereplicates sequences", "Dereplicates sequences"\n+\n+\n+.. class:: infomark page-header h2\n+\n+Advices/details on parameters\n+\n+.. class:: h3\n+\n+Primers parameters\n+\n+The (`Kozich et al. 2013 &lt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/&gt;`_ ) 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: ATGCC\n+ \n+ Value for parameter 3\' primer: ATTTCAG\n+\n+.. class:: h3\n+\n+Amplicons sizes parameters\n+\n+ The two following images show two examples of perfect values fors sizes parameters.\n+\n+ .. image:: static/images/FROGS_preprocess_ampliconSize_unimodal.png\n+    :height: 415\n+    :width: 676\n+ \n+ .. image:: static/images/FROGS_preprocess_ampliconSize_multimodal.png\n+    :height: 415\n+    :width: 676\n+\n+ Don\'t worry the "Expected amplicon size" does not need to be very accurate.\n+\n+.. class:: h3\n+\n+If the filter \'overlapped\' reduce drasticaly the number of sequences:\n+\n+ In un-merged Illumina data, the reduction of dataset by the overlapped 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 &lt;http://www.bioinformatics.babraham.ac.uk/projects/fastqc/&gt;`_) you can try to cut the end of your sequences and relaunch the preprocess tool. \n+ You can either raise the mismatch percent in the overlapped region, but not too much!\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs@inra.fr\n+\n+Repository: https://github.com/geraldinepascal/FROGS\n+\n+Please cite the FROGS Publication: *Frederic Escudie, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, Katia Vidal, Sarah Maman, Guillermina Hernandez-Raquet, Sylvie Combes, Geraldine Pascal; FROGS: Find, Rapidly, OTUs with Galaxy Solution, Bioinformatics, , btx791,* https://doi.org/10.1093/bioinformatics/btx791\n+\n+Depending on the help provided you can cite us in acknowledgements, references or both.\n+\t</help> \n+\t<citations>\n+\t\t<citation type="doi">10.1093/bioinformatics/btx791</citation>\n+\t\t<citation type="doi">10.1128/AEM.01043-13</citation>\n+\t\t<citation type="doi">10.14806/ej.17.1.200</citation>\n+\t\t<citation type="doi">10.1093/bioinformatics/btr507</citation>\n+\t</citations>\n+</tool>\n'
b
diff -r 000000000000 -r 76c750c5f0d1 r_alpha_diversity.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/r_alpha_diversity.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,128 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="1.0.0">
+ <description>with richness plot</description>
+ <requirements>
+ <requirement type="package" version="2.0.1">frogs</requirement>
+ </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>r_alpha_diversity.py
+                                             --rdata $data 
+                                             --varExp $varExp
+                                             --alpha-measures $measures
+                                             --alpha-out $alphaD 
+                                             --html $html
+ </command>
+    <inputs>
+ <!-- Files -->
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This file is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ <!-- Parameters -->
+ <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>        
+     <param name="measures" type="select" label="The alpha diversity indices to compute" multiple="true" display="checkboxes">
+             <option value="Observed" selected="True">Observed</option>
+             <option value="Chao1" selected="True">Chao1</option>
+             <option value="Shannon" selected="True">Shannon</option>
+             <option value="InvSimpson" selected="True">InvSimpson</option>
+             <option value="Simpson">Simpson</option>
+             <option value="ACE">ACE</option>
+             <option value="Fisher">Fisher</option>
+        </param>
+ </inputs>
+ <outputs>
+ <data format="tabular" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/>
+ <data format="html" name="html" label="${tool.name}: alpha_diversity.html" from_work_dir="alpha_diversity.html"/>
+ </outputs>
+        <tests>
+                <test>
+                        <param name="data" value="references/11-phylo_import.Rdata" />
+                        <param name="varExp" value="EnvType" />
+                        <param name="measures" value="Observed,Chao1,Shannon" />
+                        <output name="alphaD" file="references/13-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 &lt;https://joey711.github.io/phyloseq/&gt;`_ 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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): the review of richness plots and rarefaction curves.
+
+.. image:: static/images/phyloseq_plot_richness.png 
+     :height: 400
+     :width: 525 
+
+.. image:: static/images/phyloseq_plot_richness_box.png
+     :height: 400
+     :width: 499
+     
+.. image:: static/images/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/phyloseq_alpha_diversity_table.png
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 r_beta_diversity.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/r_beta_diversity.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,145 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool name="FROGSSTAT Phyloseq Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="1.0.0">
+ <description>distance matrix</description>
+ <requirements>
+ <requirement type="package" version="2.0.1">frogs</requirement>
+ </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>r_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 $html
+ </command>
+    <inputs>
+ <!-- Files -->
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ <!-- Parameters -->
+        <param name="varExp" type="text" label="Grouping variable" help="Experimental variable used to group samples (Treatment, Host type, etc)." optional="false" value="" size="20">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="methods" type="select" label="The methods of beta diversity" help="N.B. if the tree is not available in your RData, you cannot choose Unifrac or Weighted Unifrac" multiple="true" display="checkboxes">
+            <option value="unifrac" selected="False">Unifrac</option>
+            <option value="wunifrac" selected="False">Weighted Unifrac</option>
+            <option value="bray" selected="False">Bray-Curtis</option>
+            <option value="cc" selected="False">Jaccard</option>
+        </param>
+        <param type="text" name="other_method" label="Other method" help="The other methods of beta diversity that you want to use (comma separated value). c.f. details below." optional="false" value="" size="40"/>
+    </inputs>
+ <outputs>
+        <data format="html" name="html" label="${tool.name}: beta_diversity" from_work_dir="beta_diversity.html">
+            <discover_datasets pattern="__designation__" ext="tabular" directory="BetaMatrix" visible="true"/>
+        </data>
+ </outputs>
+        <tests>
+                <test>
+                        <param name="data" value="references/11-phylo_import.Rdata" />
+                        <param name="varExp" value="EnvType" />
+                        <param name="methods" value="cc,unifrac" />
+                        <!--output name="html" file="references/14-phylo_beta_div.html" compare="sim_size" delta="0" /-->
+                        <output name="html">
+                                <assert_contents>
+                                        <has_text_matching expression="html\sxmlns=.*" />
+                                        <has_text_matching expression="Phyloseq\s+\d+\.\d+\.\d+" />
+                                </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 &lt;https://joey711.github.io/phyloseq/&gt;`_ 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 &lt;https://www.bioconductor.org/packages/devel/bioc/manuals/phyloseq/man/phyloseq.pdf&gt;`_ .
+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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
+
+The review of beta diversity with heatmap plots:
+
+.. image:: static/images/phyloseq_beta_diversity.png 
+     :height: 609
+     :width: 800 
+
+
+**beta diversity matrix** (format tabular):
+The distance matrix of beta diversity.
+
+ .. image:: static/images/phyloseq_beta_diversity_matrix.png 
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 r_clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/r_clustering.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,121 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="1.0.0">
+ <description>of samples using different linkage methods</description>
+ <requirements>
+ <requirement type="package" version="2.0.1">frogs</requirement>
+ </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>r_clustering.py 
+                                               --html $html 
+                                               --rdata $data 
+                                               --varExp $varExp 
+                                               --distance-matrix $method
+ </command>
+    <inputs>
+ <!-- Files -->
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ <!-- Parameters -->
+ <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ </inputs>
+ <outputs>
+ <data format="html" name="html" label="${tool.name}: clustering.html" from_work_dir="clustering.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="data" value="references/11-phylo_import.Rdata"/>
+ <param name="varExp" value="EnvType"/>
+ <param name="method" value="references/Unifrac.tsv"/>
+ <!--output name="html" file="references/16-phylo_structure.html" compare="sim_size" delta="0" /-->
+                        <output name="html">
+                                <assert_contents>
+                                        <has_text_matching expression="html\sxmlns=.*" />
+                                        <has_text_matching expression="Phyloseq\s+\d+\.\d+\.\d+" />
+                                </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 &lt;https://joey711.github.io/phyloseq/&gt;`_ 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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
+
+.. container:: row
+
+ .. image:: static/images/phyloseq_clustering_ward.png 
+   :height: 576
+   :width: 768
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 r_composition.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/r_composition.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,151 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="1.0.0">
+ <description>with bar plot and composition plot</description>
+        <requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+        <stdio> 
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>r_composition.py 
+                                              --rdata $data 
+                                              --varExp $varExp 
+                                              --taxaRank1 $taxaRank1 
+                                              --taxaSet1 $taxaSet1 
+                                              --taxaRank2 $taxaRank2 
+                                              --numberOfTaxa $numberOfTaxa
+                                              --html $html 
+ </command>
+    <inputs>
+ <!-- Files -->
+     <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>
+ <!-- Parameters -->
+ <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.html" from_work_dir="composition.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="data" value="references/11-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" file="references/12-phylo_composition.html" compare="sim_size" delta="0" /-->
+ <output name="html">
+ <assert_contents>
+         <has_text_matching expression="html\sxmlns=.*" />
+         <has_text_matching expression="application/json.*Sample: BHT0.LOT01" />
+ </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 &lt;https://joey711.github.io/phyloseq/&gt;`_ 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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): data composition plots.
+
+Bar plot of OTUs is colored with aggregated taxonomic level *i.e* "Phylum" :
+
+ .. image:: static/images/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: 5 
+
+ .. image:: static/images/phyloseq_composition_plot.png 
+     :height: 644
+     :width: 800 
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+
+ </help>
+        <citations>
+                <citation type="doi">10.1093/bioinformatics/btx791</citation>
+                <citation type="doi">10.1128/AEM.01043-13</citation>
+                <citation type="doi">10.14806/ej.17.1.200</citation>
+                <citation type="doi">10.1093/bioinformatics/btr507</citation>
+        </citations>
+
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 r_import_data.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/r_import_data.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,138 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="1.0.0">
+ <description>from 3 files: biomfile, samplefile, treefile </description>
+  <requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>r_import_data.py --biomfile $biomfile
+                                                   #if $samplefile
+                                                      --samplefile $samplefile 
+                                                   #end if
+                                                      --treefile $treefile 
+                                                      --ranks "$ranks"
+                                                #if $normalization
+                                                      --normalization
+                                                   #end if
+                                                      --html $html 
+                                                      --rdata $data
+ </command>
+    <inputs>
+ <!-- Files -->
+ <param format="biom1" name="biomfile" type="data" label="Standard biom file" help="The file contains the  OTU informations (format: biom1)." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        
+ <param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false">
+            <validator type="empty_field" message="This parameter is required." />                
+        </param>
+        
+ <param format="nhx" name="treefile" type="data" label="Tree file" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" />
+        
+        <!-- Parameters -->
+ <param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space."  value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/>
+ <param name="normalization" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before analysis." optional="false" /> 
+ </inputs>
+ <outputs>
+ <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/>
+ <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="biomfile" value="references/chaillou.biom"/>
+ <param name="samplefile" value="references/sample_metadata.tsv"/>
+ <param name="treefile" value="references/tree.nwk"/>
+ <output name="data" value="references/11-phylo_import.Rdata"/>
+ </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 &lt;https://joey711.github.io/phyloseq/&gt;`_ object.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**OTU biom file**:
+
+The OTU biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
+This file is the result of FROGS BIOM to std BIOM.
+The example of biom file: 
+
+  .. image:: static/images/biomfile.png 
+     :height: 30
+     :width: 733 
+
+**Newick file** (tree.nwk):
+
+Newick file (format `nxh &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_) is the result of FROGS Tree:
+
+  .. image:: static/images/nwk_treefile.png
+
+**Sample file**:
+The file contains the conditions of experiment with sample ID in the first column:
+  
+  .. image:: static/images/phyloseq_samplefile.png 
+     :height: 115
+     :width: 369
+      
+.. class:: h3
+
+Output
+
+**Html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The summary of phyloseq object.
+  
+  .. image:: static/images/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@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 r_manova.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/r_manova.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,115 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="1.0.0">
+        <description>perform Multivariate Analysis of Variance (MANOVA)</description>
+ <requirements>
+ <requirement type="package" version="2.0.1">frogs</requirement>
+ </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>r_manova.py 
+                                    --rdata $data
+                                    --varExp "$varExp"
+                                    --distance-matrix $method
+                                    --html $html
+ </command>
+    <inputs>
+ <!-- Files -->
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ <!-- Parameters -->
+ <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+    </inputs>
+ <outputs>
+ <data format="html" name="html" label="${tool.name}: manova.html" from_work_dir="manova.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="data" value="references/11-phylo_import.Rdata"/>
+ <param name="varExp" value="EnvType"/>
+ <param name="method" value="references/Unifrac.tsv"/>
+ <!--output name="html" file="references/17-phylo_structure.html" compare="sim_size" delta="0" /-->
+                        <output name="html">
+                                <assert_contents>
+                                        <has_text_matching expression="html\sxmlns=.*" />
+                                        <has_text_matching expression="Phyloseq\s+\d+\.\d+\.\d+" />
+                                </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 &lt;https://joey711.github.io/phyloseq/&gt;`_ and `vegan &lt;https://cran.r-project.org/web/packages/vegan/index.html&gt;`_ 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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The review of Manova test.
+
+.. image:: static/images/phyloseq_manova.png 
+     
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 r_structure.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/r_structure.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,131 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool name="FROGSSTAT Phyloseq Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="1.0.0">
+ <description>with heatmap plot and ordination plot</description>
+ <requirements>
+ <requirement type="package" version="2.0.1">frogs</requirement>
+ </requirements>
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+ <command>r_structure.py 
+                                         --html $html
+                                         --rdata $data
+                                         --varExp $varExp
+                                         --ordination-method $method
+                                         --distance-matrix $distance
+ </command>
+    <inputs>
+ <!-- Files -->
+     <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data Tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="distance" format="tabular" type="data" label="The beta diversity distance matrix file" help="These file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ <!-- Parameters -->
+ <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ <param name="method" type="select" label="Ordination method">
+ <option value="MDS" >MDS/PCoA</option>
+ <option value="NMDS" >NMDS</option>
+            <option value="DPCoA" >DPCoA</option>
+        </param>
+ </inputs>
+ <outputs>
+ <data format="html" name="html" label="${tool.name}: structure.html" from_work_dir="structure.html"/>
+ </outputs>
+        <tests>
+                <test>
+                        <param name="data" value="references/11-phylo_import.Rdata" />
+                        <param name="varExp" value="EnvType" />
+                        <param name="method" value="MDS" />
+                        <param name="distance" value="references/Unifrac.tsv" />
+                        <!--output name="html" file="references/15-phylo_structure.html" compare="sim_size" delta="10" /-->
+                 <output name="html">
+                                <assert_contents>
+                                        <has_text_matching expression="html\sxmlns=.*" />
+                                        <has_text_matching expression="application/json.*DesLardons" />
+                                </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 &lt;https://joey711.github.io/phyloseq/&gt;`_ and customized R function, this tool constructs heatmap plot and ordination plot with the `ordination methods &lt;https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html#ordination-methods&gt;`_ 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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
+
+The review of data structure with an ordination plot and with an heatmap plot:
+
+.. image:: static/images/phyloseq_plot_sample_ellipse.png 
+     :height: 343
+     :width: 450
+
+.. image:: static/images/phyloseq_plot_heatmap_red.png 
+     :height: 343
+     :width: 450
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 remove_chimera.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/remove_chimera.xml Thu Oct 25 05:01:13 2018 -0400
[
@@ -0,0 +1,178 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="1.3.0">
+ <description>Step 3 in metagenomics analysis : Remove PCR chimera in each sample.</description>
+  <requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>
+ remove_chimera.py 
+                 --nb-cpus $nb_cpus
+                 --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 $out_abundance_count
+                 #end if
+ </command>
+ <inputs>
+ <!-- Files -->
+ <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta)." optional="false" />
+ <conditional name="abundance_type">
+ <param name="abundance_type_selected" type="select" label="Abundance type" help="Select the type of file where the abundance of each sequence by sample is stored.">
+ <option value="biom" selected="true">BIOM file</option>
+ <option value="count">TSV file</option>
+ </param>
+ <when value="biom">
+ <param format="biom1" name="abundance_biom" type="data" label="Abundance file" help="It contains the count by sample for each sequence." optional="false" />
+ </when>
+ <when value="count">
+ <param format="tabular" name="abundance_count" type="data" label="Count file" help="It contains the count by sample for each sequence (see below)." optional="false" />
+ </when>
+ </conditional>
+ <!-- Parameters -->
+ <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" />
+ <!--
+ <param name="size_separator" type="text" label="Size separator" help="Fill this input only if the IDs of sequences in fasta store the abundance as suffix. Example: 'Cluster_1;size=10' => ';size='" value="" optional="true" />
+ -->
+ </inputs>
+ <outputs>
+ <data format="fasta" name="non_chimera_fasta" label="${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.fasta"/>
+ <conditional name="abundance_type">
+ <param name="abundance_type_selected" value="biom"/>
+ <param name="abundance_biom" value="references/02-clustering.biom" />
+ </conditional>
+ <output name="non_chimera_fasta" file="references/03-chimera.fasta"/>
+ </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 &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+**Abundance file**:

+ The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+OR
+
+ The abundance of each sequence in each sample (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_). This type of file is produced by *FROGS pre-process*.

+ Example::
+
+     #id splA splB
+     seq1 1289 2901
+     seq2 3415 0
+
+.. class:: h3
+
+Outputs
+
+**Sequence file** (non_chimera.fasta):
+
+ The sequence file with only non-chimera (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+**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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
+
+
+.. 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 &lt;https://github.com/torognes/vsearch&gt;`_)."
+   "3", "Remove the sequences identify as chimera in all samples where they are present."
+
+
+----
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
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diff -r 000000000000 -r 76c750c5f0d1 test-data/bergeyTrainingTree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bergeyTrainingTree.xml Thu Oct 25 05:01:13 2018 -0400
[
@@ -0,0 +1,53 @@
+<trainsetNo>1</trainsetNo><version>null</version><modversion>null</modversion><file>bergeyTrainingTree</file>
+<TreeNode name="Root" taxid="0" rank="rootrank" parentTaxid="-1" leaveCount="30" genusIndex="-1"></TreeNode>
+<TreeNode name="Bacteria [id:3]" taxid="3" rank="domain" parentTaxid="0" leaveCount="30" genusIndex="-1"></TreeNode>
+<TreeNode name="Actinobacteria [id:400]" taxid="400" rank="phylum" parentTaxid="3" leaveCount="30" genusIndex="-1"></TreeNode>
+<TreeNode name="Acidimicrobiia [id:401]" taxid="401" rank="class" parentTaxid="400" leaveCount="30" genusIndex="-1"></TreeNode>
+<TreeNode name="Acidimicrobiales [id:402]" taxid="402" rank="order" parentTaxid="401" leaveCount="30" genusIndex="-1"></TreeNode>
+<TreeNode name="Sva0996 marine group [id:417]" taxid="417" rank="family" parentTaxid="402" leaveCount="1" genusIndex="-1"></TreeNode>
+<TreeNode name="unknown genus [id:1000000001]" taxid="1000000001" rank="genus" parentTaxid="417" leaveCount="1" genusIndex="-1"></TreeNode>
+<TreeNode name="unidentified bacterium wb1_P06 [id:1000000043]" taxid="1000000043" rank="species" parentTaxid="1000000001" leaveCount="1" genusIndex="0"></TreeNode>
+<TreeNode name="OM1 clade [id:415]" taxid="415" rank="family" parentTaxid="402" leaveCount="7" genusIndex="-1"></TreeNode>
+<TreeNode name="Candidatus Actinomarina [id:416]" taxid="416" rank="genus" parentTaxid="415" leaveCount="2" genusIndex="-1"></TreeNode>
+<TreeNode name="unknown species [id:1000000003]" taxid="1000000003" rank="species" parentTaxid="416" leaveCount="1" genusIndex="1"></TreeNode>
+<TreeNode name="Candidatus Actinomarina minuta [id:1000000059]" taxid="1000000059" rank="species" parentTaxid="416" leaveCount="1" genusIndex="2"></TreeNode>
+<TreeNode name="unknown genus [id:1000000008]" taxid="1000000008" rank="genus" parentTaxid="415" leaveCount="5" genusIndex="-1"></TreeNode>
+<TreeNode name="microbial mat metagenome [id:1000000034]" taxid="1000000034" rank="species" parentTaxid="1000000008" leaveCount="1" genusIndex="3"></TreeNode>
+<TreeNode name="bacterium WH6-7 [id:1000000011]" taxid="1000000011" rank="species" parentTaxid="1000000008" leaveCount="1" genusIndex="4"></TreeNode>
+<TreeNode name="unidentified bacterium wb1_G04 [id:1000000041]" taxid="1000000041" rank="species" parentTaxid="1000000008" leaveCount="1" genusIndex="5"></TreeNode>
+<TreeNode name="unidentified bacterium wb1_J07 [id:1000000044]" taxid="1000000044" rank="species" parentTaxid="1000000008" leaveCount="1" genusIndex="6"></TreeNode>
+<TreeNode name="unknown species [id:1000000009]" taxid="1000000009" rank="species" parentTaxid="1000000008" leaveCount="1" genusIndex="7"></TreeNode>
+<TreeNode name="Acidimicrobiaceae [id:403]" taxid="403" rank="family" parentTaxid="402" leaveCount="12" genusIndex="-1"></TreeNode>
+<TreeNode name="CL500-29 marine group [id:405]" taxid="405" rank="genus" parentTaxid="403" leaveCount="4" genusIndex="-1"></TreeNode>
+<TreeNode name="bacterium enrichment culture clone B213(2011) [id:1000000054]" taxid="1000000054" rank="species" parentTaxid="405" leaveCount="1" genusIndex="8"></TreeNode>
+<TreeNode name="bacterium enrichment culture clone B97(2011) [id:1000000056]" taxid="1000000056" rank="species" parentTaxid="405" leaveCount="1" genusIndex="9"></TreeNode>
+<TreeNode name="unknown species [id:1000000000]" taxid="1000000000" rank="species" parentTaxid="405" leaveCount="1" genusIndex="10"></TreeNode>
+<TreeNode name="marine metagenome [id:1000000048]" taxid="1000000048" rank="species" parentTaxid="405" leaveCount="1" genusIndex="11"></TreeNode>
+<TreeNode name="Acidimicrobium [id:404]" taxid="404" rank="genus" parentTaxid="403" leaveCount="1" genusIndex="-1"></TreeNode>
+<TreeNode name="unknown species [id:1000000047]" taxid="1000000047" rank="species" parentTaxid="404" leaveCount="1" genusIndex="12"></TreeNode>
+<TreeNode name="Ferrithrix [id:407]" taxid="407" rank="genus" parentTaxid="403" leaveCount="3" genusIndex="-1"></TreeNode>
+<TreeNode name="actinobacterium BGR 74 [id:1000000024]" taxid="1000000024" rank="species" parentTaxid="407" leaveCount="1" genusIndex="13"></TreeNode>
+<TreeNode name="unknown species [id:1000000006]" taxid="1000000006" rank="species" parentTaxid="407" leaveCount="1" genusIndex="14"></TreeNode>
+<TreeNode name="actinobacterium BGR 77 [id:1000000021]" taxid="1000000021" rank="species" parentTaxid="407" leaveCount="1" genusIndex="15"></TreeNode>
+<TreeNode name="Ferrimicrobium [id:406]" taxid="406" rank="genus" parentTaxid="403" leaveCount="2" genusIndex="-1"></TreeNode>
+<TreeNode name="Ferrimicrobium acidiphilum [id:1000000050]" taxid="1000000050" rank="species" parentTaxid="406" leaveCount="1" genusIndex="16"></TreeNode>
+<TreeNode name="unknown species [id:1000000007]" taxid="1000000007" rank="species" parentTaxid="406" leaveCount="1" genusIndex="17"></TreeNode>
+<TreeNode name="unknown genus [id:409]" taxid="409" rank="genus" parentTaxid="403" leaveCount="2" genusIndex="-1"></TreeNode>
+<TreeNode name="unknown species [id:1000000027]" taxid="1000000027" rank="species" parentTaxid="409" leaveCount="1" genusIndex="18"></TreeNode>
+<TreeNode name="Ilumatobacter nonamiensis YM16-303 [id:1000000014]" taxid="1000000014" rank="species" parentTaxid="409" leaveCount="1" genusIndex="19"></TreeNode>
+<TreeNode name="Acidimicrobiales Incertae Sedis [id:410]" taxid="410" rank="family" parentTaxid="402" leaveCount="2" genusIndex="-1"></TreeNode>
+<TreeNode name="Aciditerrimonas [id:411]" taxid="411" rank="genus" parentTaxid="410" leaveCount="2" genusIndex="-1"></TreeNode>
+<TreeNode name="Aciditerrimonas ferrireducens [id:1000000012]" taxid="1000000012" rank="species" parentTaxid="411" leaveCount="1" genusIndex="20"></TreeNode>
+<TreeNode name="unknown species [id:1000000042]" taxid="1000000042" rank="species" parentTaxid="411" leaveCount="1" genusIndex="21"></TreeNode>
+<TreeNode name="unknown family [id:418]" taxid="418" rank="family" parentTaxid="402" leaveCount="5" genusIndex="-1"></TreeNode>
+<TreeNode name="unknown genus [id:1000000004]" taxid="1000000004" rank="genus" parentTaxid="418" leaveCount="5" genusIndex="-1"></TreeNode>
+<TreeNode name="bacterium enrichment culture clone auto73_4W [id:1000000051]" taxid="1000000051" rank="species" parentTaxid="1000000004" leaveCount="1" genusIndex="22"></TreeNode>
+<TreeNode name="bacterium enrichment culture clone auto8_4W [id:1000000053]" taxid="1000000053" rank="species" parentTaxid="1000000004" leaveCount="1" genusIndex="23"></TreeNode>
+<TreeNode name="actinobacterium YJF2-33 [id:1000000026]" taxid="1000000026" rank="species" parentTaxid="1000000004" leaveCount="1" genusIndex="24"></TreeNode>
+<TreeNode name="actinobacterium BGR 43 [id:1000000022]" taxid="1000000022" rank="species" parentTaxid="1000000004" leaveCount="1" genusIndex="25"></TreeNode>
+<TreeNode name="unknown species [id:1000000005]" taxid="1000000005" rank="species" parentTaxid="1000000004" leaveCount="1" genusIndex="26"></TreeNode>
+<TreeNode name="Iamiaceae [id:413]" taxid="413" rank="family" parentTaxid="402" leaveCount="3" genusIndex="-1"></TreeNode>
+<TreeNode name="Iamia [id:414]" taxid="414" rank="genus" parentTaxid="413" leaveCount="3" genusIndex="-1"></TreeNode>
+<TreeNode name="bacterium Ellin5273 [id:1000000038]" taxid="1000000038" rank="species" parentTaxid="414" leaveCount="1" genusIndex="27"></TreeNode>
+<TreeNode name="Iamia majanohamensis [id:1000000016]" taxid="1000000016" rank="species" parentTaxid="414" leaveCount="1" genusIndex="28"></TreeNode>
+<TreeNode name="bacterium Ellin5247 [id:1000000037]" taxid="1000000037" rank="species" parentTaxid="414" leaveCount="1" genusIndex="29"></TreeNode>
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/db.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/db.fasta Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,60 @@\n+>GQ387491.21030.22531\tRoot;Bacteria [id:3];Actinobacteria [id:400];Acidimicrobiia [id:401];Acidimicrobiales [id:402];Acidimicrobiaceae [id:403];CL500-29 marine group [id:405];unknown species [id:1000000000]\n+AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAATCCATGGTGTAGCAATACACCGGAAGATTTAGTGGCGAACGGGTGAGGATCACGTGAGAAACGTGCCCCAGACTCTGGGATAACAATTGGAAACGATTGCTAATACCGGATGACGTCGGAGAATCGCATGATTCACTGACGAAAGATATTTCGGTTTGGGAGCGTCTCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCAACGACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGCGTGCGGGATGAAGGCCTTCGGGCTGTAAACCGCTTTCAGCAGGAACGAAAATGACGGTACCTGCAGAAGAAGGAGCGGCCAACTACGTGCCAGCAGCCGCGGTGACACGTAGGCTCCAAGCGTTGTCCGGATTTATTGGGCGTAAAGAGCTCGTAGGCGGTTGAGTAAGTCGGGTGTGAAAACTCTGGGCTTAACCCGGAGACGCCATCCGATACTGCTCTGACTAGAGTTCAGGAGGGGAGTGGGGAATTCCTAGTGTAGCGGTGAAATGCGCAGATATTAGGAGGAACACCGGTGGCGAAGGCGCCACTCTGGACTGAAACTGACGCTGAGGAGCGAAAGCATGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGGTGGGCACTAGGTGTGGGTTCCAACTAACGGGATCCGCGCCGTCGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTTGCTTAATTCGATGCTACGCGAAGAACCTTACCTGGGTTTGACATGTTTGGAAAAGCCACAGAGATGTGGTGTCCGCAAGGGCCAAACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATTCTATGTTGCCAGCAAGTAATGTTGGGGACTCATGGAAGACCGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGCCCCTTATGTCCAGGGCTGCAAACACGCTACAATGGCCGATACAAAGGGTCGCTTGCCCGCGAGGGTTGGCCAATCCCATAAAGTCGGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGCTGGAGTTGCTAGTAATCCCGGATCAGCACGCCGGGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCGGCAACACCCGAAGCCGGTGGCCTAACCGAAAGGAAGGAGCCGTCGAAGGTGGGGTCGGTGATTGGGGTGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTG\n+>HQ166726.1.1343\tRoot;Bacteria [id:3];Actinobacteria [id:400];Acidimicrobiia [id:401];Acidimicrobiales [id:402];OM1 clade [id:415];Candidatus Actinomarina [id:416];unknown species [id:1000000003]\n+GACGAACGCTGGCGGTGCGCCTTATGCATGCAAGTCGAGCGAAGCTTCTCTGTAGTTTACTACCGAGAATGACTGAGCGGCGAACGGGTGAGTAACGCGTGAGCAATCTACCTTAGTTACAGGGATAGCCCGAGGAAACTCGGATTAATACCTGATATTCTTTAAATTTCGCATGAAATTAAAAGGAAAGGTCAGCCGAACTAAGATGAGCTCGCGTTCTATCAGCTAGTTGGTGAGGTAATAGCTCACCAAGGCTACGACGGATAGCTGGTCTGAGAGGACGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCTGCAGCAGGGAATATTGTGCAATGAGCGAAAGCTTGACACAGCGACACCGCGTGTGGGATGACGGATCTAGGTTTGTAAACCACTTTCAGGAGGGAAGAAAATGACGGTACCTCCACAAGAAGCCCCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGAGCTCGTAGGCGGTTCAACAAGTCGGTCGTGAAAGTTCAGGGCTCAACCCTGAAATGTCGATCGATACTGTTGTGACTAGGATACGGTAGAGGTGAGTGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAATTGCGAAGGCAGCTCACTGGGCCGCTATCGACGCTGAGGAGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCTGTAAACGATGGATACTAGACGTAGGAACTGGATTGACGGTTTCTGTGTCGCAGCTAACGCGTTAAGTATCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGCCCCGCACAAGCGGCGGAGCATGCGGCTTAATTCGATGATACCCGTAGAACCTTACCTGGACTTGACATATAGGGTCAAGCTATAGAAATATAGTGTGCATTAGCGCCCTATACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTATGTTGCCAGCATTTAGTTGGGGACTCATAGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTGCACGCATGCTACAATGGCAAGTACAACGAGTCGCAATACCGCGAGGTGGAGCAAATCTCTTAAAGCTTGTCTCAGTTCGGATAGGAGTCTGCAACTCGACTCCTTGAAGTTGGAGTCGCTAGTAATCGCAAATCAGCAATGTTGCGGTGAATACGTTCTCGGGGT\n+>KF182287.1.1248\tRoot;Bacteria [id:3];Actinobacteria [id:400];Acidimicrobiia [id:401];Acidimicrobiales [id:402];unknown family [id:418];unknown genus [id:1000000004];unknown species [id:1000000005]\n+GTTTGGGGAGGAGCCTGCGTCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGTCGATCAGTAGCTGGTCTGAGAGGATGATCAGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGACGCAGCAACGCCGCGTGGAGGAAGAAGGCCTTCGGGTTGTAAACTCCTTTCAGCAGGAAAGATTATGACGGTACCTGCAGAAGAAGCCCCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGAGCTCGTAGGCGGCTTGACAAGTCGGATGTGAAAACTCCAGGCTCAACTTGGAGACGCCATTCGATACTGTTATGGCTTGAGTCCGGTAGAGGACCACGGAATTCCTGGTGTAGCGGTGAAATGCACAGATATCAGGAGGAACACCAATGGCGAAGGCAGTGGTCTGGGCCGGTACTGACGCTGAGGAGCGAAAGCG'..b'AAGAACCTTACCTGGGTTTGACATGTGCGAAAAAGCCACAGAGATGTGGTGTCCTTCGGGGTCGCACACAGGTGATGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATTCCATGTTGCCAGCGGGTAATGCCGGGGACTCGTGGAAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGACGACGTCAAGTCATCATGCCCCTTACGTCCAGGGCTGCAAACACGCTACAATGGCCGGTACAAAGGGCTGCGAACTCGCGAGAGCAAGCCAATCCCACAAAGCCGGTCTCAGTTCGGATTGAAGGCTGCAACTCGCCTTCATGAAGCTGGAGTTGCTAGTAATCCCGGATCAGCACGCCGGGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCGGCAACACCCGAAGCCGGTGGCCTAACCGTAAGGAAGGAGCCGTCGAAGGTGGGGTCGGTGATTGGGGTGAAGTCGTAACAAGGTAACCGTAGAATC\n+>JF830216.1.1493\tRoot;Bacteria [id:3];Actinobacteria [id:400];Acidimicrobiia [id:401];Acidimicrobiales [id:402];Acidimicrobiaceae [id:403];CL500-29 marine group [id:405];bacterium enrichment culture clone B97(2011) [id:1000000056]\n+ATTAGAGTTTGATCATGGCTCAGGATGAACGCTAGCGGCGTGCTTAACACATGCAAGTCGAACGAGATCCATGGTGTAGCAATACATCGGAAGATCTAGTGGCGAACGGGTGAGGAACACGTGAGAAACCTGCCCCAGACTTTGGGATAACAAGTGGAAACGCTTGCTAATACCGAATGACGTCGGAGAACCGCATGGTTCACTGACGAAAGGAATTCCGGTTTGGGAGGGTCTCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCAACGACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAGTGGGCGAAAGCCTGACGCAGCAACGCCGCGTGCGGGATGAAGGCCTTCGGGCTGTAAACCGCTTTCAGCAGGAACGAAAATGACGGTACCTGCAGAAGAAGGAGCGGCCAACTACGTGCCAGCAGCCGCGGTGACACGTAGGCTCCAAGCGTTGTCCGGATTTATTGGGCGTAAAGAGCTCGTAGGCGGTTGAGTAAGTCGGGTGTGAAAACTCTGGGCTTAACCCGGAGACGCCATCCGATACTGCTCTGACTTGAGTTCAGGAGGGGAGTGGGGAATTCCTAGTGTAGCGGTGAAATGCGCAGATATTAGAGGAACACCGGTGGCGAAAGCGCCACTCTGGACTGAAACTGACGCTGAGGAGCGAAAGCATGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGGTGGGCACTAGGTGTGGGTTCCAACTAACGGGATCCGCGCCGTCGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTTGCTTAATTCGATGCTACGCGAAGAACCTTACCTGGGTTTGACATGTTTGGAAAAGCCACAGAGATGTGGTGTCCGCAAGGGCCAAACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTCTATGTTGCCAGCAAGTTATGTTGGGGACTCATAGAAGACCGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGCCCCTTATGTCCAGGGCTGCAAACACGCTACAATGGCCGATACAAAGGGTCGCCAGCTCGCGAGAGTTAGCTAATCCCATAAAGTCGGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGCTGGAGTTGCTAGTAATCCCGGATCAGCACGCCGGGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCGGCAACACCCGAAGCCGGTGGCCCAACCGCAAGGAAGGAGCCGTCGAAGGTGGGGTCGGTGATTGGGGTGAAGTCGTAACAAGGTAACCGTAGAATC\n+>KC811143.18830.20338\tRoot;Bacteria [id:3];Actinobacteria [id:400];Acidimicrobiia [id:401];Acidimicrobiales [id:402];OM1 clade [id:415];Candidatus Actinomarina [id:416];Candidatus Actinomarina minuta [id:1000000059]\n+AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGTGCGCCTTATGCATGCAAGTCGAGCGAAGCTTTTCAGTAGTTTACTACAGAAAATGACTGAGCGGCGAACGGGTGAGTAACGCGTGAGCAATCTACCTTAGTTACAGGGATAGCCCGAGGAAACTCGGATTAATACCTGATATTCTTTATTTCTCGCATGAGAATAAAAGGAAAGGTCAGCCGAACTAAGATGAGCTCGCGTTCTATCAGCTAGTTGGTGAGGTAAAAGCTTACCAAGGCTACGACGGATAGCTGGTCTGAGAGGACGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCTGCAGCAGGGAATATTGTGCAATGAACGAAAGTTTGACACAGCGACACCGCGTGTGGGATGACGGATCTAGGTTTGTAAACCACTTTCAGGAGGGAAGAAAATGACGGTACCTCCACAAGAAGCCCCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGAGCTCGTAGGCGGTTCAACAAGTCGGTAGTAAAAGTTCAGGGCTCAACCCTGAAATGTCTATCGATACTGTTGTGACTAGGATACGGCAGAGGTGAGTGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAATTGCGAAGGCAGCTCACTGGGCCGCTATCGACGCTGAGGAGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCTGTAAACGATGGATACTAGACGTAGGAACTGGATTGACGGTTTCTGTGTCGTAGCTAACGCGTTAAGTATCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGACCCCGCACAAGCGGCGGAGCATGCGGCTTAATTCGATGATACCCGTAGAACCTTACCTGGACTTGACATATAGGATCCAGCTATAGAGATATAGTGTGCATTAGCGTCCTATACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTATGTTGCCAGCATTTAGTTGGGGACTCATAGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGACGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTGCACGCATGCTACAATGGCAAGTACAACGAGTCGCAATACCGCGAGGTGGAGCAAATCTCTCAAAGCTTGTCCCAGTTCGGATAGGAGTCTGCAACTCGACTCCTTGAAGTTGGAGTCGCTAGTAATCGCAAATCAGCAAAGTTGCGGTGAATACGTTCTCGGGGTTTGTACACACCGCCCGTCAAGTCACGGAAGTCGGCAATACCCGAAGCCAGTGGTCCAACCCTTTTATTAGGGAGGAAGCTGTCGAAGGTAGGGTCGGTAACTGGGACTAAGTCGTAACAAGGTAGCCGTACGGGAACGTGCGGCTG\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/db.fasta.nhr
b
Binary file test-data/db.fasta.nhr has changed
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/db.fasta.nin
b
Binary file test-data/db.fasta.nin has changed
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/db.fasta.nsq
b
Binary file test-data/db.fasta.nsq has changed
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/db.fasta.properties
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/db.fasta.properties Thu Oct 25 05:01:13 2018 -0400
b
@@ -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 
+
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/db.tax
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/db.tax Thu Oct 25 05:01:13 2018 -0400
[
@@ -0,0 +1,81 @@
+0*Root*-1*0*rootrank
+3*Bacteria [id:3]*0*1*domain
+400*Actinobacteria [id:400]*3*2*phylum
+401*Acidimicrobiia [id:401]*400*3*class
+402*Acidimicrobiales [id:402]*401*4*order
+413*Iamiaceae [id:413]*402*5*family
+414*Iamia [id:414]*413*6*genus
+1000000038*bacterium Ellin5273 [id:1000000038]*414*7*species
+1000000032*unknown species [id:1000000032]*414*7*species
+1000000016*Iamia majanohamensis [id:1000000016]*414*7*species
+1000000033*Aciditerrimonas sp. [id:1000000033]*414*7*species
+1000000037*bacterium Ellin5247 [id:1000000037]*414*7*species
+418*unknown family [id:418]*402*5*family
+1000000004*unknown genus [id:1000000004]*418*6*genus
+1000000013*Acidimicrobidae bacterium YM18-244 [id:1000000013]*1000000004*7*species
+1000000022*actinobacterium BGR 43 [id:1000000022]*1000000004*7*species
+1000000026*actinobacterium YJF2-33 [id:1000000026]*1000000004*7*species
+1000000051*bacterium enrichment culture clone auto73_4W [id:1000000051]*1000000004*7*species
+1000000005*unknown species [id:1000000005]*1000000004*7*species
+1000000053*bacterium enrichment culture clone auto8_4W [id:1000000053]*1000000004*7*species
+1000000052*bacterium enrichment culture clone auto222_4W [id:1000000052]*1000000004*7*species
+1000000023*actinobacterium BGR 88 [id:1000000023]*1000000004*7*species
+403*Acidimicrobiaceae [id:403]*402*5*family
+406*Ferrimicrobium [id:406]*403*6*genus
+1000000010*Ferrimicrobium sp. [id:1000000010]*406*7*species
+1000000007*unknown species [id:1000000007]*406*7*species
+1000000050*Ferrimicrobium acidiphilum [id:1000000050]*406*7*species
+408*Ilumatobacter [id:408]*403*6*genus
+1000000020*unknown species [id:1000000020]*408*7*species
+1000000017*Ilumatobacter fluminis [id:1000000017]*408*7*species
+407*Ferrithrix [id:407]*403*6*genus
+1000000035*Ferrithrix thermotolerans [id:1000000035]*407*7*species
+1000000029*actinobacterium WJ25 [id:1000000029]*407*7*species
+1000000025*actinobacterium BGR 127 [id:1000000025]*407*7*species
+1000000006*unknown species [id:1000000006]*407*7*species
+1000000021*actinobacterium BGR 77 [id:1000000021]*407*7*species
+1000000024*actinobacterium BGR 74 [id:1000000024]*407*7*species
+405*CL500-29 marine group [id:405]*403*6*genus
+1000000055*bacterium enrichment culture clone B18(2011) [id:1000000055]*405*7*species
+1000000048*marine metagenome [id:1000000048]*405*7*species
+1000000000*unknown species [id:1000000000]*405*7*species
+1000000054*bacterium enrichment culture clone B213(2011) [id:1000000054]*405*7*species
+1000000056*bacterium enrichment culture clone B97(2011) [id:1000000056]*405*7*species
+1000000040*Iamia sp. [id:1000000040]*405*7*species
+409*unknown genus [id:409]*403*6*genus
+1000000014*Ilumatobacter nonamiensis YM16-303 [id:1000000014]*409*7*species
+1000000027*unknown species [id:1000000027]*409*7*species
+1000000015*Ilumatobacter coccineus YM16-304 [id:1000000015]*409*7*species
+404*Acidimicrobium [id:404]*403*6*genus
+1000000036*Acidimicrobium sp. [id:1000000036]*404*7*species
+1000000047*unknown species [id:1000000047]*404*7*species
+1000000019*Acidimicrobium ferrooxidans [id:1000000019]*404*7*species
+1000000039*Acidithiomicrobium sp. [id:1000000039]*404*7*species
+410*Acidimicrobiales Incertae Sedis [id:410]*402*5*family
+412*Candidatus Microthrix [id:412]*410*6*genus
+1000000046*Candidatus Microthrix parvicella RN1 [id:1000000046]*412*7*species
+1000000018*unknown species [id:1000000018]*412*7*species
+1000000057*Candidatus Microthrix calida [id:1000000057]*412*7*species
+1000000028*actinobacterium CH9 [id:1000000028]*412*7*species
+411*Aciditerrimonas [id:411]*410*6*genus
+1000000012*Aciditerrimonas ferrireducens [id:1000000012]*411*7*species
+1000000042*unknown species [id:1000000042]*411*7*species
+415*OM1 clade [id:415]*402*5*family
+1000000008*unknown genus [id:1000000008]*415*6*genus
+1000000011*bacterium WH6-7 [id:1000000011]*1000000008*7*species
+1000000044*unidentified bacterium wb1_J07 [id:1000000044]*1000000008*7*species
+1000000009*unknown species [id:1000000009]*1000000008*7*species
+1000000041*unidentified bacterium wb1_G04 [id:1000000041]*1000000008*7*species
+1000000034*microbial mat metagenome [id:1000000034]*1000000008*7*species
+416*Candidatus Actinomarina [id:416]*415*6*genus
+1000000045*actinobacterium SCGC AAA015-M09 [id:1000000045]*416*7*species
+1000000059*Candidatus Actinomarina minuta [id:1000000059]*416*7*species
+1000000003*unknown species [id:1000000003]*416*7*species
+1000000058*unidentified marine bacterioplankton [id:1000000058]*416*7*species
+1000000049*marine metagenome [id:1000000049]*416*7*species
+417*Sva0996 marine group [id:417]*402*5*family
+1000000001*unknown genus [id:1000000001]*417*6*genus
+1000000043*unidentified bacterium wb1_P06 [id:1000000043]*1000000001*7*species
+1000000002*unknown species [id:1000000002]*1000000001*7*species
+1000000031*marine metagenome [id:1000000031]*1000000001*7*species
+1000000030*actinobacterium MSI70 [id:1000000030]*1000000001*7*species
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/frogs_db.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/frogs_db.loc Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,2 @@
+db db ${__HERE__}/db.fasta
+
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/genus_wordConditionalProbList.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genus_wordConditionalProbList.txt Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,42493 @@\n+<trainsetNo>1</trainsetNo><version>null</version><modversion>null</modversion><file>genus_wordConditionalProbList</file>\n+12\t-0.64589435\n+8\t-0.5576017\n+22\t-0.5576017\n+24\t-0.5576017\n+25\t-0.5576017\n+14\t-0.6155889\n+16\t-0.6155889\n+5\t-0.6155889\n+12\t-0.6155889\n+11\t-0.64589435\n+0\t-0.35437346\n+1\t-0.35437346\n+2\t-0.35437346\n+4\t-0.35437346\n+8\t-0.35437346\n+9\t-0.35437346\n+10\t-0.35437346\n+11\t-0.35437346\n+17\t-0.35437346\n+18\t-0.35437346\n+19\t-0.35437346\n+22\t-0.35437346\n+15\t-0.64589435\n+2\t-0.64589435\n+4\t-0.64589435\n+1\t-0.6155889\n+2\t-0.6155889\n+21\t-0.64589435\n+11\t-0.64589435\n+2\t-0.64589435\n+14\t-0.586175\n+16\t-0.586175\n+20\t-0.586175\n+18\t-0.6155889\n+19\t-0.6155889\n+0\t-0.45083374\n+8\t-0.45083374\n+9\t-0.45083374\n+10\t-0.45083374\n+15\t-0.45083374\n+22\t-0.45083374\n+27\t-0.45083374\n+29\t-0.45083374\n+6\t-0.40144092\n+7\t-0.40144092\n+12\t-0.40144092\n+13\t-0.40144092\n+17\t-0.40144092\n+21\t-0.40144092\n+22\t-0.40144092\n+24\t-0.40144092\n+25\t-0.40144092\n+28\t-0.40144092\n+19\t-0.64589435\n+0\t-0.0080972025\n+1\t-0.0080972025\n+2\t-0.0080972025\n+3\t-0.0080972025\n+4\t-0.0080972025\n+5\t-0.0080972025\n+6\t-0.0080972025\n+7\t-0.0080972025\n+8\t-0.0080972025\n+9\t-0.0080972025\n+10\t-0.0080972025\n+11\t-0.0080972025\n+12\t-0.0080972025\n+13\t-0.0080972025\n+14\t-0.0080972025\n+15\t-0.0080972025\n+16\t-0.0080972025\n+17\t-0.0080972025\n+18\t-0.0080972025\n+19\t-0.0080972025\n+20\t-0.0080972025\n+21\t-0.0080972025\n+22\t-0.0080972025\n+23\t-0.0080972025\n+24\t-0.0080972025\n+25\t-0.0080972025\n+26\t-0.0080972025\n+27\t-0.0080972025\n+28\t-0.0080972025\n+29\t-0.0080972025\n+8\t-0.5576017\n+9\t-0.5576017\n+10\t-0.5576017\n+18\t-0.5576017\n+22\t-0.6155889\n+26\t-0.6155889\n+14\t-0.6155889\n+16\t-0.6155889\n+5\t-0.64589435\n+12\t-0.6155889\n+18\t-0.6155889\n+3\t-0.64589435\n+11\t-0.64589435\n+1\t-0.64589435\n+7\t-0.64589435\n+5\t-0.64589435\n+1\t-0.64589435\n+1\t-0.64589435\n+7\t-0.5298222\n+13\t-0.5298222\n+14\t-0.5298222\n+15\t-0.5298222\n+24\t-0.5298222\n+11\t-0.64589435\n+24\t-0.64589435\n+13\t-0.64589435\n+2\t-0.6155889\n+17\t-0.6155889\n+0\t-0.3776303\n+1\t-0.3776303\n+2\t-0.3776303\n+4\t-0.3776303\n+8\t-0.3776303\n+9\t-0.3776303\n+10\t-0.3776303\n+11\t-0.3776303\n+18\t-0.3776303\n+19\t-0.3776303\n+22\t-0.3776303\n+14\t-0.6155889\n+15\t-0.6155889\n+24\t-0.64589435\n+2\t-0.64589435\n+1\t-0.64589435\n+11\t-0.64589435\n+25\t-0.586175\n+27\t-0.586175\n+29\t-0.586175\n+22\t-0.64589435\n+26\t-0.64589435\n+7\t-0.6155889\n+28\t-0.6155889\n+1\t-0.6155889\n+2\t-0.6155889\n+0\t-0.11075138\n+3\t-0.11075138\n+5\t-0.11075138\n+6\t-0.11075138\n+7\t-0.11075138\n+8\t-0.11075138\n+9\t-0.11075138\n+10\t-0.11075138\n+11\t-0.11075138\n+12\t-0.11075138\n+13\t-0.11075138\n+14\t-0.11075138\n+15\t-0.11075138\n+16\t-0.11075138\n+17\t-0.11075138\n+18\t-0.11075138\n+19\t-0.11075138\n+20\t-0.11075138\n+21\t-0.11075138\n+23\t-0.11075138\n+24\t-0.11075138\n+25\t-0.11075138\n+27\t-0.11075138\n+29\t-0.11075138\n+28\t-0.64589435\n+1\t-0.6155889\n+2\t-0.6155889\n+12\t-0.64589435\n+1\t-0.6155889\n+2\t-0.6155889\n+16\t-0.64589435\n+27\t-0.6155889\n+29\t-0.6155889\n+11\t-0.64589435\n+6\t-0.6155889\n+7\t-0.6155889\n+22\t-0.64589435\n+10\t-0.64589435\n+26\t-0.64589435\n+16\t-0.6155889\n+17\t-0.6155889\n+8\t-0.6155889\n+11\t-0.6155889\n+0\t-0.11075138\n+1\t-0.11075138\n+2\t-0.11075138\n+6\t-0.11075138\n+7\t-0.11075138\n+8\t-0.11075138\n+9\t-0.11075138\n+10\t-0.11075138\n+12\t-0.11075138\n+13\t-0.11075138\n+14\t-0.11075138\n+15\t-0.11075138\n+16\t-0.11075138\n+17\t-0.11075138\n+18\t-0.11075138\n+19\t-0.11075138\n+20\t-0.11075138\n+21\t-0.11075138\n+23\t-0.11075138\n+24\t-0.11075138\n+25\t-0.11075138\n+26\t-0.11075138\n+27\t-0.11075138\n+29\t-0.11075138\n+13\t-0.586175\n+14\t-0.586175\n+15\t-0.586175\n+20\t-0.64589435\n+2\t-0.64589435\n+20\t-0.586175\n+27\t-0.586175\n+29\t-0.586175\n+2\t-0.64589435\n+1\t-0.6155889\n+2\t-0.6155889\n+5\t-0.6155889\n+6\t-0.6155889\n+4\t-0.64589435\n+0\t-0.20516105\n+5\t-0.20516105\n+6\t-0.20516105\n+8\t-0.20516105\n+9\t-0.20516105\n+10\t-0.20516105\n+11\t-0.20516105\n+12\t-0.20516105\n+13\t-0.20516105\n+14\t-0.20516105\n+15\t-0.20516105\n+16\t-0.20516105\n+18\t-0.20516105\n+19\t-0.20516105\n+21\t-0.20516105\n+24\t-0.20516105\n+25\t-0.20516105\n+26\t-0.20516105\n+28\t-0.20516105\n+4\t-0.64589435\n+1\t-0.6155889\n+2\t-0.6155889\n+0\t-0.0080972025\n+1\t-0.0080972025\n+2\t-0.0080972025\n+3\t-0.0080972025\n+4\t-0.0080972025\n+5\t-0.0080972025\n+6\t-0.0080972'..b'76017\n+12\t-0.5576017\n+26\t-0.5576017\n+28\t-0.5576017\n+0\t-0.0080972025\n+1\t-0.0080972025\n+2\t-0.0080972025\n+3\t-0.0080972025\n+4\t-0.0080972025\n+5\t-0.0080972025\n+6\t-0.0080972025\n+7\t-0.0080972025\n+8\t-0.0080972025\n+9\t-0.0080972025\n+10\t-0.0080972025\n+11\t-0.0080972025\n+12\t-0.0080972025\n+13\t-0.0080972025\n+14\t-0.0080972025\n+15\t-0.0080972025\n+16\t-0.0080972025\n+17\t-0.0080972025\n+18\t-0.0080972025\n+19\t-0.0080972025\n+20\t-0.0080972025\n+21\t-0.0080972025\n+22\t-0.0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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/logWordPrior.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/logWordPrior.txt Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,65537 @@\n+<trainsetNo>1</trainsetNo><version>null</version><modversion>null</modversion><file>logWordPrior</file>\n+0\t-4.1271343\n+1\t-4.1271343\n+2\t-4.1271343\n+3\t-4.1271343\n+4\t-4.1271343\n+5\t-4.1271343\n+6\t-4.1271343\n+7\t-4.1271343\n+8\t-4.1271343\n+9\t-4.1271343\n+10\t-4.1271343\n+11\t-4.1271343\n+12\t-4.1271343\n+13\t-4.1271343\n+14\t-4.1271343\n+15\t-3.028522\n+16\t-4.1271343\n+17\t-4.1271343\n+18\t-4.1271343\n+19\t-4.1271343\n+20\t-4.1271343\n+21\t-4.1271343\n+22\t-4.1271343\n+23\t-4.1271343\n+24\t-4.1271343\n+25\t-4.1271343\n+26\t-4.1271343\n+27\t-4.1271343\n+28\t-4.1271343\n+29\t-4.1271343\n+30\t-4.1271343\n+31\t-4.1271343\n+32\t-4.1271343\n+33\t-4.1271343\n+34\t-4.1271343\n+35\t-4.1271343\n+36\t-4.1271343\n+37\t-4.1271343\n+38\t-4.1271343\n+39\t-4.1271343\n+40\t-4.1271343\n+41\t-4.1271343\n+42\t-4.1271343\n+43\t-4.1271343\n+44\t-4.1271343\n+45\t-4.1271343\n+46\t-4.1271343\n+47\t-1.9299098\n+48\t-4.1271343\n+49\t-4.1271343\n+50\t-4.1271343\n+51\t-4.1271343\n+52\t-4.1271343\n+53\t-4.1271343\n+54\t-4.1271343\n+55\t-4.1271343\n+56\t-4.1271343\n+57\t-4.1271343\n+58\t-4.1271343\n+59\t-4.1271343\n+60\t-4.1271343\n+61\t-2.5176966\n+62\t-2.5176966\n+63\t-4.1271343\n+64\t-4.1271343\n+65\t-4.1271343\n+66\t-4.1271343\n+67\t-4.1271343\n+68\t-4.1271343\n+69\t-4.1271343\n+70\t-4.1271343\n+71\t-4.1271343\n+72\t-4.1271343\n+73\t-4.1271343\n+74\t-4.1271343\n+75\t-4.1271343\n+76\t-4.1271343\n+77\t-4.1271343\n+78\t-4.1271343\n+79\t-4.1271343\n+80\t-4.1271343\n+81\t-4.1271343\n+82\t-4.1271343\n+83\t-4.1271343\n+84\t-4.1271343\n+85\t-4.1271343\n+86\t-4.1271343\n+87\t-4.1271343\n+88\t-4.1271343\n+89\t-4.1271343\n+90\t-4.1271343\n+91\t-4.1271343\n+92\t-4.1271343\n+93\t-3.028522\n+94\t-4.1271343\n+95\t-4.1271343\n+96\t-4.1271343\n+97\t-4.1271343\n+98\t-4.1271343\n+99\t-0.90825856\n+100\t-4.1271343\n+101\t-4.1271343\n+102\t-4.1271343\n+103\t-4.1271343\n+104\t-4.1271343\n+105\t-4.1271343\n+106\t-4.1271343\n+107\t-4.1271343\n+108\t-4.1271343\n+109\t-4.1271343\n+110\t-4.1271343\n+111\t-4.1271343\n+112\t-4.1271343\n+113\t-4.1271343\n+114\t-4.1271343\n+115\t-4.1271343\n+116\t-4.1271343\n+117\t-4.1271343\n+118\t-4.1271343\n+119\t-4.1271343\n+120\t-4.1271343\n+121\t-4.1271343\n+122\t-4.1271343\n+123\t-4.1271343\n+124\t-4.1271343\n+125\t-4.1271343\n+126\t-4.1271343\n+127\t-4.1271343\n+128\t-4.1271343\n+129\t-4.1271343\n+130\t-4.1271343\n+131\t-4.1271343\n+132\t-4.1271343\n+133\t-4.1271343\n+134\t-4.1271343\n+135\t-4.1271343\n+136\t-4.1271343\n+137\t-4.1271343\n+138\t-4.1271343\n+139\t-4.1271343\n+140\t-4.1271343\n+141\t-4.1271343\n+142\t-4.1271343\n+143\t-4.1271343\n+144\t-4.1271343\n+145\t-4.1271343\n+146\t-4.1271343\n+147\t-4.1271343\n+148\t-3.028522\n+149\t-4.1271343\n+150\t-4.1271343\n+151\t-3.028522\n+152\t-4.1271343\n+153\t-4.1271343\n+154\t-4.1271343\n+155\t-4.1271343\n+156\t-4.1271343\n+157\t-4.1271343\n+158\t-4.1271343\n+159\t-3.028522\n+160\t-2.5176966\n+161\t-4.1271343\n+162\t-4.1271343\n+163\t-4.1271343\n+164\t-4.1271343\n+165\t-4.1271343\n+166\t-4.1271343\n+167\t-4.1271343\n+168\t-4.1271343\n+169\t-3.028522\n+170\t-4.1271343\n+171\t-4.1271343\n+172\t-4.1271343\n+173\t-4.1271343\n+174\t-4.1271343\n+175\t-4.1271343\n+176\t-3.028522\n+177\t-4.1271343\n+178\t-4.1271343\n+179\t-4.1271343\n+180\t-4.1271343\n+181\t-3.028522\n+182\t-2.1812243\n+183\t-2.5176966\n+184\t-4.1271343\n+185\t-4.1271343\n+186\t-4.1271343\n+187\t-4.1271343\n+188\t-1.293921\n+189\t-4.1271343\n+190\t-1.0826119\n+191\t-4.1271343\n+192\t-4.1271343\n+193\t-4.1271343\n+194\t-4.1271343\n+195\t-4.1271343\n+196\t-4.1271343\n+197\t-4.1271343\n+198\t-4.1271343\n+199\t-4.1271343\n+200\t-4.1271343\n+201\t-4.1271343\n+202\t-4.1271343\n+203\t-4.1271343\n+204\t-4.1271343\n+205\t-4.1271343\n+206\t-4.1271343\n+207\t-4.1271343\n+208\t-4.1271343\n+209\t-4.1271343\n+210\t-4.1271343\n+211\t-4.1271343\n+212\t-4.1271343\n+213\t-4.1271343\n+214\t-3.028522\n+215\t-4.1271343\n+216\t-4.1271343\n+217\t-4.1271343\n+218\t-4.1271343\n+219\t-4.1271343\n+220\t-0.016260505\n+221\t-1.9299098\n+222\t-4.1271343\n+223\t-2.5176966\n+224\t-4.1271343\n+225\t-4.1271343\n+226\t-4.1271343\n+227\t-4.1271343\n+228\t-4.1271343\n+229\t-4.1271343\n+230\t-4.1271343\n+231\t-4.1271343\n+232\t-4.1271343\n+233\t-4.1271343\n+234\t-4.1271343\n+235\t-4.1271343\n+236\t-4.1271343\n+237\t-4.1271343\n+238\t-4.1271343\n+239\t-4.1271343\n+240\t-4.1271343\n+241\t-4.1271343\n+242\t-4.1271343\n+243\t-4.1271343\n+244\t-4.1271343\n+245\t-4.1271343\n+246\t-4.1271343\n+247\t-2.5176966\n+248\t-4.1271343\n+249\t-3'..b'343\n+65313\t-4.1271343\n+65314\t-3.028522\n+65315\t-2.1812243\n+65316\t-4.1271343\n+65317\t-4.1271343\n+65318\t-4.1271343\n+65319\t-4.1271343\n+65320\t-4.1271343\n+65321\t-4.1271343\n+65322\t-4.1271343\n+65323\t-3.028522\n+65324\t-4.1271343\n+65325\t-4.1271343\n+65326\t-4.1271343\n+65327\t-4.1271343\n+65328\t-4.1271343\n+65329\t-4.1271343\n+65330\t-4.1271343\n+65331\t-4.1271343\n+65332\t-4.1271343\n+65333\t-4.1271343\n+65334\t-4.1271343\n+65335\t-4.1271343\n+65336\t-4.1271343\n+65337\t-4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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/otus_pynast.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/otus_pynast.fasta Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,500 @@\n+>592283\n+--------------------------------------------------------------------------------------------------------------------------------------------------------GG-C--G-GC-G-TG--C----C-T--AATACA-T-GC-A-AGT-CGA-G-CG----------G------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------CTC-CATC----------------G-GG--A--GT--T--AG-C-GG-C-GG-A--C-------------GGG-TGAGT-A--AC-AC-G-T-G-GG---GAA--C-CT-G--G-C-ATC--AA-G------------------------------------------------------------------T-GG----GGG-AT-AA-CGC-------------------------C-T-G-----------------------GAA-A---CGG-GTG-CTAA-TT---CC-G--C-AT-A----------G----------------------A--C-T-C--T--T-----------------TG---CT-C-----------------------------------------------------------------------------------------------------------------------G-CA-T--------------------------------------------------------------------------------------------------------------------------------------G-A-G--T-G---------------A--A-G-A-A-G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAA--G-G-C-GC-------------------------------------------------------------------------------------------------------------------------------------T-A--------------------------------------------------------------------------------------------------------------------------CGG-CG--T---C-G--------------C----T-T---G-AT-G---AT---G-G-----C-CCC-GCG--G-CGC--A------TT--A--G-CT-A----G---TTGG-T-G-GG-G-T----AAT-GG-C-C-T-CCCA--A-GG-C-G--A-CG-A------------TGC-G-T------AG-CC-G-A-CCT-G-AG----A--GG-GT--G-AC-C-GG-CCAC-A-CTGGG--A-C-TG-A-GA-C-AC-G-G-CCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TA---GG-G-A-ATC-TTCCG-C-AA-T-GG--GC-GA-A----A-G-CC-T-GA-CG-GA-GCAA-CGCC-G-TG-T---G-A-A--T--GA-A-G--A--C-G-G-TC-----TT-CG---------G-A-T-T-G-T--A---AA-G-TTC--------TG-TC-A-T--T-GGG----GA-C--G---AAGTAGG---AAGA-GA----G-----GG-A---A----T-----GC-T-CTT-CTA-GA-GA-CG-GT-A-C-CC-A-AG-G---------AG-----------GAAGC-CCC-GG-C-TAA---C--T-ACGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GT-AG-GGG-GCA-A-G-CG-TTGT-C-CGG-AA-TG-A--C-T--GGGC-GTA----AA-GCGC-GC--G-CA-G-G-C-G------------G--T-CT-T-T-T-AA----G-T-C-T---G-AGG-TG-A-AA-GG--CT-GGG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-C-T-GG-CA-T----C-G-C-C-T-T--------G--GA-A-A-C-G-G-GAA--G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-G-A-G-G-A-----C-TG--GA-G-A------------G-GC-A-AG-G----GG--AATT-CCA-C-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TG-T-GGA--GG-A-AT-A-CC-AG--T--G--GC-GAA-G--G-C---G----C--C-T-TGCTG------G-AC-AG--------------------------------------------------------------TG-'..b'-------------------------------------T-T-G-A-G-G-C-----T-CG--GC-G-G------------G-GG-G-CG-T----GG--AATT-CCG-G-GT--GG-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-C-GGA--GG-A-AC-A-CC-GA--C--G--GC-GAA-G--G-C---G----G--C-G-CCCTG------G-AC-GA--------------------------------------------------------------GT-T-C-T--GA--CG-----CT-CA-GG--C-A-CGA--AA-G-C--------------T-GGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CC--A-G-CCC-T-AAA--C-GATG-TC--CA-CC---------A-GG--T--G-C-CG-C-GG-G--T---------------------------------------------------------------------------------------AT-C---------------------------------------------------------------------------------------------------------------------------------------------------G-A-C-CCC-T-GCGGT-GC-C------GC--A----GC-TCA--CG-T-G-A--T--GA-GT--G----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------GGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCA-GC-G--G--AG-CG-T--GT-GGT-TT-AATT-C-G-ATG-CGAC-G-CG-C-AG-A-A-CC-TT-A-CC-TGGGT-TT-G-AC-A-T-G------------G--CA-G-T-----------G-C-AC-C-A-C--GG--G-TA-A-T-T--C-C-G--T-G-T-C-CC-C--------------------------------------------G--CA-A------------------------------------------------G----G---GGCGCTG--C--CA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-CC-G--TGA-GG-TGT-T-GG-G-TT-AA-GT-CCCCT-AA--------C-GAG-CGC-A-ACC-C-C-TG--GG--G-TCCG--T-T-A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTCCCTTTGCGGGGAGGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-G---T---------------C-G-G-G-C-GC-G--AC-T-G-CCG--C-G------------------------------------C-G---CAA----------------------------------C-G-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---AGC-A-C-G-G-C-C-CTT----AC-G--TC-C-A-GG-GC-GA-CAC-ACACG-C--TA--CAATG---G-CCGG-T-A--C-AAC-GG-GT--------------------------------------------------------------------------------------------------C-G-C-C-A--A-GCCG-C--G---------------------------------------A-GG-C-G-----------G--A-G-CC---A----------A-TCCC-AG-----C---AAAGC-CG-G-T-C-T-CAG-TTC--------GGA-T-TGCAG-GC--T-GCAA-CC-C-------------------------------------------------------------------------------------------------G-CCTGC-A-T-G-AA-G-TT-GGAGT-TG-C-TA--G-TA-AC-C-G-C----GGG-TC-A-G--C------AC--ACC-GC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGCA----CTCACCG-CCC-GTC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/01-prepro.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro.fasta Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,171330 @@\n+>HWI-M00185:22:000000000-A53C9:1:1111:13422:24947;size=1 1:N:0:ACTTGA \n+CACGTAAGAATTTGCCTTTTGGATGAAAGATGACCAATCCATGGAAGTTGTCGTTCAGGGAGGGGCCCGCGTCCCATTAGCTTGTTGGTAGGGTAATGGCCTACCAAGGCGACGATGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGCACTGAAACACGGGCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGGGTGAAGAAGGCTTTCGGGTCGTAAAGCCCTGTCAGGTGGGAAAAAATACTCCTGGTTAATAGCCAGGGGAGCTGATGGTACCACCAGAGGAAGCACCGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:2101:17984:4632;size=1 1:N:0:ACTTGA \n+CACGTAGGCGACCTGCCCCAAAGAGGGGGACAACCGCTGGAAACGGTGGCTAATACCCCATAATATCCTAGGGTTTGGATACCCATGGATTAAAGCTCCGGCGCTTTGGGAGGGGCCTGCGGCCCATCAGCTTGTTGGTAGGGTAATGGCCTACCAAGGCAGAGACGGGTAGGGGGCGTGAGAGCGTGATCCCCCACACTGGCACTGATACACGGGCCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGCCCAATGGACGCAAGTCTGAGGCAGCAACGCCGCGTGGATGATGAAGGCCTTCGGGTTGTAAAATCCTTTTCTGGAGGAAGGGACGGCTAACTTC\n+>HWI-M00185:22:000000000-A53C9:1:2114:23327:24384;size=1 1:N:0:CCGTCC \n+CACGTGAGAATCTACCTCTAGGAGGGGCATAAAAAACCCCATATGCCGTAAGGTGAAATGGATTTAAATAATTCGCCTGGAGATGAGCTCGCGTCTGATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCCACTATCAGTAGCTGGTCTGAGAGGACGAACAGCCACACTGGGACTGAGATACGGCCCAGACTCCTCCGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGTGAAAGCTTGACGGAGCAACGCCGCGTGGAGGATGAAGGTTTTAGGATTGTAAACTCCTTTTCTCAAAGAAAAATCGATGATAGTATTTGAGGTAAAAAGCACCGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:1108:14455:27359;size=1 1:N:0:CCGTCC \n+CGCGTAAGTAATCTACCTTTTAGTTCAGAATAATCATTTTATGAAAAAACTGAATAATTTAATAAAAAAATTTATTGCTAAAAGATGAGCTTGCGTAAGATTAGGTAGTTGGTTTTTTAACAGATAACCAAGCCGACGATCTTTAGCTGGTTTGAAAGAATGATCAGCCACACTGGGACTGAGATACGGCCCAGACTTCATTAGAAGGCAGCAGTGAGGAATTTTGGACAATGGGCGAAAGCTTGATCCAGCAATACTACGTGAGTGAGGAAGGCTATTTGGTTGTAAAGCTCTTTCGATAAGGAAGAAAAAAGACAGTACTTATAAAAGAAGTTCCGGCCAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:2110:9053:23480;size=1 1:N:0:ACTTGA \n+CGCGTGGGAACGTGCCCTCCTGCCCGGGATAACAGTTGGAAACGACTGCTAAAACCGGATGCACCCTTTGGGGGAAGGGGAGGATCGGCCCGCGCCGGATTAGGTAGTTGGTGGGGTAACGGCCTACCAAGCCTACGATCCGTACCTGGTTTGAGAGGATGATCAGGCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGGGCAACCCTGACGGAGCAACGCCGCGTGGGGGAGGAAGGTCTGTGGATTGTAAACCCCTTTTCTCAGGGAAGAAGTTCTGACGGTACCTGAGGAATCAGCATCGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:2112:5573:22659;size=1 1:N:0:ACTTGA \n+CGCGTGGGAACGTGCCCTCCTGCCCGGGATAACAGTTGGAAACGACTGCTAAAACCGGATGCGCCCTACGGGGGAAGGGGAGGATCGGCCCGCGTCGGATTAGGTAGTTGGTGGGGTAACGGCCTACCAAGCCTACGATCCGTACCTGGTTTGAGAGGATGATCAGGCACACTGGGACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCAACGCCGCGTGAACGAAGAAGGCTTTCGAGTCGTAAAGTTCTGTTATAGGGGAAGAAGAAGTGACGGTACCCTATGAGAAAGCCACGGCTAATTAC\n+>HWI-M00185:22:000000000-A53C9:1:2105:22700:25394;size=1 1:N:0:CCGTCC \n+CGCGTGGGAACGTGCCCTCTTGCCTGGGATAACCTCTGGAAACGGTGGCTAATACCGGATGAGCCCTATGGGGGAAGAGAGGATCGGCCCGCGTTGGATTAGGTAGTTGGTGGGGTAATGGCCTACCAAGCCGACGATCCATACCTGGTTTGAGAGGATGACCAGGCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGTCTTCGGATTGTAAACTTCTGTTATGAGGGAAAAATAAAATGATGGTACCTCAGTAGAAAGCCACGGCTAACTAC\n+>HWI-M00185:22:000000000-A53C9:1:1101:16802:15706;size=2 1:N:0:ACTTGA \n+TGCATCGGAACGTGCCCAGTAGTGGGGGATAGCTCGGCGAAAGCCGGATTAATACCGCATACGACCTACGGGTGAAAGCGGGGGACCGAAAGGCCTCGCGCTATTGGAGCGGCCGATGTCGGATTAGCTTGTTGGTGGGGTAAAAGCCTACCAAGGCGACGATCCGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGGCGAGAACGAAACAGCGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:1105:14233:10346;size=2 1:N:0:CCGTCC \n+CACGTAAGAATTTGCCTTTAGGAGGGGGAAAGCAGGGGATCGCAAGACCTTGCGTTATTCGAGCGGCCGACGTCTGATTAGCTAGTTGGTGGGGTAATGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGGCTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATTCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCAGCTGGAACGAAACGGTACGCTCTAACATAGCGTGCTAATGACGGTACCAGCAGAAGAAGCACCGGCTAACTAC\n+>HWI-M00185:22:000000000-A53C9:1:2108:24332:19653;size=1 1:N:0:ACTTGA \n+CACGTGAGAATCTACCTCTAGGAGGGGCATAAAAAACCCCATATGCCTATACGGGTGAAACGGATTTACATAAATTCGCCTGGAGATGAGCTCGCGGCTGATTAGCTAGTTGGTGAGG'..b'TCC\n+>HWI-M00185:22:000000000-A53C9:1:2108:18698:24708;size=1 1:N:0:CCGTCC \n+TGCATGGGTAACGTGCCCTGAACACCGGGATAGCGGCGGGCTTCGGCCCTTTAGCGAAAATGCCGGTAATACCGGGTAACATCCAGAGGCCTCATGGCTTTTGGATCAAAAGCGGGGACCCTTCGGGGCCTGGCGGGTTTGGATCGGCCCCTGCCCTATCAGCTTGTTGGGGGGGGAACGGCCTACCAAAGCGGTGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGACGAAAGTCTGACAGAGCGACGCCGCGTGAAGGATGAAATCCTTCGGGATGTAAACTTCAATAGTTTGTCAGGAAGCGAGGGGGCCTAATACGTCCCTAAGTTGACCACCAAACGAAAGGGGTGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:1110:14843:3015;size=1 1:N:0:ACTTGA \n+CACATGGGTAACGTACCTTGGACACAGGGATAGCGGCGCCCCGCAAGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATAATATCCCGGTTCGGCATCGAGCCGGGATCAAATGGTGGGGACCTTCGGGCCTGCCGGTCTGAGATCGGCCCATGCCCTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCTAAGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCGCGTGGGGGATGAAGTCCTTCGGGATGTAAACTTTAATGGTATGCTAGGAAGCGAACCGGCCTAATACGTCGGCGAGTTGACCCGCATACGAAAGGGGCGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:2104:4995:13455;size=1 1:N:0:ACTTGA \n+CACATGGGTAACGTACCTTGGACACAGGGATAGCGGCGCCCCGCAAGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATAATATCTCGGCTCGGCATCGAGCTGAGATCAGATGGTGGGGACCTTCGGGCCTGCCGGTCTGGGATCGGCCCATGCCCTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCTAAGGCGGGTAGCCGGCGTGAGAGAGCGACCGGCCACATCGGCACTAAGACCCTGCCCTGCCACCTACGGGTGGCTGCGGCCACGAAGATGCCGCAGTGAGGCATAGCATGACGGAGCGAAGCGGGGGGGGAGAGGAGGGCCCTTGGTATGAAAACTGTAAAGGTATGCTAGGAAGCGGGGCGGCCTAATACGCCGGTGAGCGGACCCGCATACGAAAGGGGCGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:2113:28426:15778;size=1 1:N:0:ACTTGA \n+CACGTGAGAAACCTGCCCTTCAGTGGGGGACAACGTCGGTTCTTCGGAACCTCGCGAAAGCGGCGCTAATACCCCATGTCATCTCTGGATCGCATGTTCCGGGGCTGAAAGCGGGGGACCCTTCGGGGCCTCGCGCTGAAGGATGGTCTCGCGCCTGATTAGCTAGTTGGTGGGGTAACGGCCTACCAAGGCTTCGATCAGTAGCTGGCCTGAGAGGGTGGTCAGCCACACTGGGATTGAGATACGGCCCAGACTCCTACGGGAGGCAACAGTCTAGAAGCTTCGGCAATGGGGGCAACCCTGACCGAGCGACGCCGTGTGAAGGATGACACAGTTTATCTGCGTAAAGTACTGTTAACCGGGACGAAAAGATGCATGGACTGCATTTATATGACGGTACCGGTAGAGGAAGCTCCGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:1101:11608:15683;size=2 1:N:0:ACTTGA \n+CACGTGAGAATCTGTCCTGAGATGGGGATAGCCCATGGAAACATGGGGTAATACCGCGTATGTCCCGATTCTTCCGGCCTGCTTCACATGAAGCGGTCCGGAAGAATCGGGATGAAAGCAGCTTTTGCTGCGTCTTAGGGTGAGCTTGCGGTCCATTAGCTAGTTGGTAGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATTCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCAGCAGGAACGAAACGGTACGCTCTAACATAGTGTGCTAATGACGGTACCTGCAGAAGAAGCACCGGCTAACTAC\n+>HWI-M00185:22:000000000-A53C9:1:2114:23288:19094;size=1 1:N:0:CCGTCC \n+TAAATAGATAACGTACCCCGGTCTCAGGGATACCAGCGGGAGCTTGCTCCCTTTGCGAAAGTGCTGTTAATACCTGATAACGTTTAGCGTAGGCATCTACGAAAAATCAAAGGTGGGGACCCTCGGGCCTACCGGACTGGGAGCGGTCTATTTCCTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCAGCGACGGGTAGCCGGACTGAGAGGTTGGACGGCCACATCGGAACTGAGACACTGTCCGGACACCTACGGGTGGCTGCAGTAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCTCGTGGAGGACGAATTCCCTCGGGATGTAAACTCCTTTTAGGGTTACGCAAGCAAGGATGGTTAATACCCATCTGCGTTGAGCTATCCCAGAAAAAGCCTCGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:1102:27166:10559;size=2 1:N:0:CCGTCC \n+TGCATGGGGAACGTACCTCGCGCACAGGGATAGCGGCGCCCTTCGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATGACATCCAGGGGCTGCATGGTTTCTGGATCAAAGATGGGGACCCTTCGGGGCCTGTCGGGGCGAGAGCGGCCCATGCCCTATCAGCTTGTTGGTGGGGTAACGGCCTACCAAGGCGATGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCGCGTGGGGGATGAAGTCTTTCGGGATGTAAACTCCATCAGTATGCCAGGAAGCGATCCTGGCTAATACCTGGGAAAGTTGACCGGCATACGAAAAGGGGCGGCTAACTCC\n+>HWI-M00185:22:000000000-A53C9:1:1110:6064:5235;size=1 1:N:0:ACTTGA \n+TGCATGGGTAACGTACCTCGCGCACAGGGATAGCGGCGCCCTTCGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATGACATCCAGGGGCTGCATGGTTTCTGGATCAAAGATGGGGACCCTTCGGGGCCTGTCGGGGCGAGAGCGGCCCATGCCCTATCAGCTTGTTGGTGGGGTAACGGCCTACGGAGGCGATGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCGCGTGGGGGATGAAGTCTTTCGGGATGTAAACTCCATCAGTATGCCAGGAAGCGATCCTGGCTAATACCTGGGAAAGTTGACCGGCATACGAAAAGGGGCGGCTAACTCC\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/01-prepro.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro.html Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,446 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<html>\n+    <head>\n+        <title>FROGS Pre-process</title>\n+        <meta charset="UTF-8">\n+        <meta name="version" content="1.2.1">\n+        <!-- CSS -->\n+        <link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>\n+        <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></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+        </style>\n+        <!-- JS -->\n+        <script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>\n+        <script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>\n+        <script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>\n+        <script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>\n+        <script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>\n+        <script type="text/javascript">\n+            /*\n+             * HTMLTable.js 0.1.0 - HTMLTable Library\n+             *\n+             * Copyright (c) 2015 Escudie Frederic\n+             * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.\n+             */\n+            function HTMLtable(e){var t,r,n=e,a=";";this.deleteColumns=function(e){for(var a=n.getElementsByTagName("tr"),o=0;o<a.length;o++){s=0;var i=a[o].getElementsByTagName("td");0==i.length&&(i=a[o].getElementsByTagName("th"));for(var v=0,s=0;s<t[1];s++)if(!r[o][s]){var f=i[v].getAttribute("colspan");if(null!=f)for(var m=0;f>m;m++){if(in_array(s+m,e)){var u=i[v].getAttribute("colspan");u-1==0?i[v].removeAttribute("colspan"):i[v].setAttribute("colspan",u-1)}if(null==i[v].getAttribute("colspan")){var h=i[v];a[o].removeChild(h),v--}}else if(in_array(s,e)){var h=i[v];a[o].removeChild(h),v--}v++}}l(),g()},this.filter=function(e,a){var l=new RegExp(e),g=new Array;null!=a&&a||(g.c0=!0);for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)r[i][f]||(l.test(v[s].innerHTML)&&(g["c"+f]=!0),s++)}for(var m=new Array,u=0;u<t[1];u++)void 0===g["c"+u]&&m.push(u);this.deleteColumns(m)},this.getModel=function(){return n};var l=function(){for(var e=0,r=0,a=n.getElementsByTagName("tr"),l=0;l<a.length;l++){var g=0;e++;var o=a[l].getElementsByTagName("td");0==o.length&&(o=a[l].getElementsByTagName("th"));for(var i=0;i<o.length;i++){var v=o[i].getAttribute("colspan");g+=null==v?1:parseInt(v)}g>r&&(r=g)}t=new Array(2),t[0]=e,t[1]=r},g=function(){r=new Array(t[0]);for(var e=0;e<t[0];e++){r[e]=new Array(t[1]);for(var a=0;a<t[1];a++)r[e][a]=!1}for(var l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){v=0;var o=l[g].getEle'..b'             $(\'#filterBySample-csv-export\').html( \'<button class="btn btn-primary"><span class="glyphicon glyphicon-open-file" aria-hidden="true">CSV</span></button>\' );\n+                $(\'#filterBySample-csv-export\').addClass( \'dataTables_filter\' );\n+                $(\'#filterBySample-csv-export\').datatableExport({\n+                    \'table_id\': "filterBySample-table",\n+                    \'omitted_columns\': [0]\n+                });\n+\n+                // Add modal listener\n+                $(\'#lengths-modal\').on(\'shown.bs.modal\', function (event) {\n+                    var button = $(event.relatedTarget); // Button that triggered the modal\n+                    var data_type = button.data(\'whatever\');\n+                    if( data_type == "before-process" ){\n+                        setLengthsGraph(before_lengths_by_sample,"Amplicon length distribution before trimming and filtering");\n+                    } else {\n+                        setLengthsGraph(after_lengths_by_sample,"Preprocessed Amplicon Length distribution");\n+                    }\n+                });\n+            }\n+\n+            $(function() {\n+                // Remove alert\n+                $(\'#js-alert\').remove();\n+                $(\'#content\').removeClass("hidden");\n+                \n+                // Display summary\n+                summaryLoad();\n+                \n+                // Display data by sample\n+                sampleDetailsLoad();\n+            });\n+        </script>\n+    </head>\n+    <body>\n+        <!-- Alert -->\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+        <!-- Content -->\n+        <div id="content" class="hidden">\n+            <div id="filter-summary"></div>\n+            <div id="filter-log">\n+                <table id="filterBySample-table" class="table table-striped">\n+                    <thead>\n+                        <tr>\n+                            <th class="title">Filtering by sample</th>\n+                        </tr>\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 btn-primary table-action fusion-right disabled" data-toggle="modal" data-target="#lengths-modal" data-whatever="before-process">Display amplicon lengths </button>\n+                                <button id="display-after-spl-lengths" class="btn btn-primary table-action disabled" data-toggle="modal" data-target="#lengths-modal" data-whatever="after-process">Display preprocessed amplicon lengths</button>\n+                            </th>\n+                        </tr>\n+                    </tfoot>\n+                </table>\n+            </div>\n+        </div>\n+        \n+        <!-- Modals -->\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+                        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>\n+                        <h4 class="modal-title">Amplicons lengths</h4>\n+                    </div>\n+                    <div class="modal-body">\n+                        <div id="lengths-chart"></div>\n+                    </div>\n+                    <div class="modal-footer">\n+                        <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+                    </div>\n+                </div>\n+            </div>\n+        </div>\n+    </body>\n+</html>\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/01-prepro.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/01-prepro.tsv Thu Oct 25 05:01:13 2018 -0400
b
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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/02-clustering.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering.biom Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16192:3924"}}, {"id": "Cluster_2", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:12521:5680"}}, {"id": "Cluster_3", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16005:1920"}}, {"id": "Cluster_4", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14417:1745"}}, {"id": "Cluster_5", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19898:5958"}}, {"id": "Cluster_6", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:10625:3122"}}, {"id": "Cluster_7", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19644:2236"}}, {"id": "Cluster_8", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19958:2207"}}, {"id": "Cluster_9", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14723:9889"}}, {"id": "Cluster_10", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:22681:4284"}}, {"id": "Cluster_11", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:27968:12864"}}, {"id": "Cluster_12", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14639:6828"}}, {"id": "Cluster_13", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:4008:12611"}}, {"id": "Cluster_14", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:21539:2936"}}, {"id": "Cluster_15", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:20802:4801"}}, {"id": "Cluster_16", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1102:16581:10470"}}, {"id": "Cluster_17", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19782:3604"}}, {"id": "Cluster_18", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:6692:9035"}}, {"id": "Cluster_19", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:20545:9379"}}, {"id": "Cluster_20", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14438:5670"}}, {"id": "Cluster_21", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:20869:4256"}}, {"id": "Cluster_22", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1102:7862:4645"}}, {"id": "Cluster_23", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13251:3399"}}, {"id": "Cluster_24", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13562:5876"}}, {"id": "Cluster_25", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13515:9183"}}, {"id": "Cluster_26", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:2885:13564"}}, {"id": "Cluster_27", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:21255:10262"}}, {"id": "Cluster_28", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14966:11238"}}, {"id": "Cluster_29", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:24472:10224"}}, {"id": "Cluster_30", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:22469:24753"}}, {"id": "Cluster_31", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13243:24549"}}, {"id": "Cluster_32", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19945:7038"}}, {"id": "Cluster_33", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:6451:8890"}}, {"id": "Cluster_34", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:24138:10320"}}, {"id": "Cluster_35", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:21317:3390"}}, {"id": "Cluster_36", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:12120:5410"}}, {"id": "Cluster_37", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:18242:4220"}}, {"id": "Cluster_38", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:5888:8430"}}, {"id": "Cluster_39", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13476:22617"}}, {"id": "Cluster_40", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:11680:15148"}}, {"id": "Cluster_41", "metadata": {"seed_id": "HWI-M0018'..b'55, 1, 1], [41956, 0, 1], [41957, 0, 1], [41958, 1, 1], [41959, 1, 1], [41960, 1, 1], [41961, 0, 2], [41962, 1, 1], [41963, 0, 1], [41964, 0, 2], [41965, 0, 1], [41966, 0, 1], [41967, 0, 1], [41968, 0, 1], [41969, 1, 1], [41970, 0, 1], [41971, 1, 1], [41972, 0, 1], [41973, 0, 1], [41974, 1, 1], [41975, 1, 1], [41976, 0, 1], [41977, 1, 1], [41978, 1, 1], [41979, 1, 1], [41980, 0, 1], [41981, 1, 1], [41982, 0, 2], [41983, 1, 1], [41984, 0, 1], [41985, 0, 1], [41986, 0, 1], [41987, 1, 1], [41988, 0, 1], [41989, 0, 1], [41990, 0, 1], [41991, 1, 1], [41992, 0, 1], [41993, 0, 1], [41994, 0, 1], [41995, 1, 1], [41996, 1, 1], [41997, 0, 1], [41998, 1, 1], [41999, 1, 1], [42000, 1, 1], [42001, 0, 1], [42002, 0, 1], [42003, 1, 1], [42004, 1, 1], [42005, 1, 1], [42006, 0, 1], [42007, 0, 1], [42008, 1, 1], [42009, 0, 1], [42010, 0, 1], [42011, 0, 1], [42012, 0, 1], [42013, 1, 1], [42014, 0, 1], [42015, 0, 1], [42016, 0, 1], [42017, 0, 1], [42018, 0, 1], [42019, 0, 1], [42020, 1, 1], [42021,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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/02-clustering.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering.fasta Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,84400 @@\n+>Cluster_1 1:N:0:ACTTGA\n+CACGTAAGAATTTGCCTTTAGGAGGGGGATAACAATTGGAAACGATTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATAGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_2 1:N:0:ACTTGA\n+CACGTAAGAATTTGCCTTTAGGAGGGGGACAACAACTGGAAACGGTTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAAAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_3 1:N:0:ACTTGA\n+TGCGTCGGAACGTACCGAGTAATGGGGGATAACGCAGCGAAAGTTGTGCTAATACCGCATACGCCCTGAGGGGGAAAGTGGGGGACCGCAAGGCCTCACGTTATTCGAGCGGCCGACGTCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATTCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCAGCAGGAACGAAACGGTACGCTCTAACATAGTGTGCTAATGACGGTACCTGCAGAAGAAGCACCGGCTAACTAC\n+>Cluster_4 1:N:0:ACTTGA\n+CACGTGAGAATCTGCCTCCAGGTCGGGGACAACAGCGGGAAACTGCTGCTAATACCCGATGTGCCTAAGGGTGAAAGATTAATTGCCTGGAGATGAGCTCGCGTCCGATTAGCTAGTTGGTAGAGTAAAAGCCTACCAAGGCTCCGATCGGTAGCTGGTCTGAGAGGATGAGCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAAGACCGCGTGGGGGATGAAGGCTCTTGGGTTGTAAACCCCTTTTCTCAGGGAAGAAGTTCTGACGGTACCTGAGGAATCAGCATCGGCTAACTCC\n+>Cluster_5 1:N:0:ACTTGA\n+CGCGTGGGAATCTGCCCTGCAGTGGGGGACAACCCGAGGAAACTCGGGCTAATACCGCATACGTCCTATGGGAGAAAGGGGGCCTTCGGGCTCTCGCTGCAGGATGAGCCCGCGTCCGATTAGCTTGTTGGTGGGGTAACGGCCCACCAAGGCTGCGATCGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTCAGTGGGGAAGAAAAGCGCGAGGTTAATACCCTTGTGTGTTGACGTTACCCACAGAAGAAGCACCGGCTAACTCC\n+>Cluster_6 1:N:0:ACTTGA\n+CACGTAAGAATTTACCTTTAGGAGGGGGACAACAGACAGAAATGACTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGATCAGTATCTGGTTTGAGAGGATGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATCTCGCGTGAGGGATGACTGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_7 1:N:0:ACTTGA\n+CGCGTGGGCAATCTACCTTCGAATCGGGGATAACATTGCGAAAGCGATGCTAATACCGGATGACATCCTGAAGGCTTCGGTTTTAAGGATCAAAGGTGGCCTCTACGAGTAAGCTACTGTTTGGAGATGAGCCCGCGTACCATTAGCTTGTTGGTAGGGTAACGGCCTACCAAGGCGACGATGGTTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAAACCACGAGGTGATAATATCGCTTTGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_8 1:N:0:ACTTGA\n+CGCGTGGGAATCTGCCCTGCAGTGGGGGACAACCCGAGGAAACTCGGGCTAATACCGCATACGTCTTACGAGAGAAAGGGGGCTTCGGCTCTCGCTGCAGGATGAGCCCGCGTCCGATTAGCTTGTTGGTAGGGTAATGGCCTACCAAGGCGACGATCGGTAGCTGGTCTGAGAGGATGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTCAGTGGGGAAGAAAAACCCGAGGTTAATACCCTTGGGTCTTGACGTTACCCACAGAAGAAGCACCGGCTAACTCC\n+>Cluster_9 1:N:0:ACTTGA\n+CGCGTGGGCAATCTACCTCCGAATCGGGGATAACATTGCGAAAGCGATGCTAATACCGGATGACATCCTGAGGACTTCGGTTTTCGGGATCAAAGGTGGCCTCTACGGGTAAGCTACTGTTTGGGGATGAGCCCGCGTACCATTAGCTTGTTGGTAGGGTAACGGCCTACCAAGGCGACGATGGTTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAAACCACGGAGCGTTAATATCGCTTTGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_10 1:N:0:ACTTGA\n+CACGTAAGAATTTGCCTTTAGGAGGGGGACAACAACTGGAAACGGTTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGATGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATCTCGCG'..b'AAGCTTCCTAATCACTAAATCATTTTTTTGAGATGCTTTAGTGATTAGGAGGCGCTTTAGGATGAGCCTACGCCGGATTAGCTTGTTGGTAAGGTAAAAGCTTACCAAGGCGACGATCCGTAGCTGGTCTGAGAGGACGATCAGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGGGAAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGAGGGTTGTAAAGCACTTTCAATAGCGAGGAAATGCATCAAGTTAATAGCTTGGTGAGCTGACGTTAGCTATAGAAGAAGCACCGTCTAACTCC\n+>Cluster_31879 1:N:0:CCGTCC\n+TGCATGGGTAACGTACCTCGCGCACAGGGATAGCGGCGCCCTTCGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATGATATCGGGGAGTCGCATGGCTTTCTGATCAAAGGTGGGGACCTTCGGGCCTACCGGAGCGAGAGCGGCCCATGTCCTATCAGCTAGTTGGTGGGGTAATGGCCTACCAAGGCGGTGACGGGTGGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGACGCAAGTCTGACGGAGCGACGCCGCGTGGAGGATGAAGTCCTTCGGGATGTAAACTCCAATGGTATGTCAGGAAGCAAACCGGCTGAACAGGCCGGGGCGTTGACCAGCATACGAAAGGGGTGGCTAACTCC\n+>Cluster_41540 1:N:0:ACTTGA\n+TGCATAGGTAACGTACCCCTCGCACGGGGATAGCAGCGGGCTTCGGCCCTTTAGCGAAAGTGCTGGTAATACCTGATAACATTCAGAGGTCTCCTGGCCTTTGGATCAAAGGTGGGGACCCTTCGGGGCCTACTGGCGTGGGATCGGCCTATGTCCTATCAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCAATGACGGGTAGTCGGCGTGAGAGCGCGACCGACCACATCGGGGCTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGACGCAAGTCTGACGGAGCGACGCCGCGTGAAGGATGAAGTCCTTCGGGATGTAAACTTCAATAGTATGTCAGGAAGCAAAGGGGCCTAATATGCCCTGGCGTTGACCATCATACGAAAGGGGTGGCTAACTCC\n+>Cluster_36176 1:N:0:ACTTGA\n+TGCATGGGTAACGTACCTTAGGCTCAGGGATAGCGGCGCCCTTCGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATGATATCCAGATTCTTCCTGGTTTCTGGATCAAAGATGGGGACCCTTCGGGGCCTGTCGGCCAAAGATCGGCCCATGTCCTATCAGCTTGTTGGTGGGGAAATGGCCTACCAAGGCGACGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTTCGGGTGGCTGCAGCAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCGCGTGGGGGATGAAGTCCTTCGGGATGTAAACTCTAATAGTATGCCAGGAAGCAAGCCGACCTAATACGTCGGTAAGTTGACCAACATATGAAAGGGGCGGCTAACTCC\n+>Cluster_34043 1:N:0:CCGTCC\n+TGCATGGGTAACGTGCCCTGAACACCGGGATAGCGGCGGGCTTCGGCCCTTTAGCGAAAATGCCGGTAATACCGGGTAACATCCAGAGGCCTCATGGCTTTTGGATCAAAAGCGGGGACCCTTCGGGGCCTGGCGGGTTTGGATCGGCCCCTGCCCTATCAGCTTGTTGGGGGGGGAACGGCCTACCAAAGCGGTGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGACGAAAGTCTGACAGAGCGACGCCGCGTGAAGGATGAAATCCTTCGGGATGTAAACTTCAATAGTTTGTCAGGAAGCGAGGGGGCCTAATACGTCCCTAAGTTGACCACCAAACGAAAGGGGTGGCTAACTCC\n+>Cluster_19598 1:N:0:ACTTGA\n+CACATGGGTAACGTACCTTGGACACAGGGATAGCGGCGCCCCGCAAGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATAATATCCCGGTTCGGCATCGAGCCGGGATCAAATGGTGGGGACCTTCGGGCCTGCCGGTCTGAGATCGGCCCATGCCCTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCTAAGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCGCGTGGGGGATGAAGTCCTTCGGGATGTAAACTTTAATGGTATGCTAGGAAGCGAACCGGCCTAATACGTCGGCGAGTTGACCCGCATACGAAAGGGGCGGCTAACTCC\n+>Cluster_29760 1:N:0:ACTTGA\n+CACATGGGTAACGTACCTTGGACACAGGGATAGCGGCGCCCCGCAAGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATAATATCTCGGCTCGGCATCGAGCTGAGATCAGATGGTGGGGACCTTCGGGCCTGCCGGTCTGGGATCGGCCCATGCCCTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCTAAGGCGGGTAGCCGGCGTGAGAGAGCGACCGGCCACATCGGCACTAAGACCCTGCCCTGCCACCTACGGGTGGCTGCGGCCACGAAGATGCCGCAGTGAGGCATAGCATGACGGAGCGAAGCGGGGGGGGAGAGGAGGGCCCTTGGTATGAAAACTGTAAAGGTATGCTAGGAAGCGGGGCGGCCTAATACGCCGGTGAGCGGACCCGCATACGAAAGGGGCGGCTAACTCC\n+>Cluster_40660 1:N:0:ACTTGA\n+CACGTGAGAAACCTGCCCTTCAGTGGGGGACAACGTCGGTTCTTCGGAACCTCGCGAAAGCGGCGCTAATACCCCATGTCATCTCTGGATCGCATGTTCCGGGGCTGAAAGCGGGGGACCCTTCGGGGCCTCGCGCTGAAGGATGGTCTCGCGCCTGATTAGCTAGTTGGTGGGGTAACGGCCTACCAAGGCTTCGATCAGTAGCTGGCCTGAGAGGGTGGTCAGCCACACTGGGATTGAGATACGGCCCAGACTCCTACGGGAGGCAACAGTCTAGAAGCTTCGGCAATGGGGGCAACCCTGACCGAGCGACGCCGTGTGAAGGATGACACAGTTTATCTGCGTAAAGTACTGTTAACCGGGACGAAAAGATGCATGGACTGCATTTATATGACGGTACCGGTAGAGGAAGCTCCGGCTAACTCC\n+>Cluster_41680 1:N:0:CCGTCC\n+TAAATAGATAACGTACCCCGGTCTCAGGGATACCAGCGGGAGCTTGCTCCCTTTGCGAAAGTGCTGTTAATACCTGATAACGTTTAGCGTAGGCATCTACGAAAAATCAAAGGTGGGGACCCTCGGGCCTACCGGACTGGGAGCGGTCTATTTCCTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCAGCGACGGGTAGCCGGACTGAGAGGTTGGACGGCCACATCGGAACTGAGACACTGTCCGGACACCTACGGGTGGCTGCAGTAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCTCGTGGAGGACGAATTCCCTCGGGATGTAAACTCCTTTTAGGGTTACGCAAGCAAGGATGGTTAATACCCATCTGCGTTGAGCTATCCCAGAAAAAGCCTCGGCTAACTCC\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/02-clustering_compo.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering_compo.tsv Thu Oct 25 05:01:13 2018 -0400
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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/03-chimera.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/03-chimera.biom Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16192:3924"}}, {"id": "Cluster_2", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:12521:5680"}}, {"id": "Cluster_3", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16005:1920"}}, {"id": "Cluster_4", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14417:1745"}}, {"id": "Cluster_5", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19898:5958"}}, {"id": "Cluster_6", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:10625:3122"}}, {"id": "Cluster_7", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19644:2236"}}, {"id": "Cluster_8", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19958:2207"}}, {"id": "Cluster_9", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14723:9889"}}, {"id": "Cluster_10", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:22681:4284"}}, {"id": "Cluster_11", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:27968:12864"}}, {"id": "Cluster_12", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14639:6828"}}, {"id": "Cluster_13", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:4008:12611"}}, {"id": "Cluster_14", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:21539:2936"}}, {"id": "Cluster_15", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:20802:4801"}}, {"id": "Cluster_16", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1102:16581:10470"}}, {"id": "Cluster_17", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19782:3604"}}, {"id": "Cluster_18", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:6692:9035"}}, {"id": "Cluster_19", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:20545:9379"}}, {"id": "Cluster_20", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14438:5670"}}, {"id": "Cluster_21", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:20869:4256"}}, {"id": "Cluster_22", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1102:7862:4645"}}, {"id": "Cluster_23", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13251:3399"}}, {"id": "Cluster_24", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13562:5876"}}, {"id": "Cluster_25", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13515:9183"}}, {"id": "Cluster_26", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:2885:13564"}}, {"id": "Cluster_27", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:21255:10262"}}, {"id": "Cluster_28", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14966:11238"}}, {"id": "Cluster_29", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:24472:10224"}}, {"id": "Cluster_30", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:22469:24753"}}, {"id": "Cluster_31", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13243:24549"}}, {"id": "Cluster_32", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19945:7038"}}, {"id": "Cluster_33", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:6451:8890"}}, {"id": "Cluster_34", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:24138:10320"}}, {"id": "Cluster_35", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:21317:3390"}}, {"id": "Cluster_36", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:12120:5410"}}, {"id": "Cluster_37", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:18242:4220"}}, {"id": "Cluster_38", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:5888:8430"}}, {"id": "Cluster_39", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13476:22617"}}, {"id": "Cluster_40", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:11680:15148"}}, {"id": "Cluster_41", "metadata": {"seed_id": "HWI-M0018'..b'64, 1, 1], [14065, 1, 1], [14066, 0, 1], [14067, 1, 1], [14068, 0, 1], [14069, 0, 1], [14070, 0, 1], [14071, 0, 1], [14072, 0, 1], [14073, 0, 1], [14074, 1, 1], [14075, 1, 1], [14076, 0, 1], [14077, 0, 1], [14078, 1, 1], [14079, 0, 1], [14080, 0, 1], [14081, 0, 1], [14082, 0, 1], [14083, 0, 1], [14084, 0, 1], [14085, 0, 1], [14086, 0, 1], [14087, 1, 1], [14088, 1, 1], [14089, 1, 1], [14090, 0, 1], [14091, 1, 1], [14092, 0, 1], [14093, 0, 1], [14094, 0, 1], [14095, 0, 1], [14096, 0, 1], [14097, 0, 1], [14098, 0, 1], [14099, 0, 1], [14100, 0, 1], [14101, 0, 1], [14102, 1, 1], [14103, 0, 1], [14104, 0, 1], [14105, 0, 1], [14106, 0, 1], [14107, 0, 1], [14108, 0, 1], [14109, 1, 1], [14110, 0, 1], [14111, 0, 1], [14112, 0, 1], [14113, 1, 1], [14114, 0, 1], [14115, 0, 1], [14116, 1, 1], [14117, 0, 1], [14118, 1, 1], [14119, 1, 1], [14120, 0, 1], [14121, 0, 1], [14122, 1, 1], [14123, 0, 1], [14124, 0, 1], [14125, 0, 1], [14126, 0, 1], [14127, 0, 1], [14128, 1, 1], [14129, 1, 1], [14130,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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/03-chimera.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/03-chimera.fasta Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,28618 @@\n+>Cluster_1 1:N:0:ACTTGA\n+CACGTAAGAATTTGCCTTTAGGAGGGGGATAACAATTGGAAACGATTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATAGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_2 1:N:0:ACTTGA\n+CACGTAAGAATTTGCCTTTAGGAGGGGGACAACAACTGGAAACGGTTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAAAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_3 1:N:0:ACTTGA\n+TGCGTCGGAACGTACCGAGTAATGGGGGATAACGCAGCGAAAGTTGTGCTAATACCGCATACGCCCTGAGGGGGAAAGTGGGGGACCGCAAGGCCTCACGTTATTCGAGCGGCCGACGTCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATTCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCAGCAGGAACGAAACGGTACGCTCTAACATAGTGTGCTAATGACGGTACCTGCAGAAGAAGCACCGGCTAACTAC\n+>Cluster_4 1:N:0:ACTTGA\n+CACGTGAGAATCTGCCTCCAGGTCGGGGACAACAGCGGGAAACTGCTGCTAATACCCGATGTGCCTAAGGGTGAAAGATTAATTGCCTGGAGATGAGCTCGCGTCCGATTAGCTAGTTGGTAGAGTAAAAGCCTACCAAGGCTCCGATCGGTAGCTGGTCTGAGAGGATGAGCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAAGACCGCGTGGGGGATGAAGGCTCTTGGGTTGTAAACCCCTTTTCTCAGGGAAGAAGTTCTGACGGTACCTGAGGAATCAGCATCGGCTAACTCC\n+>Cluster_5 1:N:0:ACTTGA\n+CGCGTGGGAATCTGCCCTGCAGTGGGGGACAACCCGAGGAAACTCGGGCTAATACCGCATACGTCCTATGGGAGAAAGGGGGCCTTCGGGCTCTCGCTGCAGGATGAGCCCGCGTCCGATTAGCTTGTTGGTGGGGTAACGGCCCACCAAGGCTGCGATCGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTCAGTGGGGAAGAAAAGCGCGAGGTTAATACCCTTGTGTGTTGACGTTACCCACAGAAGAAGCACCGGCTAACTCC\n+>Cluster_6 1:N:0:ACTTGA\n+CACGTAAGAATTTACCTTTAGGAGGGGGACAACAGACAGAAATGACTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGATCAGTATCTGGTTTGAGAGGATGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATCTCGCGTGAGGGATGACTGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_7 1:N:0:ACTTGA\n+CGCGTGGGCAATCTACCTTCGAATCGGGGATAACATTGCGAAAGCGATGCTAATACCGGATGACATCCTGAAGGCTTCGGTTTTAAGGATCAAAGGTGGCCTCTACGAGTAAGCTACTGTTTGGAGATGAGCCCGCGTACCATTAGCTTGTTGGTAGGGTAACGGCCTACCAAGGCGACGATGGTTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAAACCACGAGGTGATAATATCGCTTTGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_8 1:N:0:ACTTGA\n+CGCGTGGGAATCTGCCCTGCAGTGGGGGACAACCCGAGGAAACTCGGGCTAATACCGCATACGTCTTACGAGAGAAAGGGGGCTTCGGCTCTCGCTGCAGGATGAGCCCGCGTCCGATTAGCTTGTTGGTAGGGTAATGGCCTACCAAGGCGACGATCGGTAGCTGGTCTGAGAGGATGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTCAGTGGGGAAGAAAAACCCGAGGTTAATACCCTTGGGTCTTGACGTTACCCACAGAAGAAGCACCGGCTAACTCC\n+>Cluster_9 1:N:0:ACTTGA\n+CGCGTGGGCAATCTACCTCCGAATCGGGGATAACATTGCGAAAGCGATGCTAATACCGGATGACATCCTGAGGACTTCGGTTTTCGGGATCAAAGGTGGCCTCTACGGGTAAGCTACTGTTTGGGGATGAGCCCGCGTACCATTAGCTTGTTGGTAGGGTAACGGCCTACCAAGGCGACGATGGTTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAAACCACGGAGCGTTAATATCGCTTTGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_10 1:N:0:ACTTGA\n+CACGTAAGAATTTGCCTTTAGGAGGGGGACAACAACTGGAAACGGTTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGATGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATCTCGCG'..b'ATTATTGTAGACGTGAATTGAGATTAGTAATAATGGAGAGAAGCAGATATAATAAAGGAGAGAGATTGTAGAAAGATTGAATCGCTAGAAGAGGAGCTTTTGTAGGATTAGGTAGTTGGTGTGGTAAAGGCAGACCAAGCCGAAGATCCTTAACTGGTCTGAGAGGATGTACAGTCACACTGGGACTGAAAAAAGGCCCAGCCTTCCATGGAAGTCTGCAGTAGGGAATTCTGGACAATGGGCGAAAGCTTGATCCGGTGATACCAAATGAGTGATGAAGGTGAAAACTGTAAAACTTGATTATTAAGGAGAATAATGATGTTACTTAATAAGGAAGCCCCGGCTAATCTT\n+>Cluster_30140 1:N:0:ACTTGA\n+TACGTAGGAATCTACCCTAGAGTGGGGGACAACCCATCGAAAGATGGGCTAATACCGCATAATCTCTGAGGAGAAAAGCTTCCTAATCACTAAATCATTTTTTTGAGATGCTTTAGTGATTAGGAGGCGCTTTAGGATGAGCCTACGCCGGATTAGCTTGTTGGTAAGGTAAAAGCTTACCAAGGCGACGATCCGTAGCTGGTCTGAGAGGACGATCAGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGGGAAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGAGGGTTGTAAAGCACTTTCAATAGCGAGGAAATGCATCAAGTTAATAGCTTGGTGAGCTGACGTTAGCTATAGAAGAAGCACCGTCTAACTCC\n+>Cluster_31879 1:N:0:CCGTCC\n+TGCATGGGTAACGTACCTCGCGCACAGGGATAGCGGCGCCCTTCGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATGATATCGGGGAGTCGCATGGCTTTCTGATCAAAGGTGGGGACCTTCGGGCCTACCGGAGCGAGAGCGGCCCATGTCCTATCAGCTAGTTGGTGGGGTAATGGCCTACCAAGGCGGTGACGGGTGGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGACGCAAGTCTGACGGAGCGACGCCGCGTGGAGGATGAAGTCCTTCGGGATGTAAACTCCAATGGTATGTCAGGAAGCAAACCGGCTGAACAGGCCGGGGCGTTGACCAGCATACGAAAGGGGTGGCTAACTCC\n+>Cluster_41540 1:N:0:ACTTGA\n+TGCATAGGTAACGTACCCCTCGCACGGGGATAGCAGCGGGCTTCGGCCCTTTAGCGAAAGTGCTGGTAATACCTGATAACATTCAGAGGTCTCCTGGCCTTTGGATCAAAGGTGGGGACCCTTCGGGGCCTACTGGCGTGGGATCGGCCTATGTCCTATCAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCAATGACGGGTAGTCGGCGTGAGAGCGCGACCGACCACATCGGGGCTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGACGCAAGTCTGACGGAGCGACGCCGCGTGAAGGATGAAGTCCTTCGGGATGTAAACTTCAATAGTATGTCAGGAAGCAAAGGGGCCTAATATGCCCTGGCGTTGACCATCATACGAAAGGGGTGGCTAACTCC\n+>Cluster_36176 1:N:0:ACTTGA\n+TGCATGGGTAACGTACCTTAGGCTCAGGGATAGCGGCGCCCTTCGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATGATATCCAGATTCTTCCTGGTTTCTGGATCAAAGATGGGGACCCTTCGGGGCCTGTCGGCCAAAGATCGGCCCATGTCCTATCAGCTTGTTGGTGGGGAAATGGCCTACCAAGGCGACGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTTCGGGTGGCTGCAGCAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCGCGTGGGGGATGAAGTCCTTCGGGATGTAAACTCTAATAGTATGCCAGGAAGCAAGCCGACCTAATACGTCGGTAAGTTGACCAACATATGAAAGGGGCGGCTAACTCC\n+>Cluster_34043 1:N:0:CCGTCC\n+TGCATGGGTAACGTGCCCTGAACACCGGGATAGCGGCGGGCTTCGGCCCTTTAGCGAAAATGCCGGTAATACCGGGTAACATCCAGAGGCCTCATGGCTTTTGGATCAAAAGCGGGGACCCTTCGGGGCCTGGCGGGTTTGGATCGGCCCCTGCCCTATCAGCTTGTTGGGGGGGGAACGGCCTACCAAAGCGGTGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGACGAAAGTCTGACAGAGCGACGCCGCGTGAAGGATGAAATCCTTCGGGATGTAAACTTCAATAGTTTGTCAGGAAGCGAGGGGGCCTAATACGTCCCTAAGTTGACCACCAAACGAAAGGGGTGGCTAACTCC\n+>Cluster_19598 1:N:0:ACTTGA\n+CACATGGGTAACGTACCTTGGACACAGGGATAGCGGCGCCCCGCAAGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATAATATCCCGGTTCGGCATCGAGCCGGGATCAAATGGTGGGGACCTTCGGGCCTGCCGGTCTGAGATCGGCCCATGCCCTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCTAAGACGGGTAGCCGGCGTGAGAGCGCGACCGGCCACATCGGGACTGAGACACTGCCCGGACACCTACGGGTGGCTGCAGCAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCGCGTGGGGGATGAAGTCCTTCGGGATGTAAACTTTAATGGTATGCTAGGAAGCGAACCGGCCTAATACGTCGGCGAGTTGACCCGCATACGAAAGGGGCGGCTAACTCC\n+>Cluster_29760 1:N:0:ACTTGA\n+CACATGGGTAACGTACCTTGGACACAGGGATAGCGGCGCCCCGCAAGGGGCTTTAGCGAAAGTGCCGGTAATACCTGATAATATCTCGGCTCGGCATCGAGCTGAGATCAGATGGTGGGGACCTTCGGGCCTGCCGGTCTGGGATCGGCCCATGCCCTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCTAAGGCGGGTAGCCGGCGTGAGAGAGCGACCGGCCACATCGGCACTAAGACCCTGCCCTGCCACCTACGGGTGGCTGCGGCCACGAAGATGCCGCAGTGAGGCATAGCATGACGGAGCGAAGCGGGGGGGGAGAGGAGGGCCCTTGGTATGAAAACTGTAAAGGTATGCTAGGAAGCGGGGCGGCCTAATACGCCGGTGAGCGGACCCGCATACGAAAGGGGCGGCTAACTCC\n+>Cluster_41680 1:N:0:CCGTCC\n+TAAATAGATAACGTACCCCGGTCTCAGGGATACCAGCGGGAGCTTGCTCCCTTTGCGAAAGTGCTGTTAATACCTGATAACGTTTAGCGTAGGCATCTACGAAAAATCAAAGGTGGGGACCCTCGGGCCTACCGGACTGGGAGCGGTCTATTTCCTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCAGCGACGGGTAGCCGGACTGAGAGGTTGGACGGCCACATCGGAACTGAGACACTGTCCGGACACCTACGGGTGGCTGCAGTAACGAATATTCCGCAATGGGCGAAAGCCTGACGGAGCGACGCCTCGTGGAGGACGAATTCCCTCGGGATGTAAACTCCTTTTAGGGTTACGCAAGCAAGGATGGTTAATACCCATCTGCGTTGAGCTATCCCAGAAAAAGCCTCGGCTAACTCC\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/04-affiliation.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/04-affiliation.biom Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "CL500-29 marine group", "unknown species"], "blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 0.39, 0.29, 0.29], "blast_affiliations": [{"perc_identity": 84.31, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "evalue": "8e-68", "aln_length": 255, "perc_query_coverage": 70.83333333333334, "subject": "JQ269315.1.1487"}], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16192:3924"}}, {"id": "Cluster_2", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 0.56, 0.56, 0.39], "blast_affiliations": [{"perc_identity": 84.77, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "evalue": "5e-70", "aln_length": 256, "perc_query_coverage": 70.91412742382272, "subject": "JQ269315.1.1487"}], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:12521:5680"}}, {"id": "Cluster_3", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "unknown species"], "blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "unknown species"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 0.79, 0.79, 0.76], "blast_affiliations": [{"perc_identity": 92.06, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "unknown species"], "evalue": "2e-83", "aln_length": 214, "perc_query_coverage": 53.80710659898477, "subject": "KF182287.1.1248"}], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16005:1920"}}, {"id": "Cluster_4", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Iamiaceae", "Iamia", "Iamia majanohamensis"], "blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "Ferrithrix", "actinobacterium BGR 77"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 0.19, 0.19, 0.13], "blast_affiliations": [{"perc_identity": 86.49, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "Ferrithrix", "actinobacterium BGR 77"], "evalue": "2e-78", "aln_length": 259, "perc_query_coverage": 72.47191011235955, "subject": "GU168000.1.1473"}], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14417:1745"}}, {"id": "Cluster_5", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "Acidimicrobium", "unknown species"], "blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "unknown genus", "unknown species"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 0.31, 0.12, 0.12], "blast_affiliations": [{"perc_identity": 90.0, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "unknown genus", "unknown species"], "evalue": "2e-79", "aln_length": 220, "perc_query_coverage": 56.41025641025641, "subject": "EF471700.1.1483"}], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19898:5958"}}, {"id": "Cluster_6", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "actinobacterium BGR 43"], "blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6'..b'1], [1521, 2, 1], [1522, 0, 5], [1522, 1, 1], [1522, 2, 1], [1523, 0, 4], [1523, 1, 1], [1523, 2, 1], [1524, 0, 4], [1524, 1, 1], [1524, 2, 1], [1525, 0, 2], [1525, 1, 2], [1525, 2, 2], [1526, 0, 6], [1526, 1, 1], [1526, 2, 2], [1527, 0, 3], [1527, 1, 5], [1527, 2, 3], [1528, 0, 2], [1528, 1, 1], [1528, 2, 3], [1529, 0, 3], [1529, 1, 2], [1529, 2, 2], [1530, 0, 3], [1530, 1, 2], [1530, 2, 2], [1531, 0, 1], [1531, 1, 2], [1531, 2, 3], [1532, 0, 3], [1532, 1, 2], [1532, 2, 2], [1533, 0, 2], [1533, 1, 2], [1533, 2, 2], [1534, 0, 4], [1534, 1, 1], [1534, 2, 1], [1535, 0, 4], [1535, 1, 2], [1535, 2, 2], [1536, 0, 3], [1536, 1, 1], [1536, 2, 3], [1537, 0, 4], [1537, 1, 2], [1537, 2, 1], [1538, 0, 2], [1538, 1, 2], [1538, 2, 2], [1539, 0, 5], [1539, 1, 4], [1539, 2, 1], [1540, 0, 2], [1540, 1, 2], [1540, 2, 2], [1541, 0, 5], [1541, 1, 2], [1541, 2, 2], [1542, 0, 4], [1542, 1, 1], [1542, 2, 1], [1543, 0, 2], [1543, 1, 3], [1543, 2, 2], [1544, 0, 2], [1544, 1, 4], [1544, 2, 2], [1545, 0,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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/04-filters.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/04-filters.biom Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16192:3924"}}, {"id": "Cluster_2", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:12521:5680"}}, {"id": "Cluster_3", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16005:1920"}}, {"id": "Cluster_4", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14417:1745"}}, {"id": "Cluster_5", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19898:5958"}}, {"id": "Cluster_6", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:10625:3122"}}, {"id": "Cluster_7", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19644:2236"}}, {"id": "Cluster_8", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19958:2207"}}, {"id": "Cluster_9", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14723:9889"}}, {"id": "Cluster_10", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:22681:4284"}}, {"id": "Cluster_11", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:27968:12864"}}, {"id": "Cluster_12", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14639:6828"}}, {"id": "Cluster_13", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:4008:12611"}}, {"id": "Cluster_14", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:21539:2936"}}, {"id": "Cluster_15", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:20802:4801"}}, {"id": "Cluster_16", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1102:16581:10470"}}, {"id": "Cluster_17", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19782:3604"}}, {"id": "Cluster_18", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:6692:9035"}}, {"id": "Cluster_19", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:20545:9379"}}, {"id": "Cluster_20", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14438:5670"}}, {"id": "Cluster_21", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:20869:4256"}}, {"id": "Cluster_22", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1102:7862:4645"}}, {"id": "Cluster_23", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13251:3399"}}, {"id": "Cluster_24", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13562:5876"}}, {"id": "Cluster_25", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13515:9183"}}, {"id": "Cluster_26", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:2885:13564"}}, {"id": "Cluster_27", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:21255:10262"}}, {"id": "Cluster_28", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14966:11238"}}, {"id": "Cluster_29", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:24472:10224"}}, {"id": "Cluster_30", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:22469:24753"}}, {"id": "Cluster_31", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13243:24549"}}, {"id": "Cluster_32", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19945:7038"}}, {"id": "Cluster_33", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:6451:8890"}}, {"id": "Cluster_34", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:24138:10320"}}, {"id": "Cluster_35", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:21317:3390"}}, {"id": "Cluster_36", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:12120:5410"}}, {"id": "Cluster_37", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:18242:4220"}}, {"id": "Cluster_38", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:5888:8430"}}, {"id": "Cluster_39", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:13476:22617"}}, {"id": "Cluster_40", "metadata": {"seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:11680:15148"}}, {"id": "Cluster_41", "metadata": {"seed_id": "HWI-M0018'..b'1], [1521, 2, 1], [1522, 0, 5], [1522, 1, 1], [1522, 2, 1], [1523, 0, 4], [1523, 1, 1], [1523, 2, 1], [1524, 0, 4], [1524, 1, 1], [1524, 2, 1], [1525, 0, 2], [1525, 1, 2], [1525, 2, 2], [1526, 0, 6], [1526, 1, 1], [1526, 2, 2], [1527, 0, 3], [1527, 1, 5], [1527, 2, 3], [1528, 0, 2], [1528, 1, 1], [1528, 2, 3], [1529, 0, 3], [1529, 1, 2], [1529, 2, 2], [1530, 0, 3], [1530, 1, 2], [1530, 2, 2], [1531, 0, 1], [1531, 1, 2], [1531, 2, 3], [1532, 0, 3], [1532, 1, 2], [1532, 2, 2], [1533, 0, 2], [1533, 1, 2], [1533, 2, 2], [1534, 0, 4], [1534, 1, 1], [1534, 2, 1], [1535, 0, 4], [1535, 1, 2], [1535, 2, 2], [1536, 0, 3], [1536, 1, 1], [1536, 2, 3], [1537, 0, 4], [1537, 1, 2], [1537, 2, 1], [1538, 0, 2], [1538, 1, 2], [1538, 2, 2], [1539, 0, 5], [1539, 1, 4], [1539, 2, 1], [1540, 0, 2], [1540, 1, 2], [1540, 2, 2], [1541, 0, 5], [1541, 1, 2], [1541, 2, 2], [1542, 0, 4], [1542, 1, 1], [1542, 2, 1], [1543, 0, 2], [1543, 1, 3], [1543, 2, 2], [1544, 0, 2], [1544, 1, 4], [1544, 2, 2], [1545, 0, 4], [1545, 1, 1], [1545, 2, 2], [1546, 0, 3], [1546, 1, 1], [1546, 2, 2], [1547, 0, 4], [1547, 1, 3], [1547, 2, 1], [1548, 0, 3], [1548, 1, 2], [1548, 2, 3], [1549, 0, 5], [1549, 1, 1], [1549, 2, 2], [1550, 0, 1], [1550, 1, 3], [1550, 2, 3], [1551, 0, 5], [1551, 1, 1], [1551, 2, 1], [1552, 0, 2], [1552, 1, 4], [1552, 2, 1], [1553, 0, 3], [1553, 1, 3], [1553, 2, 2], [1554, 0, 3], [1554, 1, 2], [1554, 2, 1], [1555, 0, 4], [1555, 1, 2], [1555, 2, 1], [1556, 0, 6], [1556, 1, 2], [1556, 2, 1], [1557, 0, 3], [1557, 1, 3], [1557, 2, 1], [1558, 0, 4], [1558, 1, 1], [1558, 2, 1], [1559, 0, 4], [1559, 1, 2], [1559, 2, 1], [1560, 0, 4], [1560, 1, 1], [1560, 2, 1], [1561, 0, 7], [1561, 1, 1], [1561, 2, 1], [1562, 0, 3], [1562, 1, 1], [1562, 2, 2], [1563, 0, 1], [1563, 1, 3], [1563, 2, 2], [1564, 0, 4], [1564, 1, 1], [1564, 2, 3], [1565, 0, 9], [1565, 1, 4], [1565, 2, 2], [1566, 0, 4], [1566, 1, 1], [1566, 2, 1], [1567, 0, 1], [1567, 1, 4], [1567, 2, 1], [1568, 0, 5], [1568, 1, 3], [1568, 2, 2], [1569, 0, 5], [1569, 1, 1], [1569, 2, 1], [1570, 0, 2], [1570, 1, 5], [1570, 2, 1], [1571, 0, 3], [1571, 1, 2], [1571, 2, 1], [1572, 0, 4], [1572, 1, 2], [1572, 2, 1], [1573, 0, 1], [1573, 1, 3], [1573, 2, 2], [1574, 0, 6], [1574, 1, 4], [1574, 2, 3], [1575, 0, 4], [1575, 1, 1], [1575, 2, 2], [1576, 0, 4], [1576, 1, 1], [1576, 2, 3], [1577, 0, 2], [1577, 1, 2], [1577, 2, 2], [1578, 0, 3], [1578, 1, 1], [1578, 2, 2], [1579, 0, 2], [1579, 1, 2], [1579, 2, 2], [1580, 0, 2], [1580, 1, 2], [1580, 2, 2], [1581, 0, 3], [1581, 1, 2], [1581, 2, 1], [1582, 0, 4], [1582, 1, 2], [1582, 2, 1], [1583, 0, 3], [1583, 1, 2], [1583, 2, 2], [1584, 0, 2], [1584, 1, 2], [1584, 2, 3], [1585, 0, 2], [1585, 1, 2], [1585, 2, 2], [1586, 0, 4], [1586, 1, 2], [1586, 2, 1], [1587, 0, 2], [1587, 1, 2], [1587, 2, 2], [1588, 0, 1], [1588, 1, 2], [1588, 2, 3], [1589, 0, 3], [1589, 1, 1], [1589, 2, 2], [1590, 0, 1], [1590, 1, 2], [1590, 2, 3], [1591, 0, 2], [1591, 1, 3], [1591, 2, 1], [1592, 0, 3], [1592, 1, 2], [1592, 2, 1], [1593, 0, 4], [1593, 1, 2], [1593, 2, 2], [1594, 0, 1], [1594, 1, 3], [1594, 2, 2], [1595, 0, 2], [1595, 1, 1], [1595, 2, 3], [1596, 0, 2], [1596, 1, 4], [1596, 2, 1], [1597, 0, 5], [1597, 1, 2], [1597, 2, 1], [1598, 0, 1], [1598, 1, 4], [1598, 2, 1], [1599, 0, 4], [1599, 1, 1], [1599, 2, 1], [1600, 0, 3], [1600, 1, 3], [1600, 2, 1], [1601, 0, 2], [1601, 1, 3], [1601, 2, 1], [1602, 0, 3], [1602, 1, 2], [1602, 2, 1], [1603, 0, 4], [1603, 1, 2], [1603, 2, 2], [1604, 0, 1], [1604, 1, 2], [1604, 2, 3], [1605, 0, 2], [1605, 1, 4], [1605, 2, 1], [1606, 0, 3], [1606, 1, 1], [1606, 2, 2], [1607, 0, 3], [1607, 1, 2], [1607, 2, 1], [1608, 0, 5], [1608, 1, 1], [1608, 2, 1]], "generated_by": "swarm", "matrix_type": "sparse", "shape": [1609, 3], "format_url": "http://biom-format.org", "date": "2018-01-12T18:17:43", "type": "OTU table", "id": null, "columns": [{"id": "splA_01", "metadata": null}, {"id": "splA_02", "metadata": null}, {"id": "splA_03", "metadata": null}]}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/04-filters.excluded
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/04-filters.excluded Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,12438 @@\n+#Present in minus of 3 samples\tAbundance < 5e-05\n+Cluster_516\tCluster_1658\n+Cluster_658\tCluster_1659\n+Cluster_682\tCluster_1660\n+Cluster_708\tCluster_1661\n+Cluster_709\tCluster_1662\n+Cluster_748\tCluster_1663\n+Cluster_793\tCluster_1664\n+Cluster_822\tCluster_1670\n+Cluster_830\tCluster_1674\n+Cluster_838\tCluster_1675\n+Cluster_854\tCluster_1677\n+Cluster_856\tCluster_1678\n+Cluster_863\tCluster_1679\n+Cluster_874\tCluster_1682\n+Cluster_885\tCluster_1685\n+Cluster_899\tCluster_1687\n+Cluster_908\tCluster_1698\n+Cluster_911\tCluster_1700\n+Cluster_916\tCluster_1703\n+Cluster_919\tCluster_1706\n+Cluster_929\tCluster_1711\n+Cluster_947\tCluster_1714\n+Cluster_973\tCluster_1717\n+Cluster_995\tCluster_1718\n+Cluster_1008\tCluster_1719\n+Cluster_1056\tCluster_1720\n+Cluster_1059\tCluster_1721\n+Cluster_1065\tCluster_1724\n+Cluster_1070\tCluster_1727\n+Cluster_1074\tCluster_1728\n+Cluster_1075\tCluster_1739\n+Cluster_1076\tCluster_1744\n+Cluster_1079\tCluster_1747\n+Cluster_1083\tCluster_1748\n+Cluster_1085\tCluster_1751\n+Cluster_1086\tCluster_1752\n+Cluster_1087\tCluster_1753\n+Cluster_1094\tCluster_1754\n+Cluster_1107\tCluster_1758\n+Cluster_1122\tCluster_1762\n+Cluster_1123\tCluster_1763\n+Cluster_1139\tCluster_1764\n+Cluster_1141\tCluster_1771\n+Cluster_1147\tCluster_1777\n+Cluster_1152\tCluster_1780\n+Cluster_1159\tCluster_1783\n+Cluster_1163\tCluster_1785\n+Cluster_1170\tCluster_1789\n+Cluster_1176\tCluster_1791\n+Cluster_1179\tCluster_1793\n+Cluster_1180\tCluster_1796\n+Cluster_1195\tCluster_1799\n+Cluster_1204\tCluster_1803\n+Cluster_1206\tCluster_1810\n+Cluster_1218\tCluster_1813\n+Cluster_1219\tCluster_1815\n+Cluster_1220\tCluster_1817\n+Cluster_1222\tCluster_1818\n+Cluster_1224\tCluster_1820\n+Cluster_1228\tCluster_1821\n+Cluster_1240\tCluster_1822\n+Cluster_1248\tCluster_1826\n+Cluster_1259\tCluster_1829\n+Cluster_1264\tCluster_1832\n+Cluster_1272\tCluster_1833\n+Cluster_1288\tCluster_1834\n+Cluster_1293\tCluster_1835\n+Cluster_1294\tCluster_1839\n+Cluster_1300\tCluster_1843\n+Cluster_1307\tCluster_1844\n+Cluster_1309\tCluster_1845\n+Cluster_1318\tCluster_1846\n+Cluster_1325\tCluster_1847\n+Cluster_1332\tCluster_1849\n+Cluster_1335\tCluster_1850\n+Cluster_1341\tCluster_1851\n+Cluster_1343\tCluster_1852\n+Cluster_1355\tCluster_1853\n+Cluster_1363\tCluster_1854\n+Cluster_1368\tCluster_1856\n+Cluster_1370\tCluster_1857\n+Cluster_1372\tCluster_1859\n+Cluster_1374\tCluster_1861\n+Cluster_1376\tCluster_1862\n+Cluster_1377\tCluster_1863\n+Cluster_1378\tCluster_1868\n+Cluster_1379\tCluster_1869\n+Cluster_1384\tCluster_1878\n+Cluster_1386\tCluster_1882\n+Cluster_1387\tCluster_1883\n+Cluster_1390\tCluster_1884\n+Cluster_1391\tCluster_1888\n+Cluster_1398\tCluster_1895\n+Cluster_1403\tCluster_1897\n+Cluster_1406\tCluster_1903\n+Cluster_1418\tCluster_1904\n+Cluster_1430\tCluster_1906\n+Cluster_1438\tCluster_1909\n+Cluster_1453\tCluster_1922\n+Cluster_1457\tCluster_1923\n+Cluster_1460\tCluster_1926\n+Cluster_1461\tCluster_1928\n+Cluster_1464\tCluster_1930\n+Cluster_1471\tCluster_1939\n+Cluster_1476\tCluster_1940\n+Cluster_1478\tCluster_1950\n+Cluster_1479\tCluster_1955\n+Cluster_1481\tCluster_1957\n+Cluster_1493\tCluster_1958\n+Cluster_1497\tCluster_1959\n+Cluster_1500\tCluster_1964\n+Cluster_1501\tCluster_1966\n+Cluster_1506\tCluster_1969\n+Cluster_1508\tCluster_1973\n+Cluster_1509\tCluster_1976\n+Cluster_1511\tCluster_1978\n+Cluster_1512\tCluster_1981\n+Cluster_1513\tCluster_1982\n+Cluster_1518\tCluster_1984\n+Cluster_1523\tCluster_1986\n+Cluster_1525\tCluster_1989\n+Cluster_1527\tCluster_1994\n+Cluster_1528\tCluster_1995\n+Cluster_1530\tCluster_1997\n+Cluster_1531\tCluster_1998\n+Cluster_1534\tCluster_2001\n+Cluster_1536\tCluster_2002\n+Cluster_1538\tCluster_2005\n+Cluster_1539\tCluster_2007\n+Cluster_1542\tCluster_2010\n+Cluster_1559\tCluster_2012\n+Cluster_1561\tCluster_2013\n+Cluster_1562\tCluster_2022\n+Cluster_1564\tCluster_2026\n+Cluster_1568\tCluster_2029\n+Cluster_1571\tCluster_2030\n+Cluster_1575\tCluster_2031\n+Cluster_1577\tCluster_2036\n+Cluster_1579\tCluster_2037\n+Cluster_1580\tCluster_2038\n+Cluster_1581\tCluster_2042\n+Cluster_1587\tCluster_2049\n+Cluster_1595\tCluster_2051\n+Cluster_1597\tCluster_2055\n+Cluster_1598\tCluster_2056\n+Cluster_1611\tCluster_2057\n+Cluster_16'..b'41998\tCluster_41535\n+Cluster_41999\tCluster_41536\n+Cluster_42001\tCluster_41539\n+Cluster_42003\tCluster_41540\n+Cluster_42007\tCluster_41546\n+Cluster_42009\tCluster_41550\n+Cluster_42016\tCluster_41555\n+Cluster_42021\tCluster_41556\n+Cluster_42023\tCluster_41557\n+Cluster_42027\tCluster_41559\n+Cluster_42039\tCluster_41563\n+Cluster_42040\tCluster_41564\n+Cluster_42042\tCluster_41565\n+Cluster_42053\tCluster_41566\n+Cluster_42059\tCluster_41572\n+Cluster_42060\tCluster_41579\n+Cluster_42063\tCluster_41580\n+Cluster_42071\tCluster_41582\n+Cluster_42077\tCluster_41584\n+Cluster_42078\tCluster_41586\n+Cluster_42079\tCluster_41592\n+Cluster_42082\tCluster_41599\n+Cluster_42084\tCluster_41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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/04-filters.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/04-filters.fasta Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,3218 @@\n+>Cluster_1 1:N:0:ACTTGA\n+CACGTAAGAATTTGCCTTTAGGAGGGGGATAACAATTGGAAACGATTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATAGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_2 1:N:0:ACTTGA\n+CACGTAAGAATTTGCCTTTAGGAGGGGGACAACAACTGGAAACGGTTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAAAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_3 1:N:0:ACTTGA\n+TGCGTCGGAACGTACCGAGTAATGGGGGATAACGCAGCGAAAGTTGTGCTAATACCGCATACGCCCTGAGGGGGAAAGTGGGGGACCGCAAGGCCTCACGTTATTCGAGCGGCCGACGTCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATTCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCAGCAGGAACGAAACGGTACGCTCTAACATAGTGTGCTAATGACGGTACCTGCAGAAGAAGCACCGGCTAACTAC\n+>Cluster_4 1:N:0:ACTTGA\n+CACGTGAGAATCTGCCTCCAGGTCGGGGACAACAGCGGGAAACTGCTGCTAATACCCGATGTGCCTAAGGGTGAAAGATTAATTGCCTGGAGATGAGCTCGCGTCCGATTAGCTAGTTGGTAGAGTAAAAGCCTACCAAGGCTCCGATCGGTAGCTGGTCTGAGAGGATGAGCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAAGACCGCGTGGGGGATGAAGGCTCTTGGGTTGTAAACCCCTTTTCTCAGGGAAGAAGTTCTGACGGTACCTGAGGAATCAGCATCGGCTAACTCC\n+>Cluster_5 1:N:0:ACTTGA\n+CGCGTGGGAATCTGCCCTGCAGTGGGGGACAACCCGAGGAAACTCGGGCTAATACCGCATACGTCCTATGGGAGAAAGGGGGCCTTCGGGCTCTCGCTGCAGGATGAGCCCGCGTCCGATTAGCTTGTTGGTGGGGTAACGGCCCACCAAGGCTGCGATCGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTCAGTGGGGAAGAAAAGCGCGAGGTTAATACCCTTGTGTGTTGACGTTACCCACAGAAGAAGCACCGGCTAACTCC\n+>Cluster_6 1:N:0:ACTTGA\n+CACGTAAGAATTTACCTTTAGGAGGGGGACAACAGACAGAAATGACTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGATCAGTATCTGGTTTGAGAGGATGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATCTCGCGTGAGGGATGACTGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_7 1:N:0:ACTTGA\n+CGCGTGGGCAATCTACCTTCGAATCGGGGATAACATTGCGAAAGCGATGCTAATACCGGATGACATCCTGAAGGCTTCGGTTTTAAGGATCAAAGGTGGCCTCTACGAGTAAGCTACTGTTTGGAGATGAGCCCGCGTACCATTAGCTTGTTGGTAGGGTAACGGCCTACCAAGGCGACGATGGTTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAAACCACGAGGTGATAATATCGCTTTGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_8 1:N:0:ACTTGA\n+CGCGTGGGAATCTGCCCTGCAGTGGGGGACAACCCGAGGAAACTCGGGCTAATACCGCATACGTCTTACGAGAGAAAGGGGGCTTCGGCTCTCGCTGCAGGATGAGCCCGCGTCCGATTAGCTTGTTGGTAGGGTAATGGCCTACCAAGGCGACGATCGGTAGCTGGTCTGAGAGGATGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTCAGTGGGGAAGAAAAACCCGAGGTTAATACCCTTGGGTCTTGACGTTACCCACAGAAGAAGCACCGGCTAACTCC\n+>Cluster_9 1:N:0:ACTTGA\n+CGCGTGGGCAATCTACCTCCGAATCGGGGATAACATTGCGAAAGCGATGCTAATACCGGATGACATCCTGAGGACTTCGGTTTTCGGGATCAAAGGTGGCCTCTACGGGTAAGCTACTGTTTGGGGATGAGCCCGCGTACCATTAGCTTGTTGGTAGGGTAACGGCCTACCAAGGCGACGATGGTTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAAACCACGGAGCGTTAATATCGCTTTGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_10 1:N:0:ACTTGA\n+CACGTAAGAATTTGCCTTTAGGAGGGGGACAACAACTGGAAACGGTTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGATGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATCTCGCGT'..b'GGATGACGGCCCTACGGGTTGTAAACTGCTTTTATACGGGAAGAAACCTCCTTACGTGTAGGGAGCTGACGGTACCGTAAGAATAAGCATCGGCTAACTCC\n+>Cluster_4252 1:N:0:CCGTCC\n+CGCGTAGGTGATCTACCTTCAAGTGGGGGACAACCCAGGGAAACTTGGGCTAATACCGCATGTGGCAGTAATGCTAAAGCCGGCCTCTGAATATGCTGGTGCTTGGAGATGAGCTTGCGTCTGATTAGCTAGTTGGTGGGGTAATGGCCTACCGAGGCGATGATAAGTAGGCGGCTTTAACGAGTGGTCGCCCACACTGGGATTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTCGAGAATAGTCTACAATGGTCGAAAGATTGATAGTGCGACGCCGCGTGAACGATGAAGCATTTCGGTGTGTAAAGTTCTTTTCTATGGGAGCAGTGCTTTTTATGTTAATAGCATGAGAGGAGAGATATTACTGTAGGAATAAGCCACGGCTAACTCC\n+>Cluster_13801 1:N:0:ACTTGA\n+CACGTAAATAACTTACCCTTAAGTTTGGGATACCATTGCTAACGCGATGTTAATACCGGATGTGGATAGAGAGTCACCTGGTTTTCTATTTAAAGGTCCTTCGGGACTGCTTAAGGATGGATTTGCGCACCATTAGCTTGTTGGTGGGGTAACGGCCTACCAAGGCGATGATGGTTAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATATTGCGCAATGGACGAAAGTCTGACGCAGCAACTCCGCGTGAAGGATGAAGGTTCTCGGATCGTAAACTTCTTTTATTTGGGAAGAAATGTCTAAGTAGGTAATGGCTTAGATTTGACGGTACCATTTGAATAAGCTCCGGCTAAATAC\n+>Cluster_15144 1:N:0:ACTTGA\n+TACATGGGTAATTTGCCCCTTTGTTCGGAATAGCCACCGGAAACGGTGATTAATTCCGGATGTGTTCGGGTGCCGCATGGCACCTTATATAAAGGCGGGGATCTTCGGACCTGTCGCAAAGGGATAAGCCCATGTCCTATCAGCTTGTTGGTGAGGTAACGGCTCACCAAGGCTTACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACTGCCCAGACTCCTACGGGAGGCTGCAGTCGAGAATCATTGTCAATGCACGAAAGTGTGAACATGCGACGCCGCGTGGAGGAAGACGGCCTTCGGGTTGTAAACTCCTGTCAGCAGGGAGGAAAGACAGTACCATTAATACCGGTGCGGTTTGACAGTACCTGCAGAGGAAGTCACGGCTAACTCT\n+>Cluster_5432 1:N:0:ACTTGA\n+CACGTGATCAATCTGCCCTGAAGTCGGGGATAGCTATTCGAAAGGATAGGTAATACCTGATAAGACCACAGCATCGCATGGTGCAGTGGTAAAACGGTGGGGACCTTCGGGCCTTCCGCTTCAGGATGAGATCGCGGCCTATTAGCTTGTTGGTGAGGTAACGGCTCACCAAGGCTTTGATGGGTAACCGGCCTGAGAGGGTGAACGGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGCTGAATCATTCGCCAATGCGCGAAAGCGTGACGGTGCGACGCCGCGTGAAGGATGAAGGCCCTAGGGTCGTAAACTTCTGTCAGATTCTAGAAAACTACAAGGGTTAATAGCTTTTGTACTGATCAGAATCAGAGGAAGCACAGGCTAATCTC\n+>Cluster_7257 1:N:0:ACTTGA\n+CGCGTAGATAACCTGTCTTCATGTCTGGAATAATACACCGAAAGGGGTACTAATACCGGATATTCTTGCTTTATATAAGTTTTGCAAGCAAAGGTGGCCTCTGATTCAAGCTACTGCATGTAGAGGGGTCTGCGTACCATTAGCTAGTAGGTAGGGTAATGGCCTACCTAGGCTACGATGGTTAGCGGGTCTGAGAGGATTATCCGCCACACTGGCACTGGAACACGGGCCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGCGCAATGGGGGCAACCCTGACGCAGCGACGCCGCGTGAGTGAGGAAGGCCTTCGGGTCGTAAAGCTCTGTCAAGAGGAAAGAAATGCATATCGGTTAATACCCGATATGTTTGACGGTACCTCTAAAGGAAGCACCGGCTAACTCC\n+>Cluster_6485 1:N:0:ACTTGA\n+CGCGTGGGTAACCTACCTCCGAACCTGGGATAACTTCGCGAAAGCGTTGCTAATACCGGATATTGCCCCATAGTCCGTGGACCGTGGGGTGAAAGGTGACCTCTTCTTGAAAGTTGCCATTCGGAGATGGGCTCGCGTCCCATTAGCTTGTTGGTAGGGTAATGGCCTACCAAGGCGACGATGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGCGCTGAAACACGGGCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTGTCAGGTGGGAAAAAAGGCCCACAGTAAATAGCTTCGGGATCTGATGGTACCACCAGAGGAAGCACCGGCTAACTCC\n+>Cluster_6916 1:N:0:CCGTCC\n+CACGTGGGTAATCTACCTTCAAATCGGGAATAACGTTGCGAAAGCGACGCTAATACCGGATAACATCGATGAGGTCTCGGCCTTTTCGATCAAAGATGGCCTCTACATGTAAGCTGTCGTTCGAAGATGAGCCCGCGTCCCATTAGCTTGTTGGTAGGGTAAAGGCCTACCAAGGCGACGATGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACATGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAACCCACGTGGTAATAATACTGCCACGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_13089 1:N:0:ACTTGA\n+CACATGGCTGACCTGCCCTTCAGAGGGGGACAACCGCTGGAAACGGTGGCTAATACCCCATACGCTCACGACGATTAGAAGGTTGTGAGGAAAGTGTTTAGCGCTGAAGGAGGGGGCTGTGGCCCATCAGCTAGTTGGTGAGGTAACGGCTTACCAAGGCGAAGACGGGTAGGGGGCCTGAGAGGGTGACCCCCCACACGGGTACTGAGACACGGACCCGACTCCTACGGGAGGCAGCAGTAAGGGATATTGCGACAATGGGCGAAAGCCTGACGCAGCAACGCCGCGTGCGGGAGGAAGGCCTTCGGGTTGTAAACCGCTTTTCGGGGGGAAGAGGAAGGACGGTACCCCCGGAATAAGTCTCGGCTAACTAC\n+>Cluster_11351 1:N:0:CCGTCC\n+CGCGTATGCAACCTACCCTTAACTATGGGATAGCCCGGGGAAACTCGGATTAATATCGTATAACATCATAAAATGGCATCATTAAATGATTAAAGCTGCGGCGGTTAAGGATGGGCATGCGTGCCATTAGATAGTTGGTGAGGTAACGGCTCACCAAGTCAACGATGGCTACGGGGTCTTAAAGGATGATCCCGCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGCAAGCCTGAACCAGCCATGCCGCGTGTAGGATGACGGCCTTCTGGGTTGTAAACTACTTTTATATGGGAAGAAAGTCAGATACTTGTATCTGTTTGCCGGTACCATATGAATAAGCATCGGCTAACTCC\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/05-clustersStat.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/05-clustersStat.html Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,780 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\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="1.4.1">\n+\t\t<!-- CSS -->\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>\n+\t\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>\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: 500px;\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.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+\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: #3871A8;\n+\t\t\t\tbackground: radial-gradient( #649DD4, #3871A8);\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+\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: steelblue;\n+\t\t\t\tstroke-width: 3px;\n+\t\t\t}\n+\t\t\t.d3-collapsed-node {\n+\t\t\t\tfill: #B0C4DE;\n+\t\t\t\tstroke: #663399;\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: #ccc;\n+\t\t\t\tstroke-width: 2px;\n+\t\t\t}\n+\t\t</style>\n+\t\t<!-- JS -->\n+\t\t<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts-more.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>\n+\t\t<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>\n+\t\t<script type="text/javascript">\n+\t\t\t/*\n+\t\t\t * d3 v3 - JavaScript d3 Library\n+\t\t\t * (http://d3js.org/)\n+\t\t\t */\n+\t\t\t!function(){function n(n){return n&&(n.ownerDocument||n.document||n).documentElement}function t(n){return n&&(n.ownerDocument&&n.ownerDocument.defaultView||n.document&&n||n.defaultView)}function e(n,t){return t>n?-1:n>t?1:n>=t?0:0/0}function r(n){return null===n?0/0:+n}function u(n){return!isNaN(n)}function i(n){return{left:function(t,e,r,u){for(arguments.length<3&&(r=0),arguments.length<4&&(u=t.length'..b' 267, 283, 288, 289, 298, 304, 317, 320, 322, 325, 326, 330, 336, 341, 343, 352, 366, 372, 386, 388, 414, 417, 422, 427, 479, 487, 504, 525, 559, 572, 606, 618, 665, 688, 740, 744, 779, 831, 832, 860, 1133, 1139, 1140, 1269, 1293, 1390, 1572, 2356, 2370, 3113, 3433, 4282] ;\n+\t\t\tvar series = [{\n+\t\t\t\t\'name\': "All",\n+\t\t\t\t\'data\': [141, 140, 80, 94, 71, 64, 62, 53, 51, 41, 43, 36, 34, 25, 35, 15, 24, 17, 22, 27, 11, 11, 20, 13, 12, 10, 11, 10, 7, 5, 12, 10, 9, 10, 6, 8, 2, 6, 6, 8, 7, 11, 5, 6, 5, 5, 5, 10, 1, 5, 4, 7, 4, 2, 2, 2, 7, 4, 2, 2, 6, 3, 5, 8, 2, 4, 1, 1, 4, 3, 3, 3, 2, 3, 7, 3, 2, 4, 2, 1, 2, 2, 2, 3, 1, 2, 1, 2, 4, 3, 3, 2, 1, 3, 2, 3, 1, 4, 3, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 1, 2, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]\n+\t\t\t}];\n+\t\t\tvar sum_series = new Array() ;\n+\t\t\tvar samples_distrib = {"splA_01": {"shared_observations": 1609, "own_seq": 0, "shared_seq": 47633, "own_observations": 0}, "splA_02": {"shared_observations": 1609, "own_seq": 0, "shared_seq": 27088, "own_observations": 0}, "splA_03": {"shared_observations": 1609, "own_seq": 0, "shared_seq": 17297, "own_observations": 0}} ;\n+\t\t\tvar newick = "((splA_02,(splA_01,splA_03):0.098):0.114);" ;\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 role="presentation" class="active"><a href="#cluster-distrib">Clusters distribution</a></li>\n+\t\t\t\t<li role="presentation"><a href="#sequence-distrib">Sequences distribution</a></li>\n+\t\t\t\t<li role="presentation"><a 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<h1 class="page-header">Sequences count</h1>\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<h1 class="page-header">Hierarchical clustering</h1>\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'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/06-affiliationsStat.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/06-affiliationsStat.html Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,952 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\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="1.3.0">\n+\t\t<!-- CSS -->\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>\n+\t\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>\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;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:#b0c4de;border:0;border-radius:8px;pointer-events:none}.jDistrib-empty-details{color:#31708F;background-color:#D9EDF7;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 input {\n+\t\t\t\tmargin-right: 10px;\n+\t\t\t}\n+\t\t\t#display-global-sunburst {\n+\t\t\t\tmargin-bottom: 40px;\n+\t\t\t}\n+\t\t</style>\n+\t\t<!-- JS -->\n+\t\t<script typ'..b'e 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 role="presentation" class="active"><a href="#tax-distrib">Taxonomy distribution</a></li>\n+\t\t\t\t<li role="presentation" id="bootstrap-nav-tab"><a href="#bootstrap-distrib">Bootstrap distribution</a></li>\n+\t\t\t\t<li role="presentation" id="alignment-nav-tab"><a 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 btn-primary center-block" data-toggle="modal" data-target="#sunburst-modal">\n+\t\t\t\t\t\t<span class="glyphicon glyphicon-stats" 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\t<tr>\n+\t\t\t\t\t\t\t\t<th class="title">Taxonomies by sample</th>\n+\t\t\t\t\t\t    </tr>\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 btn-primary table-action fusion-right disabled" data-toggle="modal" data-target="#rarefaction-modal">Display rarefaction</button>\n+\t\t\t\t\t\t\t\t\t<button id="display-spl-sunburst" class="btn btn-primary table-action disabled" data-toggle="modal" data-target="#sunburst-modal">Display distribution</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-primary btn-md btn-block">by OTUs</button>\n+\t\t\t\t\t\t<button id="bootstrap-seq-btn" type="button" class="btn btn-default 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-primary btn-md btn-block">by OTUs</button>\n+\t\t\t\t\t\t<button id="heatmap-seq-btn" type="button" class="btn btn-default 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<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>\n+\t\t\t\t\t\t<h4 class="modal-title">Taxa distribution</h4>\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<h4>Detail on selected:</h4>\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">Close</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<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>\n+\t\t\t\t\t\t<h4 class="modal-title">Rarefaction</h4>\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">Close</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'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/07-biom2tsv.multi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-biom2tsv.multi Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,131 @@\n+#observation_name\tblast_taxonomy\t blast_subject\tblast_perc_identity\tblast_perc_query_coverage\tblast_evalue\tblast_aln_length\n+Cluster_16\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;bacterium enrichment culture clone auto8_4W\tGU731331.1.1375\t88.07\t57.9787234043\t4e-71\t218\n+Cluster_16\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium YJF2-33\tFJ405887.1.1482\t89.0\t55.3191489362\t4e-71\t209\n+Cluster_16\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium BGR 43\tGU167988.1.1472\t89.0\t55.3191489362\t4e-71\t209\n+Cluster_65\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species\tEF471700.1.1483\t85.71\t58.0213903743\t8e-63\t217\n+Cluster_65\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium YJF2-33\tFJ405887.1.1482\t85.2\t59.6256684492\t8e-63\t223\n+Cluster_70\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrimicrobium;Ferrimicrobium acidiphilum\tAF251436.1.1466\t90.91\t47.461928934\t2e-69\t187\n+Cluster_70\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Acidimicrobium;unknown species\tEU419133.1.1468\t90.91\t47.461928934\t2e-69\t187\n+Cluster_70\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrithrix;actinobacterium BGR 77\tGU168000.1.1473\t88.46\t52.7918781726\t2e-69\t208\n+Cluster_96\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;bacterium enrichment culture clone auto8_4W\tGU731331.1.1375\t89.22\t49.2753623188\t5e-70\t204\n+Cluster_96\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;unknown species\tGQ387491.21030.22531\t88.26\t51.2077294686\t5e-70\t213\n+Cluster_120\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species\tEF471700.1.1483\t86.08\t63.2432432432\t6e-69\t237\n+Cluster_120\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t84.96\t66.4864864865\t6e-69\t246\n+Cluster_150\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Acidimicrobium;unknown species\tEU419133.1.1468\t89.22\t49.3917274939\t5e-70\t204\n+Cluster_150\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrithrix;actinobacterium BGR 77\tGU168000.1.1473\t89.22\t49.3917274939\t5e-70\t204\n+Cluster_164\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;bacterium enrichment culture clone auto8_4W\tGU731331.1.1375\t84.54\t48.3790523691\t1e-51\t194\n+Cluster_164\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Iamiaceae;Iamia;Iamia majanohamensis\tAB360448.1.1474\t84.54\t48.3790523691\t1e-51\t194\n+Cluster_230\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species\tEF471700.1.1483\t91.93\t40.6565656566\t1e-61\t161\n+Cluster_230\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;Ilumatobacter nonamiensis YM16-303\tAB360345.1.1443\t91.93\t40.6565656566\t1e-61\t161\n+Cluster_261\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;bacterium enrichment culture clone auto8_4W\tGU731331.1.1375\t89.22\t49.2753623188\t5e-70\t204\n+Cluster_261\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;unknown species\tGQ387491.21030.22531\t88.26\t51.2077294686\t5e-70\t213\n+Cluster_315\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Iamiaceae;Iamia;bacterium Ellin5273\tAY234624.1.1446\t85.92\t53.68956743\t4e-61\t213\n+Cluster_315\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Iamiaceae;Iamia;bacterium Ellin5247\tAY234598.1.1446\t85.92\t53.68956743\t4e-61\t213\n+Cluster_317\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiales Incertae Sedis;Aciditerrimonas;unknown species\tAF225451.1.1418\t82'..b'cidimicrobium;unknown species\tEU419133.1.1468\t87.95\t56.4885496183\t3e-72\t224\n+Cluster_1454\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species\tEF471700.1.1483\t87.39\t58.0152671756\t3e-72\t230\n+Cluster_1553\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrimicrobium;Ferrimicrobium acidiphilum\tAF251436.1.1466\t87.56\t55.5269922879\t7e-69\t217\n+Cluster_1553\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrithrix;actinobacterium BGR 77\tGU168000.1.1473\t87.56\t55.5269922879\t7e-69\t217\n+Cluster_1563\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;bacterium enrichment culture clone auto8_4W\tGU731331.1.1375\t88.73\t49.2753623188\t3e-68\t204\n+Cluster_1563\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;unknown species\tGQ387491.21030.22531\t91.62\t43.2367149758\t3e-68\t179\n+Cluster_1710\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;unidentified bacterium wb1_G04\tAF317765.1.1443\t89.25\t52.7227722772\t7e-74\t214\n+Cluster_1710\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium BGR 43\tGU167988.1.1472\t90.24\t50.495049505\t7e-74\t205\n+Cluster_1837\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Iamiaceae;Iamia;bacterium Ellin5273\tAY234624.1.1446\t86.38\t53.9641943734\t9e-63\t213\n+Cluster_1837\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Iamiaceae;Iamia;bacterium Ellin5247\tAY234598.1.1446\t86.38\t53.9641943734\t9e-63\t213\n+Cluster_2588\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;bacterium enrichment culture clone auto8_4W\tGU731331.1.1375\t87.28\t58.7628865979\t3e-72\t228\n+Cluster_2588\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium YJF2-33\tFJ405887.1.1482\t87.61\t57.9896907216\t3e-72\t226\n+Cluster_2588\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium BGR 43\tGU167988.1.1472\t87.89\t57.2164948454\t3e-72\t223\n+Cluster_2840\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Acidimicrobium;unknown species\tEU419133.1.1468\t82.76\t76.8\t2e-69\t290\n+Cluster_2840\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiales Incertae Sedis;Aciditerrimonas;unknown species\tAF225451.1.1418\t82.59\t77.6\t2e-69\t293\n+Cluster_2931\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium BGR 43\tGU167988.1.1472\t86.7\t46.1728395062\t4e-56\t188\n+Cluster_2931\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;unknown species\tGQ387491.21030.22531\t86.63\t46.1728395062\t4e-56\t187\n+Cluster_3079\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrimicrobium;Ferrimicrobium acidiphilum\tAF251436.1.1466\t86.98\t51.8337408313\t2e-65\t215\n+Cluster_3079\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrithrix;actinobacterium BGR 77\tGU168000.1.1473\t87.1\t51.8337408313\t2e-65\t217\n+Cluster_3079\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrithrix;unknown species\tKF182221.1.1489\t87.1\t51.8337408313\t2e-65\t217\n+Cluster_3175\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium BGR 43\tGU167988.1.1472\t88.7\t66.7605633803\t4e-81\t239\n+Cluster_3175\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t87.21\t72.1126760563\t4e-81\t258\n+Cluster_5016\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;bacterium enrichment culture clone B213(2011)\tJF830237.1.1494\t83.86\t67.9144385027\t4e-66\t254\n+Cluster_5016\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;unknown species\tGQ387491.21030.22531\t83.98\t67.9144385027\t4e-66\t256\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/07-biom2tsv.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/07-biom2tsv.tsv Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,1610 @@\n+#rdp_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\tsplA_01\tsplA_02\tsplA_03\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);Acidimicrobiaceae;(0.39);CL500-29 marine group;(0.29);unknown species;(0.29);\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t84.31\t70.8333333333\t8e-68\t255\tHWI-M00185:22:000000000-A53C9:1:1101:16192:3924\tCACGTAAGAATTTGCCTTTAGGAGGGGGATAACAATTGGAAACGATTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATAGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\tCluster_1\t3433\t1856\t971\t606\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);OM1 clade;(0.56);unknown genus;(0.56);bacterium WH6-7;(0.39);\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t84.77\t70.9141274238\t5e-70\t256\tHWI-M00185:22:000000000-A53C9:1:1101:12521:5680\tCACGTAAGAATTTGCCTTTAGGAGGGGGACAACAACTGGAAACGGTTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAAAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\tCluster_2\t4282\t2211\t1307\t764\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);unknown family;(0.79);unknown genus;(0.79);unknown species;(0.76);\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t92.06\t53.807106599\t2e-83\t214\tHWI-M00185:22:000000000-A53C9:1:1101:16005:1920\tTGCGTCGGAACGTACCGAGTAATGGGGGATAACGCAGCGAAAGTTGTGCTAATACCGCATACGCCCTGAGGGGGAAAGTGGGGGACCGCAAGGCCTCACGTTATTCGAGCGGCCGACGTCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATTCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCAGCAGGAACGAAACGGTACGCTCTAACATAGTGTGCTAATGACGGTACCTGCAGAAGAAGCACCGGCTAACTAC\tCluster_3\t2356\t1221\t683\t452\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);Iamiaceae;(0.19);Iamia;(0.19);Iamia majanohamensis;(0.13);\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrithrix;actinobacterium BGR 77\tGU168000.1.1473\t86.49\t72.4719101124\t2e-78\t259\tHWI-M00185:22:000000000-A53C9:1:1101:14417:1745\tCACGTGAGAATCTGCCTCCAGGTCGGGGACAACAGCGGGAAACTGCTGCTAATACCCGATGTGCCTAAGGGTGAAAGATTAATTGCCTGGAGATGAGCTCGCGTCCGATTAGCTAGTTGGTAGAGTAAAAGCCTACCAAGGCTCCGATCGGTAGCTGGTCTGAGAGGATGAGCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAAGACCGCGTGGGGGATGAAGGCTCTTGGGTTGTAAACCCCTTTTCTCAGGGAAGAAGTTCTGACGGTACCTGAGGAATCAGCATCGGCTAACTCC\tCluster_4\t3113\t1591\t931\t591\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);Acidimicrobiaceae;(0.31);Acidimicrobium;(0.12);unknown species;(0.12);\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species\tEF471700.1.1483\t90.0\t56.4102564103\t2e-79\t220\tHWI-M00185:22:000000000-A53C9:1:1101:19898:5958\tCGCGTGGGAATCTGCCCTGCAGTGGGGGACAACCCGAGGAAACTCGGGCTAATACCGCATACGTCCTATGGGAGAAAGGGGGCCTTCGGGCTCTCGCTGCAGGATGAGCCCGCGTCCGATTAGCTTGTTGGTGGGGTAACGGCCCACCAAGGCTGCGATCGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTCAGTGGGGAAGAAAAGCGCGAGGTTAATACCCTTGTGTGTTGACGTTACCCACAGAAGAAGCACCGGCTAACTCC\tCluster_5\t2370\t1197\t711\t462\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobii'..b'C9:1:1105:24844:7034\tCACGTGATCAATCTGCCCTGAAGTCGGGGATAGCTATTCGAAAGGATAGGTAATACCTGATAAGACCACAGCATCGCATGGTGCAGTGGTAAAACGGTGGGGACCTTCGGGCCTTCCGCTTCAGGATGAGATCGCGGCCTATTAGCTTGTTGGTGAGGTAACGGCTCACCAAGGCTTTGATGGGTAACCGGCCTGAGAGGGTGAACGGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGCTGAATCATTCGCCAATGCGCGAAAGCGTGACGGTGCGACGCCGCGTGAAGGATGAAGGCCCTAGGGTCGTAAACTTCTGTCAGATTCTAGAAAACTACAAGGGTTAATAGCTTTTGTACTGATCAGAATCAGAGGAAGCACAGGCTAATCTC\tCluster_5432\t7\t3\t2\t2\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);unknown family;(0.39);unknown genus;(0.39);bacterium enrichment culture clone auto73_4W;(0.3);\tNone\tno data\tno data\tno data\tno data\tno data\tHWI-M00185:22:000000000-A53C9:1:1107:13467:3519\tCGCGTAGATAACCTGTCTTCATGTCTGGAATAATACACCGAAAGGGGTACTAATACCGGATATTCTTGCTTTATATAAGTTTTGCAAGCAAAGGTGGCCTCTGATTCAAGCTACTGCATGTAGAGGGGTCTGCGTACCATTAGCTAGTAGGTAGGGTAATGGCCTACCTAGGCTACGATGGTTAGCGGGTCTGAGAGGATTATCCGCCACACTGGCACTGGAACACGGGCCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGCGCAATGGGGGCAACCCTGACGCAGCGACGCCGCGTGAGTGAGGAAGGCCTTCGGGTCGTAAAGCTCTGTCAAGAGGAAAGAAATGCATATCGGTTAATACCCGATATGTTTGACGGTACCTCTAAAGGAAGCACCGGCTAACTCC\tCluster_7257\t8\t4\t2\t2\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);unknown family;(0.25);unknown genus;(0.25);actinobacterium BGR 43;(0.13);\tNone\tno data\tno data\tno data\tno data\tno data\tHWI-M00185:22:000000000-A53C9:1:1106:20977:17309\tCGCGTGGGTAACCTACCTCCGAACCTGGGATAACTTCGCGAAAGCGTTGCTAATACCGGATATTGCCCCATAGTCCGTGGACCGTGGGGTGAAAGGTGACCTCTTCTTGAAAGTTGCCATTCGGAGATGGGCTCGCGTCCCATTAGCTTGTTGGTAGGGTAATGGCCTACCAAGGCGACGATGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGCGCTGAAACACGGGCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTGTCAGGTGGGAAAAAAGGCCCACAGTAAATAGCTTCGGGATCTGATGGTACCACCAGAGGAAGCACCGGCTAACTCC\tCluster_6485\t6\t3\t1\t2\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);Acidimicrobiales Incertae Sedis;(0.29);Aciditerrimonas;(0.29);Aciditerrimonas ferrireducens;(0.26);\tNone\tno data\tno data\tno data\tno data\tno data\tHWI-M00185:22:000000000-A53C9:1:1106:5800:18584\tCACGTGGGTAATCTACCTTCAAATCGGGAATAACGTTGCGAAAGCGACGCTAATACCGGATAACATCGATGAGGTCTCGGCCTTTTCGATCAAAGATGGCCTCTACATGTAAGCTGTCGTTCGAAGATGAGCCCGCGTCCCATTAGCTTGTTGGTAGGGTAAAGGCCTACCAAGGCGACGATGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACATGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAACCCACGTGGTAATAATACTGCCACGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\tCluster_6916\t6\t3\t2\t1\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);OM1 clade;(0.56);unknown genus;(0.56);unidentified bacterium wb1_J07;(0.2);\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;bacterium enrichment culture clone B213(2011)\tJF830237.1.1494\t88.24\t54.5454545455\t1e-66\t204\tHWI-M00185:22:000000000-A53C9:1:2110:23327:18106\tCACATGGCTGACCTGCCCTTCAGAGGGGGACAACCGCTGGAAACGGTGGCTAATACCCCATACGCTCACGACGATTAGAAGGTTGTGAGGAAAGTGTTTAGCGCTGAAGGAGGGGGCTGTGGCCCATCAGCTAGTTGGTGAGGTAACGGCTTACCAAGGCGAAGACGGGTAGGGGGCCTGAGAGGGTGACCCCCCACACGGGTACTGAGACACGGACCCGACTCCTACGGGAGGCAGCAGTAAGGGATATTGCGACAATGGGCGAAAGCCTGACGCAGCAACGCCGCGTGCGGGAGGAAGGCCTTCGGGTTGTAAACCGCTTTTCGGGGGGAAGAGGAAGGACGGTACCCCCGGAATAAGTCTCGGCTAACTAC\tCluster_13089\t8\t4\t2\t2\n+Bacteria;(1.0);Actinobacteria;(1.0);Acidimicrobiia;(1.0);Acidimicrobiales;(1.0);OM1 clade;(0.76);unknown genus;(0.61);microbial mat metagenome;(0.54);\tNone\tno data\tno data\tno data\tno data\tno data\tHWI-M00185:22:000000000-A53C9:1:1111:5626:9662\tCGCGTATGCAACCTACCCTTAACTATGGGATAGCCCGGGGAAACTCGGATTAATATCGTATAACATCATAAAATGGCATCATTAAATGATTAAAGCTGCGGCGGTTAAGGATGGGCATGCGTGCCATTAGATAGTTGGTGAGGTAACGGCTCACCAAGTCAACGATGGCTACGGGGTCTTAAAGGATGATCCCGCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGCAAGCCTGAACCAGCCATGCCGCGTGTAGGATGACGGCCTTCTGGGTTGTAAACTACTTTTATATGGGAAGAAAGTCAGATACTTGTATCTGTTTGCCGGTACCATATGAATAAGCATCGGCTAACTCC\tCluster_11351\t6\t3\t2\t1\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/08-affiliation_multihit.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/08-affiliation_multihit.tsv Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,947 @@\n+#OTUID\ttaxonomy\tsubject\tevalue\tperc_identity\tperc_query_coverage\taln_length\n+Cluster_1\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t8e-68\t84.31\t70.8333333333\t255\n+Cluster_2\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t5e-70\t84.77\t70.9141274238\t256\n+Cluster_3\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t2e-83\t92.06\t53.807106599\t214\n+Cluster_4\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrithrix;actinobacterium BGR 77\tGU168000.1.1473\t2e-78\t86.49\t72.4719101124\t259\n+Cluster_5\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species\tEF471700.1.1483\t2e-79\t90.0\t56.4102564103\t220\n+Cluster_6\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t2e-59\t82.35\t70.8333333333\t255\n+Cluster_8\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t8e-78\t89.86\t55.9278350515\t217\n+Cluster_10\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t1e-66\t83.98\t70.9141274238\t256\n+Cluster_11\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t2e-69\t84.71\t70.8333333333\t255\n+Cluster_12\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t2e-69\t84.71\t71.2290502793\t255\n+Cluster_13\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t2e-83\t92.72\t53.0927835052\t206\n+Cluster_15\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t8e-63\t82.95\t71.6666666667\t258\n+Cluster_16\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;bacterium enrichment culture clone auto8_4W\tGU731331.1.1375\t4e-71\t88.07\t57.9787234043\t218\n+Cluster_16\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium YJF2-33\tFJ405887.1.1482\t4e-71\t89.0\t55.3191489362\t209\n+Cluster_16\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium BGR 43\tGU167988.1.1472\t4e-71\t89.0\t55.3191489362\t209\n+Cluster_17\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t8e-68\t84.31\t71.0306406685\t255\n+Cluster_18\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t2e-69\t84.71\t71.0306406685\t255\n+Cluster_19\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t8e-78\t91.22\t52.8350515464\t205\n+Cluster_25\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species\tEF471700.1.1483\t4e-56\t81.04\t70.9333333333\t269\n+Cluster_26\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t8e-78\t91.22\t52.8350515464\t205\n+Cluster_27\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrimicrobium;Ferrimicrobium acidiphilum\tAF251436.1.1466\t5e-70\t87.91\t54.9872122762\t215\n+Cluster_28\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t9e-83\t90.27\t57.3604060914\t226\n+Cluster_30\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t8e-78\t91.22\t52.8350515464\t205\n+Cluster_32\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t2e-79\t90.32\t55.9278350515\t217\n+Cluster_33\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 c'..b'cidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;unidentified bacterium wb1_J07\tAF317767.1.1444\t3e-67\t88.94\t47.9318734793\t199\n+Cluster_3617\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t5e-65\t87.68\t51.5228426396\t203\n+Cluster_3662\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t5e-75\t90.64\t51.6539440204\t203\n+Cluster_3676\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium BGR 43\tGU167988.1.1472\t3e-72\t90.82\t49.4923857868\t196\n+Cluster_3696\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;Ilumatobacter nonamiensis YM16-303\tAB360345.1.1443\t2e-78\t90.91\t53.0456852792\t209\n+Cluster_3746\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t2e-68\t89.69\t48.743718593\t194\n+Cluster_3934\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t7e-69\t87.79\t54.0609137056\t213\n+Cluster_4037\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Acidimicrobium;unknown species\tEU419133.1.1468\t2e-73\t89.57\t51.7326732673\t211\n+Cluster_4748\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species\tEF471700.1.1483\t2e-73\t89.47\t53.0456852792\t209\n+Cluster_5016\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;bacterium enrichment culture clone B213(2011)\tJF830237.1.1494\t4e-66\t83.86\t67.9144385027\t254\n+Cluster_5016\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;unknown species\tGQ387491.21030.22531\t4e-66\t83.98\t67.9144385027\t256\n+Cluster_5432\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t6e-55\t85.15\t49.0243902439\t202\n+Cluster_6431\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t2e-79\t86.25\t73.4806629834\t269\n+Cluster_6858\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t2e-74\t89.25\t54.3147208122\t214\n+Cluster_7323\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7\tJQ269315.1.1487\t8e-68\t83.77\t70.4\t265\n+Cluster_7769\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species\tEF471700.1.1483\t1e-56\t88.51\t46.6307277628\t174\n+Cluster_9149\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t1e-80\t91.08\t54.0609137056\t213\n+Cluster_9174\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium YJF2-33\tFJ405887.1.1482\t5e-75\t91.79\t49.2385786802\t195\n+Cluster_9447\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium BGR 43\tGU167988.1.1472\t8e-78\t86.21\t68.8829787234\t261\n+Cluster_10958\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species\tKF182287.1.1248\t2e-79\t91.71\t52.8350515464\t205\n+Cluster_13089\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;bacterium enrichment culture clone B213(2011)\tJF830237.1.1494\t1e-66\t88.24\t54.5454545455\t204\n+Cluster_13801\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrithrix;actinobacterium BGR 77\tGU168000.1.1473\t2e-63\t86.6\t51.8610421836\t209\n+Cluster_13977\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;unknown species\tGQ387491.21030.22531\t5e-70\t84.82\t68.2666666667\t257\n+Cluster_15144\tBacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrimicrobium;Ferrimicrobium acidiphilum\tAF251436.1.1466\t4e-71\t87.61\t54.0342298289\t226\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/08-affiliation_std.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/08-affiliation_std.biom Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"blast_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7", "rdp_bootstrap": "1.0;1.0;1.0;1.0;0.39;0.29;0.29", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16192:3924", "rdp_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group;unknown species"}}, {"id": "Cluster_2", "metadata": {"blast_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7", "rdp_bootstrap": "1.0;1.0;1.0;1.0;0.56;0.56;0.39", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:12521:5680", "rdp_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7"}}, {"id": "Cluster_3", "metadata": {"blast_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species", "rdp_bootstrap": "1.0;1.0;1.0;1.0;0.79;0.79;0.76", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "unknown species"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:16005:1920", "rdp_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species"}}, {"id": "Cluster_4", "metadata": {"blast_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Ferrithrix;actinobacterium BGR 77", "rdp_bootstrap": "1.0;1.0;1.0;1.0;0.19;0.19;0.13", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "Ferrithrix", "actinobacterium BGR 77"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:14417:1745", "rdp_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Iamiaceae;Iamia;Iamia majanohamensis"}}, {"id": "Cluster_5", "metadata": {"blast_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;unknown genus;unknown species", "rdp_bootstrap": "1.0;1.0;1.0;1.0;0.31;0.12;0.12", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "unknown genus", "unknown species"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19898:5958", "rdp_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Acidimicrobiaceae;Acidimicrobium;unknown species"}}, {"id": "Cluster_6", "metadata": {"blast_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1 clade;unknown genus;bacterium WH6-7", "rdp_bootstrap": "1.0;1.0;1.0;1.0;0.4;0.4;0.32", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:10625:3122", "rdp_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;actinobacterium BGR 43"}}, {"id": "Cluster_7", "metadata": {"blast_taxonomy": null, "rdp_bootstrap": "1.0;1.0;1.0;1.0;0.32;0.32;0.32", "taxonomy": ["Unclassified", "Unclassified", "Unclassified", "Unclassified", "Unclassified", "Unclassified", "Unclassified"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1101:19644:2236", "rdp_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;Sva0996 marine group;unknown genus;unidentified bacterium wb1_P06"}}, {"id": "Cluster_8", "metadata": {"blast_taxonomy": "Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;unknown family;unknown genus;unknown species", "rdp_bootstrap": "1.0;1.0;1.0;1.0;0.56;0.56;0.23", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "unknown species"], "seed_id": "HWI-M00185:22:000000000-A5'..b'1], [1521, 2, 1], [1522, 0, 5], [1522, 1, 1], [1522, 2, 1], [1523, 0, 4], [1523, 1, 1], [1523, 2, 1], [1524, 0, 4], [1524, 1, 1], [1524, 2, 1], [1525, 0, 2], [1525, 1, 2], [1525, 2, 2], [1526, 0, 6], [1526, 1, 1], [1526, 2, 2], [1527, 0, 3], [1527, 1, 5], [1527, 2, 3], [1528, 0, 2], [1528, 1, 1], [1528, 2, 3], [1529, 0, 3], [1529, 1, 2], [1529, 2, 2], [1530, 0, 3], [1530, 1, 2], [1530, 2, 2], [1531, 0, 1], [1531, 1, 2], [1531, 2, 3], [1532, 0, 3], [1532, 1, 2], [1532, 2, 2], [1533, 0, 2], [1533, 1, 2], [1533, 2, 2], [1534, 0, 4], [1534, 1, 1], [1534, 2, 1], [1535, 0, 4], [1535, 1, 2], [1535, 2, 2], [1536, 0, 3], [1536, 1, 1], [1536, 2, 3], [1537, 0, 4], [1537, 1, 2], [1537, 2, 1], [1538, 0, 2], [1538, 1, 2], [1538, 2, 2], [1539, 0, 5], [1539, 1, 4], [1539, 2, 1], [1540, 0, 2], [1540, 1, 2], [1540, 2, 2], [1541, 0, 5], [1541, 1, 2], [1541, 2, 2], [1542, 0, 4], [1542, 1, 1], [1542, 2, 1], [1543, 0, 2], [1543, 1, 3], [1543, 2, 2], [1544, 0, 2], [1544, 1, 4], [1544, 2, 2], [1545, 0,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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/09-tsv2biom.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/09-tsv2biom.biom Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1899", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "microbial mat metagenome"], "blast_taxonomy": ["None"], "rdp_bootstrap": ["1.0", "1.0", "1.0", "1.0", "0.38", "0.36", "0.26"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1108:3723:19540", "blast_affiliations": [{"perc_identity": "no data", "taxonomy": ["None"], "evalue": "no data", "aln_length": "no data", "perc_query_coverage": "no data", "subject": "no data"}]}}, {"id": "Cluster_1898", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "microbial mat metagenome"], "blast_taxonomy": ["None"], "rdp_bootstrap": ["1.0", "1.0", "1.0", "1.0", "0.4", "0.4", "0.26"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1108:19503:8413", "blast_affiliations": [{"perc_identity": "no data", "taxonomy": ["None"], "evalue": "no data", "aln_length": "no data", "perc_query_coverage": "no data", "subject": "no data"}]}}, {"id": "Cluster_1891", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "microbial mat metagenome"], "blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "unknown genus", "unknown species"], "rdp_bootstrap": ["1.0", "1.0", "1.0", "1.0", "0.44", "0.44", "0.4"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1107:24576:18163", "blast_affiliations": [{"perc_identity": "85.32", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "unknown genus", "unknown species"], "evalue": "4e-61", "aln_length": "218", "perc_query_coverage": "57.8666666667", "subject": "EF471700.1.1483"}]}}, {"id": "Cluster_1722", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "CL500-29 marine group", "unknown species"], "blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "unknown species"], "rdp_bootstrap": ["1.0", "1.0", "1.0", "1.0", "0.54", "0.33", "0.19"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:2105:16715:26852", "blast_affiliations": [{"perc_identity": "87.55", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "unknown species"], "evalue": "5e-85", "aln_length": "265", "perc_query_coverage": "70.2917771883", "subject": "HQ183925.1.1489"}]}}, {"id": "Cluster_1893", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "rdp_bootstrap": ["1.0", "1.0", "1.0", "1.0", "0.38", "0.38", "0.31"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:1107:8983:19826", "blast_affiliations": [{"perc_identity": "86.63", "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "bacterium WH6-7"], "evalue": "4e-56", "aln_length": "187", "perc_query_coverage": "45.7212713936", "subject": "JQ269315.1.1487"}]}}, {"id": "Cluster_1726", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "unknown species"], "blast_taxonomy": ["None"], "rdp_bootstrap": ["1.0", "1.0", "1.0", "1.0", "0.49", "0.49", "0.29"], "seed_id": "HWI-M00185:22:000000000-A53C9:1:2105:28320:20098", "blast_affiliations": [{"perc_identity": "no data", "taxonomy": ["None"], "evalue": "no data", "aln_length": "no data", "perc_query_coverage": "no data", "subject": "no data"}]}}, {"id": "Cluster_1725", "metadata": {"rdp_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "unknown'..b'3, 1, 2], [1523, 2, 2], [1524, 0, 2], [1524, 1, 3], [1524, 2, 1], [1525, 0, 2], [1525, 1, 2], [1525, 2, 3], [1526, 0, 2], [1526, 1, 4], [1526, 2, 1], [1527, 0, 3], [1527, 1, 3], [1527, 2, 1], [1528, 0, 18], [1528, 1, 11], [1528, 2, 5], [1529, 0, 20], [1529, 1, 8], [1529, 2, 8], [1530, 0, 4], [1530, 1, 4], [1530, 2, 3], [1531, 0, 8], [1531, 1, 3], [1531, 2, 2], [1532, 0, 24], [1532, 1, 4], [1532, 2, 10], [1533, 0, 39], [1533, 1, 27], [1533, 2, 16], [1534, 0, 5], [1534, 1, 5], [1534, 2, 3], [1535, 0, 27], [1535, 1, 10], [1535, 2, 11], [1536, 0, 23], [1536, 1, 10], [1536, 2, 3], [1537, 0, 21], [1537, 1, 7], [1537, 2, 8], [1538, 0, 18], [1538, 1, 15], [1538, 2, 4], [1539, 0, 24], [1539, 1, 8], [1539, 2, 7], [1540, 0, 5], [1540, 1, 2], [1540, 2, 1], [1541, 0, 3], [1541, 1, 3], [1541, 2, 1], [1542, 0, 1], [1542, 1, 3], [1542, 2, 2], [1543, 0, 4], [1543, 1, 4], [1543, 2, 2], [1544, 0, 3], [1544, 1, 1], [1544, 2, 3], [1545, 0, 4], [1545, 1, 1], [1545, 2, 1], [1546, 0, 5], [1546, 1, 2], [1546, 2, 1], [1547, 0, 5], [1547, 1, 2], [1547, 2, 4], [1548, 0, 3], [1548, 1, 3], [1548, 2, 3], [1549, 0, 1], [1549, 1, 5], [1549, 2, 1], [1550, 0, 2], [1550, 1, 2], [1550, 2, 3], [1551, 0, 2], [1551, 1, 1], [1551, 2, 3], [1552, 0, 48], [1552, 1, 41], [1552, 2, 12], [1553, 0, 57], [1553, 1, 23], [1553, 2, 16], [1554, 0, 56], [1554, 1, 14], [1554, 2, 19], [1555, 0, 49], [1555, 1, 24], [1555, 2, 15], [1556, 0, 42], [1556, 1, 30], [1556, 2, 23], [1557, 0, 48], [1557, 1, 26], [1557, 2, 16], [1558, 0, 49], [1558, 1, 25], [1558, 2, 18], [1559, 0, 60], [1559, 1, 22], [1559, 2, 14], [1560, 0, 49], [1560, 1, 25], [1560, 2, 19], [1561, 0, 53], [1561, 1, 22], [1561, 2, 14], [1562, 0, 16], [1562, 1, 6], [1562, 2, 3], [1563, 0, 6], [1563, 1, 4], [1563, 2, 1], [1564, 0, 7], [1564, 1, 1], [1564, 2, 1], [1565, 0, 5], [1565, 1, 3], [1565, 2, 2], [1566, 0, 4], [1566, 1, 1], [1566, 2, 2], [1567, 0, 7], [1567, 1, 1], [1567, 2, 1], [1568, 0, 4], [1568, 1, 2], [1568, 2, 2], [1569, 0, 3], [1569, 1, 4], [1569, 2, 3], [1570, 0, 1], [1570, 1, 3], [1570, 2, 3], [1571, 0, 7], [1571, 1, 2], [1571, 2, 2], [1572, 0, 7], [1572, 1, 4], [1572, 2, 2], [1573, 0, 8], [1573, 1, 5], [1573, 2, 5], [1574, 0, 18], [1574, 1, 3], [1574, 2, 2], [1575, 0, 11], [1575, 1, 3], [1575, 2, 1], [1576, 0, 2], [1576, 1, 4], [1576, 2, 2], [1577, 0, 17], [1577, 1, 3], [1577, 2, 7], [1578, 0, 10], [1578, 1, 3], [1578, 2, 1], [1579, 0, 8], [1579, 1, 5], [1579, 2, 2], [1580, 0, 11], [1580, 1, 3], [1580, 2, 3], [1581, 0, 11], [1581, 1, 7], [1581, 2, 3], [1582, 0, 10], [1582, 1, 5], [1582, 2, 4], [1583, 0, 10], [1583, 1, 9], [1583, 2, 6], [1584, 0, 22], [1584, 1, 8], [1584, 2, 7], [1585, 0, 15], [1585, 1, 10], [1585, 2, 3], [1586, 0, 10], [1586, 1, 5], [1586, 2, 5], [1587, 0, 10], [1587, 1, 11], [1587, 2, 3], [1588, 0, 29], [1588, 1, 5], [1588, 2, 10], [1589, 0, 9], [1589, 1, 3], [1589, 2, 7], [1590, 0, 7], [1590, 1, 9], [1590, 2, 5], [1591, 0, 5], [1591, 1, 1], [1591, 2, 1], [1592, 0, 23], [1592, 1, 16], [1592, 2, 9], [1593, 0, 22], [1593, 1, 15], [1593, 2, 10], [1594, 0, 2], [1594, 1, 3], [1594, 2, 2], [1595, 0, 27], [1595, 1, 12], [1595, 2, 8], [1596, 0, 3], [1596, 1, 1], [1596, 2, 2], [1597, 0, 24], [1597, 1, 17], [1597, 2, 9], [1598, 0, 20], [1598, 1, 12], [1598, 2, 14], [1599, 0, 4], [1599, 1, 3], [1599, 2, 2], [1600, 0, 5], [1600, 1, 6], [1600, 2, 2], [1601, 0, 2], [1601, 1, 4], [1601, 2, 1], [1602, 0, 32], [1602, 1, 18], [1602, 2, 8], [1603, 0, 9], [1603, 1, 4], [1603, 2, 2], [1604, 0, 6], [1604, 1, 4], [1604, 2, 3], [1605, 0, 3], [1605, 1, 4], [1605, 2, 3], [1606, 0, 3], [1606, 1, 3], [1606, 2, 2], [1607, 0, 35], [1607, 1, 16], [1607, 2, 12], [1608, 0, 3], [1608, 1, 5], [1608, 2, 3]], "generated_by": null, "matrix_type": "sparse", "shape": [1609, 3], "format_url": "http://biom-format.org", "date": "2018-01-12T18:20:39", "type": "OTU table", "id": null, "columns": [{"id": "splA_01", "metadata": null}, {"id": "splA_02", "metadata": null}, {"id": "splA_03", "metadata": null}]}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/09-tsv2biom.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/09-tsv2biom.fasta Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,3218 @@\n+>Cluster_1\n+CACGTAAGAATTTGCCTTTAGGAGGGGGATAACAATTGGAAACGATTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATAGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_2\n+CACGTAAGAATTTGCCTTTAGGAGGGGGACAACAACTGGAAACGGTTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAAAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGACGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_3\n+TGCGTCGGAACGTACCGAGTAATGGGGGATAACGCAGCGAAAGTTGTGCTAATACCGCATACGCCCTGAGGGGGAAAGTGGGGGACCGCAAGGCCTCACGTTATTCGAGCGGCCGACGTCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATTCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCAGCAGGAACGAAACGGTACGCTCTAACATAGTGTGCTAATGACGGTACCTGCAGAAGAAGCACCGGCTAACTAC\n+>Cluster_4\n+CACGTGAGAATCTGCCTCCAGGTCGGGGACAACAGCGGGAAACTGCTGCTAATACCCGATGTGCCTAAGGGTGAAAGATTAATTGCCTGGAGATGAGCTCGCGTCCGATTAGCTAGTTGGTAGAGTAAAAGCCTACCAAGGCTCCGATCGGTAGCTGGTCTGAGAGGATGAGCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAAGACCGCGTGGGGGATGAAGGCTCTTGGGTTGTAAACCCCTTTTCTCAGGGAAGAAGTTCTGACGGTACCTGAGGAATCAGCATCGGCTAACTCC\n+>Cluster_5\n+CGCGTGGGAATCTGCCCTGCAGTGGGGGACAACCCGAGGAAACTCGGGCTAATACCGCATACGTCCTATGGGAGAAAGGGGGCCTTCGGGCTCTCGCTGCAGGATGAGCCCGCGTCCGATTAGCTTGTTGGTGGGGTAACGGCCCACCAAGGCTGCGATCGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTCAGTGGGGAAGAAAAGCGCGAGGTTAATACCCTTGTGTGTTGACGTTACCCACAGAAGAAGCACCGGCTAACTCC\n+>Cluster_6\n+CACGTAAGAATTTACCTTTAGGAGGGGGACAACAGACAGAAATGACTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGATCAGTATCTGGTTTGAGAGGATGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATCTCGCGTGAGGGATGACTGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_7\n+CGCGTGGGCAATCTACCTTCGAATCGGGGATAACATTGCGAAAGCGATGCTAATACCGGATGACATCCTGAAGGCTTCGGTTTTAAGGATCAAAGGTGGCCTCTACGAGTAAGCTACTGTTTGGAGATGAGCCCGCGTACCATTAGCTTGTTGGTAGGGTAACGGCCTACCAAGGCGACGATGGTTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAAACCACGAGGTGATAATATCGCTTTGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_8\n+CGCGTGGGAATCTGCCCTGCAGTGGGGGACAACCCGAGGAAACTCGGGCTAATACCGCATACGTCTTACGAGAGAAAGGGGGCTTCGGCTCTCGCTGCAGGATGAGCCCGCGTCCGATTAGCTTGTTGGTAGGGTAATGGCCTACCAAGGCGACGATCGGTAGCTGGTCTGAGAGGATGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTCAGTGGGGAAGAAAAACCCGAGGTTAATACCCTTGGGTCTTGACGTTACCCACAGAAGAAGCACCGGCTAACTCC\n+>Cluster_9\n+CGCGTGGGCAATCTACCTCCGAATCGGGGATAACATTGCGAAAGCGATGCTAATACCGGATGACATCCTGAGGACTTCGGTTTTCGGGATCAAAGGTGGCCTCTACGGGTAAGCTACTGTTTGGGGATGAGCCCGCGTACCATTAGCTTGTTGGTAGGGTAACGGCCTACCAAGGCGACGATGGTTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAAACCACGGAGCGTTAATATCGCTTTGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_10\n+CACGTAAGAATTTGCCTTTAGGAGGGGGACAACAACTGGAAACGGTTGCTAATACCCCATATGCTTTCGAGTGAAATGGATTTTTCCGCCTAGAGAGAAGCTTGCGGCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCAGTATCTGGTTTGAGAGGATGATCAGACACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATCTCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAACAAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCC\n+>Cluster_11\n+CACGTAAGAATTTGCCTTTAGGAGGGG'..b'GGTCTAAAAGGATGATCCCCCACACTGGTACTGAGACACGGACCAGGCTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAAGGGGCGAAAGCCTGAACCAGCCATGCCGCGTGCAGGATGACGGCCCTACGGGTTGTAAACTGCTTTTATACGGGAAGAAACCTCCTTACGTGTAGGGAGCTGACGGTACCGTAAGAATAAGCATCGGCTAACTCC\n+>Cluster_4252\n+CGCGTAGGTGATCTACCTTCAAGTGGGGGACAACCCAGGGAAACTTGGGCTAATACCGCATGTGGCAGTAATGCTAAAGCCGGCCTCTGAATATGCTGGTGCTTGGAGATGAGCTTGCGTCTGATTAGCTAGTTGGTGGGGTAATGGCCTACCGAGGCGATGATAAGTAGGCGGCTTTAACGAGTGGTCGCCCACACTGGGATTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTCGAGAATAGTCTACAATGGTCGAAAGATTGATAGTGCGACGCCGCGTGAACGATGAAGCATTTCGGTGTGTAAAGTTCTTTTCTATGGGAGCAGTGCTTTTTATGTTAATAGCATGAGAGGAGAGATATTACTGTAGGAATAAGCCACGGCTAACTCC\n+>Cluster_13801\n+CACGTAAATAACTTACCCTTAAGTTTGGGATACCATTGCTAACGCGATGTTAATACCGGATGTGGATAGAGAGTCACCTGGTTTTCTATTTAAAGGTCCTTCGGGACTGCTTAAGGATGGATTTGCGCACCATTAGCTTGTTGGTGGGGTAACGGCCTACCAAGGCGATGATGGTTAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATATTGCGCAATGGACGAAAGTCTGACGCAGCAACTCCGCGTGAAGGATGAAGGTTCTCGGATCGTAAACTTCTTTTATTTGGGAAGAAATGTCTAAGTAGGTAATGGCTTAGATTTGACGGTACCATTTGAATAAGCTCCGGCTAAATAC\n+>Cluster_15144\n+TACATGGGTAATTTGCCCCTTTGTTCGGAATAGCCACCGGAAACGGTGATTAATTCCGGATGTGTTCGGGTGCCGCATGGCACCTTATATAAAGGCGGGGATCTTCGGACCTGTCGCAAAGGGATAAGCCCATGTCCTATCAGCTTGTTGGTGAGGTAACGGCTCACCAAGGCTTACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACTGCCCAGACTCCTACGGGAGGCTGCAGTCGAGAATCATTGTCAATGCACGAAAGTGTGAACATGCGACGCCGCGTGGAGGAAGACGGCCTTCGGGTTGTAAACTCCTGTCAGCAGGGAGGAAAGACAGTACCATTAATACCGGTGCGGTTTGACAGTACCTGCAGAGGAAGTCACGGCTAACTCT\n+>Cluster_5432\n+CACGTGATCAATCTGCCCTGAAGTCGGGGATAGCTATTCGAAAGGATAGGTAATACCTGATAAGACCACAGCATCGCATGGTGCAGTGGTAAAACGGTGGGGACCTTCGGGCCTTCCGCTTCAGGATGAGATCGCGGCCTATTAGCTTGTTGGTGAGGTAACGGCTCACCAAGGCTTTGATGGGTAACCGGCCTGAGAGGGTGAACGGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGCTGAATCATTCGCCAATGCGCGAAAGCGTGACGGTGCGACGCCGCGTGAAGGATGAAGGCCCTAGGGTCGTAAACTTCTGTCAGATTCTAGAAAACTACAAGGGTTAATAGCTTTTGTACTGATCAGAATCAGAGGAAGCACAGGCTAATCTC\n+>Cluster_7257\n+CGCGTAGATAACCTGTCTTCATGTCTGGAATAATACACCGAAAGGGGTACTAATACCGGATATTCTTGCTTTATATAAGTTTTGCAAGCAAAGGTGGCCTCTGATTCAAGCTACTGCATGTAGAGGGGTCTGCGTACCATTAGCTAGTAGGTAGGGTAATGGCCTACCTAGGCTACGATGGTTAGCGGGTCTGAGAGGATTATCCGCCACACTGGCACTGGAACACGGGCCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGCGCAATGGGGGCAACCCTGACGCAGCGACGCCGCGTGAGTGAGGAAGGCCTTCGGGTCGTAAAGCTCTGTCAAGAGGAAAGAAATGCATATCGGTTAATACCCGATATGTTTGACGGTACCTCTAAAGGAAGCACCGGCTAACTCC\n+>Cluster_6485\n+CGCGTGGGTAACCTACCTCCGAACCTGGGATAACTTCGCGAAAGCGTTGCTAATACCGGATATTGCCCCATAGTCCGTGGACCGTGGGGTGAAAGGTGACCTCTTCTTGAAAGTTGCCATTCGGAGATGGGCTCGCGTCCCATTAGCTTGTTGGTAGGGTAATGGCCTACCAAGGCGACGATGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGCGCTGAAACACGGGCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTGTCAGGTGGGAAAAAAGGCCCACAGTAAATAGCTTCGGGATCTGATGGTACCACCAGAGGAAGCACCGGCTAACTCC\n+>Cluster_6916\n+CACGTGGGTAATCTACCTTCAAATCGGGAATAACGTTGCGAAAGCGACGCTAATACCGGATAACATCGATGAGGTCTCGGCCTTTTCGATCAAAGATGGCCTCTACATGTAAGCTGTCGTTCGAAGATGAGCCCGCGTCCCATTAGCTTGTTGGTAGGGTAAAGGCCTACCAAGGCGACGATGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGACACATGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAGCTCTGTCAAGTGGGAAGAACCCACGTGGTAATAATACTGCCACGTGCTGACGGTACCACTGAAGGAAGCACCGGCTAACTCC\n+>Cluster_13089\n+CACATGGCTGACCTGCCCTTCAGAGGGGGACAACCGCTGGAAACGGTGGCTAATACCCCATACGCTCACGACGATTAGAAGGTTGTGAGGAAAGTGTTTAGCGCTGAAGGAGGGGGCTGTGGCCCATCAGCTAGTTGGTGAGGTAACGGCTTACCAAGGCGAAGACGGGTAGGGGGCCTGAGAGGGTGACCCCCCACACGGGTACTGAGACACGGACCCGACTCCTACGGGAGGCAGCAGTAAGGGATATTGCGACAATGGGCGAAAGCCTGACGCAGCAACGCCGCGTGCGGGAGGAAGGCCTTCGGGTTGTAAACCGCTTTTCGGGGGGAAGAGGAAGGACGGTACCCCCGGAATAAGTCTCGGCTAACTAC\n+>Cluster_11351\n+CGCGTATGCAACCTACCCTTAACTATGGGATAGCCCGGGGAAACTCGGATTAATATCGTATAACATCATAAAATGGCATCATTAAATGATTAAAGCTGCGGCGGTTAAGGATGGGCATGCGTGCCATTAGATAGTTGGTGAGGTAACGGCTCACCAAGTCAACGATGGCTACGGGGTCTTAAAGGATGATCCCGCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGCAAGCCTGAACCAGCCATGCCGCGTGTAGGATGACGGCCTTCTGGGTTGTAAACTACTTTTATATGGGAAGAAAGTCAGATACTTGTATCTGTTTGCCGGTACCATATGAATAAGCATCGGCTAACTCC\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/10b-tree.nwk
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/10b-tree.nwk Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,1 @@\n+((((((((Cluster_255:0.0801006,Cluster_1269:0.013881937)0.993:0.117315838,Cluster_1463:0.107206794)0.895:0.098029426,Cluster_379:0.201572703)1:0.919271068,Cluster_991:0.135869787)0.746:0.071388493,Cluster_1281:0.224971103)0.198:0.087233601,(Cluster_1016:0.08474538,(Cluster_1529:0.10904065,((((Cluster_427:0.009531235,(Cluster_194:5e-09,Cluster_351:0.009594468)0.988:0.05697923)0.994:0.048449906,(Cluster_254:0.027425721,Cluster_313:0.019028685)0.887:0.013849884)0.896:0.014402239,((Cluster_1627:0.055043487,(Cluster_377:0.025375501,Cluster_896:0.020832557)0.888:0.020999626)0.962:0.03566252,((Cluster_114:0.008177621,(Cluster_720:0.008044723,(((((Cluster_1196:0.024550703,Cluster_1292:0.02622158)0.87:0.013672042,(Cluster_1437:0.021495914,Cluster_1456:0.019514287)0.953:0.023495512)0.968:0.028639757,((Cluster_914:0.010854126,(Cluster_3204:0.034251824,Cluster_1840:0.006311411)0.893:0.018716219)0.927:0.023007583,((Cluster_361:5e-09,Cluster_970:0.017907685)0.761:0.003617048,(Cluster_1050:0.018354616,(Cluster_1246:0.022279662,Cluster_1301:0.009234553)0.864:0.008991357)0.892:0.009361888)0.868:0.014673322)0.857:0.014088014)0.861:0.015174123,(Cluster_477:0.046153993,Cluster_858:0.061476076)0.6:0.027719858)0.794:0.010541699,((Cluster_1574:0.083264226,Cluster_1784:0.021585822)0.901:0.023713426,(Cluster_459:0.015312539,(Cluster_46:5e-09,Cluster_148:0.027647579)0.746:0.002956639)0.161:0.004332796)0.977:0.028834205)0.848:0.009548686)0.97:0.034720626)0.944:0.024693492,(Cluster_1902:0.033657757,(Cluster_1394:0.057604236,Cluster_1592:5e-09)0.987:0.047902629)0.931:0.022636253)0.584:0.001129592)0.89:0.021156789)0.877:0.017264697,(Cluster_586:0.076971897,(Cluster_1306:0.153473255,Cluster_837:0.023287587)0.588:0.019469235)0.798:0.010881191)0.963:0.045118951)0.968:0.054535927)0.909:0.043415335)0.748:0.021119619,(Cluster_1227:0.147689864,(Cluster_1319:0.074705557,((Cluster_1802:0.027227347,((Cluster_1304:0.021007039,Cluster_1096:0.074184998)0.928:0.0378177,Cluster_3175:0.006255294)0.772:0.007934766)0.224:0.002348731,Cluster_1150:0.033604233)0.992:0.085852048)0.182:0.029599625)0.352:0.025392953)0.751:0.0323149365,(((((((((((((Cluster_1533:0.509082208,(Cluster_1005:0.191883151,(Cluster_1543:0.142870954,(Cluster_716:0.040595392,(Cluster_604:0.009531209,(Cluster_395:0.002890592,Cluster_1710:0.017789727)0.701:0.002074408)0.754:0.009621153)0.896:0.042786461)0.862:0.051672433)0.967:0.129986042)0.631:0.02066595,(((Cluster_550:0.014521388,Cluster_626:0.008998843)0.91:0.05901059,((((Cluster_1105:0.018574867,Cluster_1504:0.002762452)1:0.035368371,Cluster_493:5e-09)0.913:0.009126488,Cluster_329:5e-09)0.946:0.028049817,(Cluster_1250:0.01339077,(Cluster_1186:0.006952989,Cluster_4252:0.008254756)0.191:0.006357758)0.245:0.01664117)0.99:0.123436187)1:0.335019406,((Cluster_617:0.0773468,(Cluster_396:0.0509766,Cluster_473:0.030243642)1:0.144966491)0.953:0.082830343,((Cluster_2070:0.120179371,(Cluster_1364:0.06173005,((Cluster_643:0.003376648,Cluster_1468:0.027939991)0.88:0.022867435,(Cluster_1169:0.025774885,Cluster_2848:0.025610561)0.98:0.050121609)0.914:0.046174442)0.528:0.040511029)0.928:0.037495099,(((((Cluster_1643:0.182674862,(Cluster_340:0.081212379,(Cluster_826:0.056661519,(Cluster_766:0.007010283,(Cluster_755:0.005899593,Cluster_1951:0.011070147)0.548:0.007351951)0.995:0.06181351)0.95:0.039733708)0.883:0.026736343)0.625:0.006865605,((Cluster_1949:0.091098053,(Cluster_164:0.145663857,((((Cluster_742:0.010622976,((Cluster_984:0.039300328,Cluster_1570:0.029366477)0.969:0.033356272,Cluster_979:0.026941742)0.929:0.026134988)0.949:0.028019827,(((Cluster_486:0.006611613,Cluster_488:0.057869465)0.919:0.014219722,(Cluster_2882:0.013567329,(Cluster_599:0.005724739,Cluster_1689:0.005645976)0.794:0.005020539)0.754:0.004720925)0.691:0.003683993,Cluster_1211:0.021201549)0.72:0.006604993)0.992:0.067245639,(Cluster_846:0.073224686,Cluster_1155:0.021618954)0.887:0.032470121)0.927:0.053085009,(Cluster_588:0.039768339,Cluster_912:0.132221715)0.977:0.070285885)0.606:0.0'..b'ster_13:0.002778368,Cluster_756:0.010095303)1:0.054112291,(((Cluster_30:0.006650709,(Cluster_26:0.003286338,Cluster_265:0.016914009)0.923:0.010102534)0.738:0.003214524,Cluster_19:0.027671993)0.757:0.003343244,(Cluster_674:5e-09,Cluster_10958:0.034154985)0.453:0.003304017)0.852:0.008190681)0.681:0.018728401,Cluster_1996:6e-09)0.947:0.03061495)0.997:0.047481286,(Cluster_1048:0.006478486,(Cluster_1130:0.027376289,Cluster_794:0.042729164)0.859:0.014498541)0.986:0.030554368)0.752:0.00345367,((Cluster_189:0.017152585,(Cluster_894:0.022469209,(Cluster_692:0.014825237,(Cluster_59:0.007054399,Cluster_1651:0.015833571)0.835:0.014064751)0.248:0.004211949)0.784:0.007256559)0.979:0.026033205,(Cluster_253:0.003246696,(Cluster_301:0.0234116,Cluster_1291:0.003019835)0.776:0.006885326)0.983:0.025432939)0.719:0.003546096)0.957:0.019213142,(Cluster_227:0.009641996,((((((Cluster_1175:0.009501967,(Cluster_8:5e-09,(Cluster_32:0.012128544,(Cluster_2588:0.007700481,Cluster_174:0.019007248)0.307:0.007154235)0.882:0.009761984)0.184:0.006502514)0.976:0.016691468,Cluster_424:0.00632723)0.874:0.006382769,Cluster_280:5e-09)0.619:0.009179308,(Cluster_629:5e-09,Cluster_1558:0.013305071)0.997:0.034202365)0.749:0.003672157,(Cluster_910:0.015889953,Cluster_1440:0.017592319)0.928:0.014411779)0.598:0.006604906,((Cluster_5:0.012538697,Cluster_368:0.000820724)0.956:0.016332837,(Cluster_45:6e-09,Cluster_976:0.012921149)0.888:0.00970698)0.796:0.00555905)0.766:0.004760517)0.243:0.009440148)0.748:0.003445734,Cluster_719:0.038100843)0.718:0.003852615)0.691:0.005402064)0.76:0.007260223)0.929:0.021320888,((Cluster_77:0.019500184,((Cluster_621:0.016850646,Cluster_1057:0.019246015)0.992:0.032333804,(Cluster_1125:0.009906738,(Cluster_810:0.006259857,Cluster_905:0.012636122)0.94:0.012341014)0.719:0.002814594)0.473:0.003272924)0.807:0.005318901,(Cluster_55:0.015590443,Cluster_52:0.100460037)0.785:0.008196734)0.852:0.014717423)0.986:0.043332705)0.913:0.026388384)0.856:0.012876119)0.916:0.019058634)0.774:0.009822076)0.654:0.031782935,((Cluster_942:0.101854885,(((((Cluster_645:0.006049316,Cluster_201:0.026022051)0.59:0.011587816,((Cluster_49:5e-09,Cluster_580:0.025945782)0.852:0.006602735,(Cluster_480:0.003097799,Cluster_703:0.012378655)0.674:0.002593346)0:5e-09)0.528:0.005484109,((Cluster_1484:0.012667179,Cluster_3098:0.02421268)0.923:0.019822464,((Cluster_777:0.004997305,Cluster_6339:0.013565766)0.971:0.026299373,(Cluster_1866:0.025520403,Cluster_3746:0.002881705)0.981:0.030172893)0.945:0.025009693)0.697:0.03464156)0.999:0.109347181,Cluster_270:0.099107962)0:0.011620839,(Cluster_1970:0.059994999,((Cluster_901:0.040017062,Cluster_1613:0.115052214)0.39:0.035022015,(Cluster_699:0.043473737,Cluster_779:0.009708582)0.974:0.056568505)0.309:0.019360981)0.687:0.03256184)0.926:0.044124221)0.275:0.040119522,((Cluster_840:0.042885412,(((Cluster_1696:0.021947229,((Cluster_831:0.035108135,(Cluster_132:0.012569166,Cluster_2495:0.002908952)0.783:0.006296516)0.245:5e-09,Cluster_634:0.012758039)0.987:0.015935206)0:5e-09,(Cluster_1585:0.012091873,(Cluster_3:0.006807185,Cluster_449:0.008780213)0.866:0.009215309)0.765:0.003520603)0.745:0.007749686,Cluster_405:0.007995405)0.997:0.070681417)0.974:0.04946206,(((Cluster_1295:0.120166847,((((Cluster_256:0.007068331,(Cluster_1350:0.064231161,Cluster_1676:0.018085646)0.997:0.049395429)0:5e-09,(Cluster_274:0.009228419,Cluster_670:0.00290196)0.726:0.005699532)0.937:0.016377465,Cluster_2517:0.024134488)0.698:0.013013739,Cluster_879:0.075682686)0.978:0.065568462)0.947:0.051406579,(Cluster_671:0.048135631,Cluster_1865:0.043175514)0.998:0.081328141)0.564:0.014848368,Cluster_1138:0.119122421)0.827:0.025683973)0.755:0.016931603)1:0.117866683)0.218:0.056163339,Cluster_733:0.196836798)0.138:0.027033019)0.967:0.072277993,((Cluster_383:0.073196119,Cluster_888:0.120345089)0.965:0.079286338,((Cluster_1283:5e-09,Cluster_1628:0.014076201)0.97:0.074688144,(Cluster_620:0.028016799,Cluster_1645:5e-09)1:0.198385003)0.924:0.050271983)0.441:0.02812559)0.751:0.0086825685)NA;\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/11-phylo_import.Rdata
b
Binary file test-data/references/11-phylo_import.Rdata has changed
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/12-phylo_composition.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/12-phylo_composition.html Thu Oct 25 05:01:13 2018 -0400
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 \n+ggplotly(p, tooltip = c(&quot;x&quot;, &quot;y&quot;, &quot;fill&quot;))</code></pre>\n+<div id="code-r-file" style="display:none; charset=UTF-8">\n+<p>library(plotly) \n+source(&quot;<code>https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R</code>&quot;) \n+# if in new session \n+# data &lt;- path to Rdata file \n+# load(data) \n+ \n+varExp &lt;- #Experiment variable \n+taxaRank1 &lt;- #Taxonomic rank at which to filter your data \n+taxaRank2 &lt;- #Taxonomic rank used for aggregation \n+taxaSet1 &lt;- #Taxa (at previously specified taxonomic rank) to keep in the dataset \n+taxaRank &lt;- #Taxonomic rank used for coloring (typically &quot;Phylum&quot;) \n+numberOfTaxa &lt;- #Number of most abundant taxa to keep</p>\n+<p>\n+# Bar plot \n+e &lt;- paste(\'facet_wrap(~\', varExp, \', scales = &quot;free_x&quot;, nrow = 1)\') \n+p &lt;- plot_bar(data,fill= taxaRank) + eval(parse(text = e)) + ggtitle(paste(&quot;Bar plot colored by&quot;, taxaRank))+ theme(plot.title = element_text(hjust = 0.5)) \n+plot(p) \n+ \n+# composition plot \n+taxaSet1 &lt;- unlist(strsplit(taxaSet1, &quot; &quot;)) \n+p &lt;- plot_composition(data, taxaRank1, taxaSet1, taxaRank2, numberOfTaxa, fill=taxaRank2) \n+p &lt;- p + eval(parse(text = e)) + theme(plot.title = element_text(hjust = 0.5)) \n+ggplotly(p, tooltip = c(&quot;x&quot;, &quot;y&quot;, &quot;fill&quot;))</p>\n+</div>\n+<script>\n+  function download1(){\n+    var text = document.getElementById("code-r-file").textContent;\n+    var blob = new Blob([text],{type:"text/plain;charset=utf-8"});\n+    saveAs(blob,"composition_code.R");\n+   }\n+</script>\n+<p><input type="button" value="Download R code" class="button" onclick="download1();"></input></p>\n+<script>\n+function download(filename, mysrc) {\n+var element = document.createElement(\'a\');\n+    element.setAttribute(\'href\', mysrc);\n+    element.setAttribute(\'download\', filename);\n+    element.style.display = \'none\';\n+    document.body.appendChild(element);\n+    element.click();\n+    document.body.removeChild(element);\n+}\n+document.getElementById("dwn-bar-plot").addEventListener("click", function(){\n+var div = document.getElementById(\'bar-plot\');\n+var myimg = div.getElementsByTagName(\'img\')[0];\n+var mysrc = myimg.src;\n+var filename = "bar_plot.png";\n+download(filename, mysrc);\n+}, false);\n+</script>\n+</div>\n+</div>\n+\n+\n+\n+\n+</div>\n+\n+<script>\n+\n+// add bootstrap table styles to pandoc tables\n+function bootstrapStylePandocTables() {\n+  $(\'tr.header\').parent(\'thead\').parent(\'table\').addClass(\'table table-condensed\');\n+}\n+$(document).ready(function () {\n+  bootstrapStylePandocTables();\n+});\n+\n+\n+</script>\n+\n+<!-- dynamically load mathjax for compatibility with self-contained -->\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'
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diff -r 000000000000 -r 76c750c5f0d1 test-data/references/13-phylo_alpha_div.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/13-phylo_alpha_div.tsv Thu Oct 25 05:01:13 2018 -0400
b
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diff -r 000000000000 -r 76c750c5f0d1 test-data/references/14-phylo_beta_div.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/14-phylo_beta_div.html Thu Oct 25 05:01:13 2018 -0400
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ary(reshape2)\n+source(&quot;https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R&quot;)\n+#if in new session \n+#data &lt;- path to Rdata file \n+#load(data) \n+varExp &lt;- #Experiment variable to split plot\n+method &lt;- #Beta diversity method name  #To show all available distances: distanceMethodList\n+fileBeta &lt;- &quot;beta_diversity.tsv&quot;  # output file path</code></pre>\n+<h4>\n+Dist as heatmap plot\n+</h4>\n+<pre class="r"><code>## Order samples according to grouping variable\n+sampleOrder &lt;- levels(reorder(sample_names(data), as.numeric(get_variable(data, varExp)))) \n+\n+dist.a &lt;- distance(data, method = method)\n+\n+pa &lt;- plot_dist_as_heatmap(dist.a, order = sampleOrder, title = method) + \n+  theme(plot.title = element_text(hjust = 0.5))\n+plot(pa)</code></pre>\n+<h4>\n+Save distance matrix\n+</h4>\n+<pre class="r"><code>a &lt;- as.matrix(dist.a)\n+write.table(a, fileBeta, sep=&quot;\\t&quot;, quote=FALSE, col.names=NA)</code></pre>\n+<div id="code-r-file" style="display:none;">\n+<p>library(phyloseq) \n+library(ggplot2) \n+library(gridExtra) \n+library(reshape2) \n+source(&quot;<code>https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R</code>&quot;) \n+#if in new session \n+#data &lt;- path to Rdata file \n+#load(data) \n+varExp &lt;- #Experiment variable to split plot \n+method &lt;- #Beta diversity method name \n+fileBeta &lt;- #path to output Beta diversity file \n+#To show all available distances: distanceMethodList \n+ \n+## Order samples according to grouping variable \n+sampleOrder &lt;- levels(reorder(sample_names(data), as.numeric(get_variable(data, varExp)))) \n+ \n+dist.a &lt;- distance(data, method = method) \n+ \n+pa &lt;- plot_dist_as_heatmap(dist.a, order = sampleOrder, title = method) + \n+ theme(plot.title = element_text(hjust = 0.5)) \n+plot(pa) \n+ \n+a &lt;- as.matrix(dist.a) \n+write.table(a, fileBeta , sep=&quot;\\t&quot;, quote=FALSE, col.names=NA)</p>\n+</div>\n+<script>\n+  function download(){\n+    var text = document.getElementById("code-r-file").textContent;\n+    var blob = new Blob([text],{type:"text/plain;charset=utf-8"});\n+    saveAs(blob,"beta_diversity_code.R");\n+   }\n+</script>\n+<p><input type="button" value="Download R code" class="button" onclick="download();"></input></p>\n+</div>\n+</div>\n+\n+\n+\n+\n+</div>\n+\n+<script>\n+\n+// add bootstrap table styles to pandoc tables\n+function bootstrapStylePandocTables() {\n+  $(\'tr.header\').parent(\'thead\').parent(\'table\').addClass(\'table table-condensed\');\n+}\n+$(document).ready(function () {\n+  bootstrapStylePandocTables();\n+});\n+\n+\n+</script>\n+\n+<!-- dynamically load mathjax for compatibility with self-contained -->\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'
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diff -r 000000000000 -r 76c750c5f0d1 test-data/references/15-phylo_structure.html
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+++ b/test-data/references/15-phylo_structure.html Thu Oct 25 05:01:13 2018 -0400
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oad R code file\n+</button>\n+<script>\n+function download1(filename, text) {\n+    var element = document.createElement(\'a\');\n+    element.setAttribute(\'href\', \'data:text/plain;charset=utf-8,\' + encodeURIComponent(text));\n+    element.setAttribute(\'download\', filename);\n+\n+    element.style.display = \'none\';\n+    document.body.appendChild(element);\n+    element.click();\n+    document.body.removeChild(element);\n+}\n+\n+// Start file download.\n+document.getElementById("dwn-btn").addEventListener("click", function(){\n+    // Generate download of hello.txt file with some content\n+    var text = document.getElementById("code-r-file").innerText;\n+    var filename = "structure_visualization_code.R";\n+    download1(filename, text);\n+}, false);\n+</script>\n+<script>\n+function download(filename, mysrc) {\n+var element = document.createElement(\'a\');\n+    element.setAttribute(\'href\', mysrc);\n+    element.setAttribute(\'download\', filename);\n+    element.style.display = \'none\';\n+    document.body.appendChild(element);\n+    element.click();\n+    document.body.removeChild(element);\n+}\n+document.getElementById("dwn-plot1").addEventListener("click", function(){\n+    var div = document.getElementById(\'plot1\');\n+    var myimg = div.getElementsByTagName(\'img\')[0];\n+    var mysrc = myimg.src;\n+    var filename = "ordination_plot_no_sample_name.png";\n+    download(filename, mysrc);\n+}, false);\n+\n+document.getElementById("dwn-plot2").addEventListener("click", function(){\n+    var div = document.getElementById(\'plot2\');\n+    var myimg = div.getElementsByTagName(\'img\')[0];\n+    var mysrc = myimg.src;\n+    var filename = "ordination_plot_with_sample_name.png";\n+    download(filename, mysrc);\n+}, false);\n+\n+document.getElementById("dwn-plot22").addEventListener("click", function(){\n+    var div = document.getElementById(\'plot22\');\n+    var myimg = div.getElementsByTagName(\'img\')[0];\n+    var mysrc = myimg.src;\n+    var filename = "ordination_plot_with_sample_name_and_ellipse.png";\n+    download(filename, mysrc);\n+}, false);\n+\n+document.getElementById("dwn-heatmap-plot").addEventListener("click", function(){\n+    var div = document.getElementById(\'heatmap-plot\');\n+    var myimg = div.getElementsByTagName(\'img\')[0];\n+    var mysrc = myimg.src;\n+    var filename = "heatmap_plot.png";\n+    download(filename, mysrc);\n+}, false);\n+\n+</script>\n+</div>\n+</div>\n+\n+\n+\n+\n+</div>\n+\n+<script>\n+\n+// add bootstrap table styles to pandoc tables\n+function bootstrapStylePandocTables() {\n+  $(\'tr.header\').parent(\'thead\').parent(\'table\').addClass(\'table table-condensed\');\n+}\n+$(document).ready(function () {\n+  bootstrapStylePandocTables();\n+});\n+\n+\n+</script>\n+\n+<!-- dynamically load mathjax for compatibility with self-contained -->\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'
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diff -r 000000000000 -r 76c750c5f0d1 test-data/references/16-phylo_structure.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/16-phylo_structure.html Thu Oct 25 05:01:13 2018 -0400
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 \n+#if in new session \n+#library(phyloseq) \n+#source(&quot;<code>https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R</code>&quot;) \n+#data &lt;- path to Rdata file \n+#load(data) \n+ \n+##get dist object from distance matrix file \n+distance &lt;- # path to Beta diversity tsv file \n+A &lt;- read.table(file=distance, row.names=1) \n+dist &lt;- as.dist(A) \n+ \n+## Env types \n+varExp &lt;- #(discrete) experimental variable used to color samples \n+ \n+## Clustering Trees \n+plot_clust(data, dist, method = &quot;ward.D2&quot;, color = varExp) \n+plot_clust(data, dist, method = &quot;complete&quot;, color = varExp) \n+plot_clust(data, dist, method = &quot;single&quot;, color = varExp) \n+</p>\n+</div>\n+<script>\n+  function download1(){\n+    var text = document.getElementById("code-r-file").textContent;\n+    var blob = new Blob([text],{type:"text/plain;charset=utf-8"});\n+    saveAs(blob,"sample_clustering_code.R");\n+   }\n+</script>\n+<p><input type="button" value="Download R code" class="button" onclick="download1();"></input></p>\n+<script>\n+function download(filename, mysrc) {\n+var element = document.createElement(\'a\');\n+    element.setAttribute(\'href\', mysrc);\n+    element.setAttribute(\'download\', filename);\n+    element.style.display = \'none\';\n+    document.body.appendChild(element);\n+    element.click();\n+    document.body.removeChild(element);\n+}\n+document.getElementById("dwn-ward-d2").addEventListener("click", function(){\n+    var div = document.getElementById(\'ward-d2\');\n+    var myimg = div.getElementsByTagName(\'img\')[0];\n+    var mysrc = myimg.src;\n+    var filename = "sample_clustering_wardD2.png";\n+    download(filename, mysrc);\n+}, false);\n+\n+document.getElementById("dwn-complete").addEventListener("click", function(){\n+    var div = document.getElementById(\'complete\');\n+    var myimg = div.getElementsByTagName(\'img\')[0];\n+    var mysrc = myimg.src;\n+    var filename = "sample_clustering_complete.png";\n+    download(filename, mysrc);\n+}, false);\n+\n+document.getElementById("dwn-single").addEventListener("click", function(){\n+    var div = document.getElementById(\'single\');\n+    var myimg = div.getElementsByTagName(\'img\')[0];\n+    var mysrc = myimg.src;\n+    var filename = "sample_clustering_single.png";\n+    download(filename, mysrc);\n+}, false);\n+</script>\n+</div>\n+</div>\n+\n+\n+\n+\n+</div>\n+\n+<script>\n+\n+// add bootstrap table styles to pandoc tables\n+function bootstrapStylePandocTables() {\n+  $(\'tr.header\').parent(\'thead\').parent(\'table\').addClass(\'table table-condensed\');\n+}\n+$(document).ready(function () {\n+  bootstrapStylePandocTables();\n+});\n+\n+\n+</script>\n+\n+<!-- dynamically load mathjax for compatibility with self-contained -->\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'
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diff -r 000000000000 -r 76c750c5f0d1 test-data/references/17-phylo_structure.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/17-phylo_structure.html Thu Oct 25 05:01:13 2018 -0400
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et tabset-fade tabset-pills">\n+<h1></h1>\n+<div id="multivariate-anova-performed-with-adonis" class="section level2">\n+<h2>Multivariate ANOVA performed with adonis</h2>\n+<pre><code>\n+Call:\n+adonis(formula = dist ~ EnvType, data = metadata, permutations = 9999) \n+\n+Permutation: free\n+Number of permutations: 9999\n+\n+Terms added sequentially (first to last)\n+\n+          Df SumsOfSqs MeanSqs F.Model      R2 Pr(&gt;F)    \n+EnvType    7    7.6565 1.09379  13.699 0.63132  1e-04 ***\n+Residuals 56    4.4713 0.07984         0.36868           \n+Total     63   12.1278                 1.00000           \n+---\n+Signif. codes:  0 \'***\' 0.001 \'**\' 0.01 \'*\' 0.05 \'.\' 0.1 \' \' 1</code></pre>\n+</div>\n+<div id="r-code" class="section level2">\n+<h2>R code</h2>\n+<h4>\n+Loading packages &amp; data\n+</h4>\n+<pre class="r"><code>library(vegan)\n+## if in new session\n+# library(phyloseq)\n+#\n+## load phyloseq object\n+# data &lt;- path to Rdata file\n+# load(data)\n+# extract sample metadata in a dataframe\n+metadata &lt;- as(sample_data(data), &quot;data.frame&quot;)\n+\n+## load beta distance matrix\n+beta_file &lt;- # path to Beta diversity tsv file\n+A &lt;- read.table(file=beta_file, row.names=1)\n+beta_dist &lt;- as.dist(A)</code></pre>\n+<h4>\n+With adonis\n+</h4>\n+<pre><code>## change experiment variable (currently EnvType )if you wish\n+## Multivariate ANOVA performed with adonis\n+adonis(beta_dist ~ EnvType, data = metadata, perm = 9999)</code></pre>\n+<div id="code-r-file" style="display:none;">\n+<p>library(vegan) \n+#if in new session \n+#library(phyloseq) \n+#data &lt;- path to Rdata file \n+#load(data) \n+metadata &lt;- as(sample_data(data), &quot;data.frame&quot;) \n+ \n+varExp &lt;- #Experiment variable \n+ \n+beta_file &lt;- # path to Beta diversity tsv file \n+A &lt;- read.table(file=beta_file, row.names=1) \n+beta_dist &lt;- as.dist(A) \n+ \n+f &lt;- paste(&quot;beta_dist ~ &quot; , varExp) \n+ \n+## Multivariate ANOVA performed with adonis \n+adonis(as.formula(f), data = metadata, perm = 9999) \n+</p>\n+</div>\n+<script>\n+  function download(){\n+    var text = document.getElementById("code-r-file").textContent;\n+    var blob = new Blob([text],{type:"text/plain;charset=utf-8"});\n+    saveAs(blob,"manova_code.R");\n+   }\n+</script>\n+<p><input type="button" value="Download R code" class="button" onclick="download();"></input></p>\n+</div>\n+</div>\n+\n+\n+\n+\n+</div>\n+\n+<script>\n+\n+// add bootstrap table styles to pandoc tables\n+function bootstrapStylePandocTables() {\n+  $(\'tr.header\').parent(\'thead\').parent(\'table\').addClass(\'table table-condensed\');\n+}\n+$(document).ready(function () {\n+  bootstrapStylePandocTables();\n+});\n+\n+\n+</script>\n+\n+<!-- dynamically load mathjax for compatibility with self-contained -->\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'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/Blast_affiliation.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/Blast_affiliation.biom Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "bacterium enrichment culture clone auto73_4W"], "blast_affiliations": [{"perc_identity": 80.964, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "bacterium enrichment culture clone auto73_4W"], "evalue": "2.32e-83", "aln_length": 394, "perc_query_coverage": 100.0, "subject": "GU731322.1.1376"}], "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:12000:2130.1"}}, {"id": "Cluster_2", "metadata": {"blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Iamiaceae", "Iamia", "Multi-affiliation"], "blast_affiliations": [{"perc_identity": 81.026, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Iamiaceae", "Iamia", "bacterium Ellin5273"], "evalue": "4.97e-85", "aln_length": 390, "perc_query_coverage": 100.0, "subject": "AY234624.1.1446"}, {"perc_identity": 81.026, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Iamiaceae", "Iamia", "bacterium Ellin5247"], "evalue": "4.97e-85", "aln_length": 390, "perc_query_coverage": 100.0, "subject": "AY234598.1.1446"}], "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:14982:2858.1"}}, {"id": "Cluster_3", "metadata": {"blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "Acidimicrobium", "unknown species"], "blast_affiliations": [{"perc_identity": 80.818, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Acidimicrobiaceae", "Acidimicrobium", "unknown species"], "evalue": "6.42e-84", "aln_length": 391, "perc_query_coverage": 100.0, "subject": "EU419133.1.1468"}], "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:18137:2514.1"}}, {"id": "Cluster_4", "metadata": {"blast_taxonomy": null, "blast_affiliations": [], "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:17819:2697.1"}}, {"id": "Cluster_5", "metadata": {"blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "unknown species"], "blast_affiliations": [{"perc_identity": 76.65, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "unknown species"], "evalue": "1.44e-55", "aln_length": 394, "perc_query_coverage": 100.0, "subject": "HQ183925.1.1489"}], "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:9726:3180.1"}}, {"id": "Cluster_6", "metadata": {"blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Multi-affiliation", "Multi-affiliation", "Multi-affiliation"], "blast_affiliations": [{"perc_identity": 77.215, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "bacterium enrichment culture clone auto73_4W"], "evalue": "6.69e-59", "aln_length": 395, "perc_query_coverage": 100.0, "subject": "GU731322.1.1376"}, {"perc_identity": 76.845, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "OM1 clade", "unknown genus", "unidentified bacterium wb1_G04"], "evalue": "6.69e-59", "aln_length": 393, "perc_query_coverage": 100.0, "subject": "AF317765.1.1443"}], "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:16808:2898.1"}}, {"id": "Cluster_7", "metadata": {"blast_taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "Multi-affiliation", "Multi-affiliation", "Multi-affiliation"], "blast_affiliations": [{"perc_identity": 79.795, "taxonomy": ["Bacteria", "Actinobacteria", "Acidimicrobiia", "Acidimicrobiales", "unknown family", "unknown genus", "bacterium enrichment culture clone auto73_4W"], "evalue": "1.08e-76", "aln_length": 391, "perc_query_coverage": 100.0, "subject": "GU731322.1.1376"}, {"perc_identity": 79.795, "taxonomy": ["B'..b'11892, 0, 1], [11893, 0, 1], [11894, 0, 1], [11895, 0, 1], [11896, 0, 1], [11897, 0, 1], [11898, 0, 1], [11899, 0, 1], [11900, 0, 1], [11901, 0, 1], [11902, 0, 1], [11903, 0, 1], [11904, 0, 1], [11905, 0, 1], [11906, 0, 1], [11907, 0, 1], [11908, 0, 1], [11909, 0, 1], [11910, 0, 1], [11911, 0, 1], [11912, 0, 1], [11913, 0, 1], [11914, 0, 1], [11915, 0, 1], [11916, 0, 1], [11917, 0, 1], [11918, 0, 1], [11919, 0, 1], [11920, 0, 1], [11921, 0, 1], [11922, 0, 1], [11923, 0, 1], [11924, 0, 1], [11925, 0, 1], [11926, 0, 1], [11927, 0, 1], [11928, 0, 1], [11929, 0, 1], [11930, 0, 1], [11931, 0, 1], [11932, 0, 1], [11933, 0, 1], [11934, 0, 1], [11935, 0, 1], [11936, 0, 1], [11937, 0, 1], [11938, 0, 1], [11939, 0, 1], [11940, 0, 1], [11941, 0, 1], [11942, 0, 1], [11943, 0, 1], [11944, 0, 1], [11945, 0, 1], [11946, 0, 1], [11947, 0, 1], [11948, 0, 1], [11949, 0, 1], [11950, 0, 1], [11951, 0, 2], [11952, 0, 1], [11953, 0, 1], [11954, 0, 1], [11955, 0, 1], [11956, 0, 1], [11957, 0, 1], [119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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/Blast_affiliation.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/Blast_affiliation.html Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,321 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\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="1.0.2">\n+\t\t<!-- CSS -->\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>\n+\t\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>\n+\t\t<style type="text/css">\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</style>\n+\t\t<!-- JS -->\n+\t\t<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>\n+\t\t<script type="text/javascript">\n+\t\t\t/*\n+\t\t\t * HTMLTable.js 0.1.0 - 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){var t,r,n=e,a=";";this.deleteColumns=function(e){for(var a=n.getElementsByTagName("tr"),o=0;o<a.length;o++){s=0;var i=a[o].getElementsByTagName("td");0==i.length&&(i=a[o].getElementsByTagName("th"));for(var v=0,s=0;s<t[1];s++)if(!r[o][s]){var f=i[v].getAttribute("colspan");if(null!=f)for(var m=0;f>m;m++){if(in_array(s+m,e)){var u=i[v].getAttribute("colspan");u-1==0?i[v].removeAttribute("colspan"):i[v].setAttribute("colspan",u-1)}if(null==i[v].getAttribute("colspan")){var h=i[v];a[o].removeChild(h),v--}}else if(in_array(s,e)){var h=i[v];a[o].removeChild(h),v--}v++}}l(),g()},this.filter=function(e,a){var l=new RegExp(e),g=new Array;null!=a&&a||(g.c0=!0);for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)r[i][f]||(l.test(v[s].innerHTML)&&(g["c"+f]=!0),s++)}for(var m=new Array,u=0;u<t[1];u++)void 0===g["c"+u]&&m.push(u);this.deleteColumns(m)},this.getModel=function(){return n};var l=function(){for(var e=0,r=0,a=n.getElementsByTagName("tr"),l=0;l<a.length;l++){var g=0;e++;var o=a[l].getElementsByTagName("td");0==o.length&&(o=a[l].getElementsByTagName("th"));for(var i=0;i<o.length;i++){var v=o[i].getAttribute("colspan");g+=null==v?1:parseInt(v)}g>r&&(r=g)}t=new Array(2),t[0]=e,t[1]=r},g=function(){r=new Array(t[0]);for(var e=0;e<t[0];e++){r[e]=new Array(t[1]);for(var a=0;a<t[1];a++)r[e][a]=!1}for(var l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){v=0;var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)if(!r[g][v]){var s=0,f=0,m=o[i].getAttribute("rowspan");null!=m&&(s=parseInt(m)-1);var u=o[i].getAttribute("colspan");null!=u&&(f=parseInt(u)-1);for(var h=s;h>=0;h--)for(var y=f;y>=0;y--)(0!=h||0!=y)&&(r[g+h][v+y]=!0);i++}}};this.replace=function(e,a,l){var g=new RegExp(e);null==a&&(a=""),null==l&&(l="");for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f'..b'removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Display summary\n+\t\t\t\tvar std_color = Highcharts.getOptions().colors ;\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(-0.3).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) );\t\t\t\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});\n+\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn btn-primary"><span class="glyphicon glyphicon-open-file" aria-hidden="true">CSV</span></button>\' );\n+\t\t\t\t$(\'#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<h1 class="page-header">Blast affiliation summary</h1>\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<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<h1 class="page-header">Blast affiliation by sample</h1>\n+\t\t\t</div>\n+\t\t</div>\n+\t</body>\n+</html>\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/Unifrac.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/Unifrac.tsv Thu Oct 25 05:01:13 2018 -0400
b
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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/chaillou.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/chaillou.biom Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "otu_01778", "metadata": {"taxonomy": ["k__Bacteria", "p__Tenericutes", "c__Mollicutes", "o__Mycoplasmatales", "f__Mycoplasmataceae", "g__Candidatus Lumbricincola", "s__NA"]}}, {"id": "otu_01838", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Prevotellaceae", "g__Prevotella", "s__NA"]}}, {"id": "otu_01386", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Xanthomonadales", "f__Xanthomonadaceae", "g__Dyella", "s__Ginsengisoli"]}}, {"id": "otu_01835", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Planococcaceae", "g__Incertae Sedis", "s__NA"]}}, {"id": "otu_01837", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Flavobacteria", "o__Flavobacteriales", "f__Flavobacteriaceae", "g__Flavobacterium", "s__NA"]}}, {"id": "otu_01832", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "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", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lactobacillus", "s__Brevis"]}}, {"id": "otu_00011", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Soli"]}}, {"id": "otu_00010", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Junii"]}}, {"id": "otu_00013", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Kyonggiensis"]}}, {"id": "otu_00012", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Johnsonii"]}}, {"id": "otu_00018", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "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'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/demultiplex_barcode.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/demultiplex_barcode.txt Thu Oct 25 05:01:13 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/demultiplex_log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/demultiplex_log.txt Thu Oct 25 05:01:13 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/demultiplex_test2_R1.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/demultiplex_test2_R1.fq Thu Oct 25 05:01:13 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/demultiplex_test2_R2.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/demultiplex_test2_R2.fq Thu Oct 25 05:01:13 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/normalisation_report.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/normalisation_report.html Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,203 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\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="1.0.1">\n+\t\t<!-- CSS -->\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>\n+\t\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>\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</style>\n+\t\t<!-- JS -->\n+\t\t<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>\n+\t\t<script type="text/javascript">\n+\t\t\t/*\n+\t\t\t * HTMLTable.js 0.1.0 - 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){var t,r,n=e,a=";";this.deleteColumns=function(e){for(var a=n.getElementsByTagName("tr"),o=0;o<a.length;o++){s=0;var i=a[o].getElementsByTagName("td");0==i.length&&(i=a[o].getElementsByTagName("th"));for(var v=0,s=0;s<t[1];s++)if(!r[o][s]){var f=i[v].getAttribute("colspan");if(null!=f)for(var m=0;f>m;m++){if(in_array(s+m,e)){var u=i[v].getAttribute("colspan");u-1==0?i[v].removeAttribute("colspan"):i[v].setAttribute("colspan",u-1)}if(null==i[v].getAttribute("colspan")){var h=i[v];a[o].removeChild(h),v--}}else if(in_array(s,e)){var h=i[v];a[o].removeChild(h),v--}v++}}l(),g()},this.filter=function(e,a){var l=new RegExp(e),g=new Array;null!=a&&a||(g.c0=!0);for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)r[i][f]||(l.test(v[s].innerHTML)&&(g["c"+f]=!0),s++)}for(var m=new Array,u=0;u<t[1];u++)void 0===g["c"+u]&&m.push(u);this.deleteColumns(m)},this.getModel=function(){return n};var l=function(){for(var e=0,r=0,a=n.getElementsByTagName("tr"),l=0;l<a.length;l++){var g=0;e++;var o=a[l].getElementsByTagName("td");0==o.length&&(o=a[l].getElementsByTagName("th"));for(var i=0;i<o.length;i++){var v=o[i].getAttribute("colspan");g+=null==v?1:parseInt(v)}g>r&&(r=g)}t=new Array(2),t[0]=e,t[1]=r},g=function(){r=new Array(t[0]);for(var e=0;e<t[0];e++){r[e]=new Array(t[1]);for(var a=0;a<t[1];a++)r[e][a]=!1}for(var l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){v=0;var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)if(!r[g][v]){var s=0,f=0,m=o[i].getAttribute("rowspan");null!=m&&(s=parseInt(m)-1);var u=o[i].getAttribute("colspan");null!=u&&(f=parseInt(u)-1);for(var h=s;h>=0;h--)for(var y=f;y>=0;y--)(0!=h||0!=y)&&(r[g+h][v+y]=!0);i++}}};this.replace=function(e,a,l){var g=new RegExp(e);null==a&&(a=""),null==l&&(l="");for(var o=n.getElementsByTagName('..b'< pCategories.length ; idx++){\n+\t\t\t\t\ttable_header_line += "      <th>" + pCategories[idx] + "</th>\\n" ;\n+\t\t\t\t}\n+\t\t\t\ttable_header += "    <tr>\\n" + table_header_line + "    </tr>\\n" ;\n+\t\t\t\ttable_header = "  <thead>\\n" + table_header + "  </thead>\\n" ;\n+\t\t\t\t\n+\t\t\t\t// Body\n+\t\t\t\tvar table_body = \'\' ;\n+\t\t\t\tfor(var data_idx = 0 ; data_idx < pData.length ; data_idx++){\n+\t\t\t\t\tvar table_body_row = "" ;\n+\t\t\t\t\tfor(var category_idx = 0 ; category_idx < pCategories.length ; category_idx++){\n+\t\t\t\t\t\tif( typeof pData[data_idx][category_idx] === "number" ) {\n+\t\t\t\t\t\t\ttable_body_row += "      <td>" + numberDisplay(pData[data_idx][category_idx]) + "</td>\\n" ;\n+\t\t\t\t\t\t} else {\n+\t\t\t\t\t\t\ttable_body_row += "      <td>" + pData[data_idx][category_idx] + "</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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/sample_metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/sample_metadata.tsv Thu Oct 25 05:01:13 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/references/tree.nwk
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/tree.nwk Thu Oct 25 05:01:13 2018 -0400
b
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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b
diff -r 000000000000 -r 76c750c5f0d1 test-data/swarm.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/swarm.biom Thu Oct 25 05:01:13 2018 -0400
[
b'@@ -0,0 +1,133557 @@\n+{\n+    "rows": [\n+        {\n+            "id": "Cluster_1", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:12000:2130.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_2", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:14982:2858.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_3", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:18137:2514.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_4", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:17819:2697.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_5", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:9726:3180.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_6", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:16808:2898.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_7", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:17587:4049.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_8", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:11076:3780.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_9", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:17125:4154.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_10", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:16691:8627.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_11", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:13834:5524.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_12", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:19361:8993.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_13", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:22692:10677.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_14", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:14865:5961.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_15", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:19687:6450.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_16", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:13867:2303.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_17", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:22102:8029.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_18", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:25665:8233.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_19", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1102:14693:6578.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_20", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1101:10312:5888.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_21", \n+            "metadata": {\n+                "seed_id": "ERR619083.M00704:57:000000000-A5HJE:1:1102:21790:3059.1"\n+            }\n+        }, \n+        {\n+            "id": "Cluster_22", \n+            "meta'..b'   12093, \n+            0, \n+            1\n+        ], \n+        [\n+            12094, \n+            0, \n+            1\n+        ], \n+        [\n+            12095, \n+            0, \n+            1\n+        ], \n+        [\n+            12096, \n+            0, \n+            1\n+        ], \n+        [\n+            12097, \n+            0, \n+            1\n+        ], \n+        [\n+            12098, \n+            0, \n+            1\n+        ], \n+        [\n+            12099, \n+            0, \n+            1\n+        ], \n+        [\n+            12100, \n+            0, \n+            1\n+        ], \n+        [\n+            12101, \n+            0, \n+            1\n+        ], \n+        [\n+            12102, \n+            0, \n+            1\n+        ], \n+        [\n+            12103, \n+            0, \n+            1\n+        ], \n+        [\n+            12104, \n+            0, \n+            1\n+        ], \n+        [\n+            12105, \n+            0, \n+            1\n+        ], \n+        [\n+            12106, \n+            0, \n+            1\n+        ], \n+        [\n+            12107, \n+            0, \n+            1\n+        ], \n+        [\n+            12108, \n+            0, \n+            1\n+        ], \n+        [\n+            12109, \n+            0, \n+            1\n+        ], \n+        [\n+            12110, \n+            0, \n+            1\n+        ], \n+        [\n+            12111, \n+            0, \n+            1\n+        ], \n+        [\n+            12112, \n+            0, \n+            1\n+        ], \n+        [\n+            12113, \n+            0, \n+            1\n+        ], \n+        [\n+            12114, \n+            0, \n+            1\n+        ], \n+        [\n+            12115, \n+            0, \n+            1\n+        ], \n+        [\n+            12116, \n+            0, \n+            1\n+        ], \n+        [\n+            12117, \n+            0, \n+            2\n+        ], \n+        [\n+            12118, \n+            0, \n+            1\n+        ], \n+        [\n+            12119, \n+            0, \n+            1\n+        ], \n+        [\n+            12120, \n+            0, \n+            1\n+        ], \n+        [\n+            12121, \n+            0, \n+            1\n+        ], \n+        [\n+            12122, \n+            0, \n+            1\n+        ], \n+        [\n+            12123, \n+            0, \n+            1\n+        ], \n+        [\n+            12124, \n+            0, \n+            1\n+        ], \n+        [\n+            12125, \n+            0, \n+            1\n+        ], \n+        [\n+            12126, \n+            0, \n+            1\n+        ], \n+        [\n+            12127, \n+            0, \n+            1\n+        ], \n+        [\n+            12128, \n+            0, \n+            1\n+        ], \n+        [\n+            12129, \n+            0, \n+            1\n+        ], \n+        [\n+            12130, \n+            0, \n+            1\n+        ], \n+        [\n+            12131, \n+            0, \n+            1\n+        ], \n+        [\n+            12132, \n+            0, \n+            1\n+        ], \n+        [\n+            12133, \n+            0, \n+            1\n+        ], \n+        [\n+            12134, \n+            0, \n+            1\n+        ], \n+        [\n+            12135, \n+            0, \n+            1\n+        ], \n+        [\n+            12136, \n+            0, \n+            1\n+        ], \n+        [\n+            12137, \n+            0, \n+            1\n+        ], \n+        [\n+            12138, \n+            0, \n+            1\n+        ]\n+    ], \n+    "generated_by": "swarm", \n+    "matrix_type": "sparse", \n+    "shape": [\n+        12139, \n+        2\n+    ], \n+    "format_url": "http://biom-format.org", \n+    "date": "15-01-09T11:09:52", \n+    "type": "OTU table", \n+    "id": null, \n+    "columns": [\n+        {\n+            "id": "sampleA_R1", \n+            "metadata": null\n+        }, \n+        {\n+            "id": "sampleB_R1", \n+            "metadata": null\n+        }\n+    ]\n+}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/swarm.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/swarm.fasta Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,24278 @@\n+>Cluster_1\n+TTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCAGCACTAAGGGGCGGAAACCCCCTAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGATCCCCACGCTTTCGCACATCAGCGTCAGTTACAGACCAGAAAGTCGCCTTCGCCACTGGTGTTCCTCCATATCTCTGCGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTTTTCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAAAAACCGCCTACGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACGTATTA\n+>Cluster_2\n+TTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTATTGCGTTAGCTCCGGCACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTACCCACGCTTTCGAGCCTCAGCGTCAGTGACAGACCAGAGAGCCGCTTTCGCCACTGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCAGACAGTTTCCAGAGCACACTATGGTTGAGCCATAGCCTTTTACTCCAGACTTTCCTGACCGCCTGCGCTCCCTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGTATTA\n+>Cluster_3\n+TTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGAATACTTAATGCGTTAGCGGCGGCACAGAGGTCATGACAACCCCTACACCTAGTATTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGTGTCAGTTACAGTCCAGAAAGTCGCCTTCGCCACTGGTATTCTTCCTAATCTCTACGCATTTCACCGCTACACTAGGAATTCTACTTTCCTCTCCTGCACTCTAGATATCCAGTTTGGAATGCAGCACCCAGGTTAAGCCCGAGTATTTCACATCCCACTTAAATATCCACCTACGCTCCCTTTACGCCCAGTAAATCCGGACAACGCTTGCCACCTACGTATTA\n+>Cluster_4\n+TTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATACTTAACGCTTTCGCTTGGCCGCTTGCCGTATATCGCAAACAGCGAGTATTCATCGTTTACCGTGTGGACTACCAGGGTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTCAACTGCACTCAAGATATCCAGTATCAACTGCAATTTTACGGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCCATCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCTCGGATCCTCCGTATTA\n+>Cluster_5\n+TTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGTCAATTTCACGCGTTAGCTACGCTACCAAGCAATCAGGTTGCCCAACAGCTAATTGACATCGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTACCCACGCTTTCGGGCATGAACGTCAGTGTTGTCCCAGGAGGCTGCCTTCGCCATCGGTATTCCTCCACATCTCTACGCATTTCACTGCTACACGTGGAATTCTACCTCCCTCTGACACACTCGAGTCACCCAGTTCAGAACGCAGTTCCCGGGTTGAGCCCGGGGATTTCACATCCTGCTTAAGTAACCGTCTGCGCCCGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTACGTATTA\n+>Cluster_6\n+TTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGGATGCTTAATGCGTTAGCTGCATTACTGGAGAGACTAAGCCCTCCAACAACTAGCATCCATCGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCGCAATCAGCGTCAGTAATGTTCCAGCAGGTCGCCTTCGCAATGAGTATTCCTCTTGATCTCTACGGATTTTACCCCTACACCAAGAATTCCACCTACCTCTCCCACACTCTAGAATAGTAGTTTCAAATGCAGTTCTATGGTTAAGCCATAGGATTTCACACCTGACTGACTATCCCGCCTACGCGCTCTTTACGCCCAGTGATTCCGAGTAACGCTTGCACCCTCCGTATTA\n+>Cluster_7\n+TTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCGGCACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCAAAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGTATTA\n+>Cluster_8\n+TTTGAGTTTCAACCTTGCGGCCGTACTTCCCAGGCGGTACGTTTATCGCGTTAGCTTCGCCAAGCACAGCATCCTGCGCTTAGCCAACGTACATCGTTTAGGGTGTGGACTACCCGGGTATCTAATCCGGTTTGCTCCCCACACTTTCGCGCCTCAGCGTCACCTTCTGTCCAGTAACTTGCCTTCGCCATTGGTGTTCCTCCTGGTATCTACGCATTCCACCGCTACACCAGGAATTCCAGTTACCTCTCCAGAGGTCAAGAAATCCAGTATCCAGTCCATCCCCGAGGTTGAGCCCCGGTCTTTAAAACCAGACTTAAATTTCCGCCTACACGCCCTTTACGCCCAGTGATTCCGGGTAACGCTTGCACCCTCCGTATTA\n+>Cluster_9\n+TTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAAAGCGTTAGCTACGGCACGGAACCCGTGGAATGGACCCCACACCTAGTACCCACCGTTTACAGCGTGGACTACCAGGGTATCTAAGCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGGAAAGGCCCAGAGAACCGCCTTCGCCACTGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTCCACCAGGAATTCCATTCTCCCCTACCTTCCTCAAGTCAACCCGTATCGAAAGCACGCTCAGGGTTAAGCCCCAAGATTACACTTCCGACGCGATCAACCACCTACGAGCCCTTTACGCCCAATAAATCCGGACAACGCTCGCACCCTACGTATCA\n+>Cluster_10\n+TTTGAGTTTTAACCTTGCGGCCGTACTCCCCAGGCGGAATGCTTAATCCGTTAGGTGTGTCACCGAACAGCATGCTGCCCGACGACTGGCATTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATCGAGCCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATTTCACCTCTACACTCGGAATTCCACTCACCTCTCTCGACCTCAAGATCGGGAGTTTCAAAGGCAGTTCCAGGGTTGAGCCCTGGGATTTCACCTCTGACTTTCCGATCCGCCTACGTGCGCTTTACGCCCAGTAATTCCGAATAACGCTAGCCCCC'..b'CACGGAACCCGTGGAATGGACCCCACACCTAGTACCCACCGTTTACAGCGTGGACTACCAGGGTATCTAAGCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGGAAAGGCCCAGAGAACCGCCTTCGCCACTGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACGTATTA\n+>Cluster_12131\n+TTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAAAGCGTTAGCTACGGCACGGAACCCGTGGAATGGACCCCACACCTAGTACCCACCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTACCCATGCTTTCGAGCCTCAGCGTCAGTTGCAGACCAGAGAGCCGCCTTCGCCACTGGTGTTCCTCCATATCTCTGCGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTTTTCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACGTATTA\n+>Cluster_12132\n+TTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAAAGCGTTAGCTACGGCACGGAACCCGTGGAATGGACCCCACACCTAGTACCCACCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAAGCCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCCCTCTTGCACTCAAGTTAAACAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACGTATTA\n+>Cluster_12133\n+TTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAAAGCGTTAGCTACGGCACGGAACCCGTGGAATGGACCCCACACCTAGTACCCACCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACTGGTATTCTTCCTAATCTCTACGCATTTCACCGCTACACGTGGAATTCTACCTCCCTCTGACACACTCGAGTCACCCAGTTCAGAACGCAGTTCCCGGGTTGAGCCCGGGGATTTCACATCCTGCTTAAGTAACCGTCTGCGCCCGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTACGTATTA\n+>Cluster_12134\n+TTTTTGAGTTTCAGCCTTGCGGCCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAACTTCAGCACTAAAGGGCGGAAACCCTCTAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGGGCATCTAATCCTGTTTGCTCCCCACGCTTTCGCGCCTCAGTGTCAGTTACAGACCAGAAAGTCGCCTTCGCCACTGGTGTTCCTCCATATCTCTACGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAATAATGCCGGATAACGCTTGCCACCTACGTATTA\n+>Cluster_12135\n+TTTTTGAGTTTCAGCCTTGCGGCCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAACTTCAGCACTAAAGGGCGGAAACCCTCTAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCGCCTCAGTGTCAGTTACAGACCAGAAAGTCGCCTTCGCCACTGGTGTTCCTCCATATCTCTACGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGAAACCGCCTGCGCTCGCTTTACGCCCAATAAAGCCGGACAACGCTTGCCACCTACGTATTA\n+>Cluster_12136\n+ATTTGAGTTTCAACCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAAAGCGTTAGCTACGGCACGGAACCCGTGGAATGGACCCCACACCTAGTACCCACCGTTTACAGCGTGGACTACCAGGGTATCTAAGCCTGTTCGCTCCCCACGCTTTCGCGCAATCAGCGTCAGTAATGTTCCAGCAGGTCGCCTTCGCAATGAGTATTCCTCTTGATCTCTACGGATTTTACCCCTACACCAAGAATTCCACCTACCTCTCCCACACTCTAGAATAGTAGTTTCAAATGCAGTTCTATGGTTAAGCCATAGGATTTCACACCTGACTGACTATCCCGCCTACGCGCTCTTTACGCCCAGTGATTCCGAGTAACGCTTGCACCCTCCGTATTA\n+>Cluster_12137\n+CTTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGGGTACTTAAAGCGTTAGCTACGGCACGGAACCCGTGGAATGGACCCCACACCTAGTACCCACCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCGCAATCAGCGTCAGTAATGTTCCAGCAGGTCGCCTTCGCAATGAGTATTCCTCTTGATCTCTACGGATTTTACCCCTACACCAAGAATTCCACCTACCTCTCCCACACTCTAGAATAGTAGTTTCAAATGCAGTTCTATGGTTAAGCCATAGGATTTCACACCTGACTGACTATCCCGCCTACGCGCTCTTTACGCCCAGTGATTCCGAGTAACGCTTGCACCCTCCGTATTA\n+>Cluster_12138\n+TTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTATTGCGTTAGCTCCGGCACTAAGCCCCGGAAAGGGCGGAAACCCTCTAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCGCCTCAGTGTCAGTTACAGACCAGAAAGTCGCCTTCGCCACTGGTGTTCCTCCATATCTCTACGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACGTATTA\n+>Cluster_12139\n+CTTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGGATGCTTAATGCGTTAGCTGCATTACTGGAGAGACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCTTCCTGATATCTGCGCATTCCACCGCTACACCAGGAGTTCCAGTCTCCCCTACCGCACTCAAGTCAGCCCGTACCCACCGCACGCCCCCAGTTAAGCCAGAGGATTTCACGGCAGACGCGACCAACCGCCTACAAGCCCTTTACGCCCAATAATTCCGGACAACGCTCGCGCCCTACGTATTA\n'
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/test_dataset.tar.gz
b
Binary file test-data/test_dataset.tar.gz has changed
b
diff -r 000000000000 -r 76c750c5f0d1 test-data/wordConditionalProbIndexArr.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wordConditionalProbIndexArr.txt Thu Oct 25 05:01:13 2018 -0400
b
b'@@ -0,0 +1,65538 @@\n+<trainsetNo>1</trainsetNo><version>null</version><modversion>null</modversion><file>wordConditionalProbIndexArr</file>\n+0\t0\n+1\t0\n+2\t0\n+3\t0\n+4\t0\n+5\t0\n+6\t0\n+7\t0\n+8\t0\n+9\t0\n+10\t0\n+11\t0\n+12\t0\n+13\t0\n+14\t0\n+15\t0\n+16\t1\n+17\t1\n+18\t1\n+19\t1\n+20\t1\n+21\t1\n+22\t1\n+23\t1\n+24\t1\n+25\t1\n+26\t1\n+27\t1\n+28\t1\n+29\t1\n+30\t1\n+31\t1\n+32\t1\n+33\t1\n+34\t1\n+35\t1\n+36\t1\n+37\t1\n+38\t1\n+39\t1\n+40\t1\n+41\t1\n+42\t1\n+43\t1\n+44\t1\n+45\t1\n+46\t1\n+47\t1\n+48\t5\n+49\t5\n+50\t5\n+51\t5\n+52\t5\n+53\t5\n+54\t5\n+55\t5\n+56\t5\n+57\t5\n+58\t5\n+59\t5\n+60\t5\n+61\t5\n+62\t7\n+63\t9\n+64\t9\n+65\t9\n+66\t9\n+67\t9\n+68\t9\n+69\t9\n+70\t9\n+71\t9\n+72\t9\n+73\t9\n+74\t9\n+75\t9\n+76\t9\n+77\t9\n+78\t9\n+79\t9\n+80\t9\n+81\t9\n+82\t9\n+83\t9\n+84\t9\n+85\t9\n+86\t9\n+87\t9\n+88\t9\n+89\t9\n+90\t9\n+91\t9\n+92\t9\n+93\t9\n+94\t10\n+95\t10\n+96\t10\n+97\t10\n+98\t10\n+99\t10\n+100\t22\n+101\t22\n+102\t22\n+103\t22\n+104\t22\n+105\t22\n+106\t22\n+107\t22\n+108\t22\n+109\t22\n+110\t22\n+111\t22\n+112\t22\n+113\t22\n+114\t22\n+115\t22\n+116\t22\n+117\t22\n+118\t22\n+119\t22\n+120\t22\n+121\t22\n+122\t22\n+123\t22\n+124\t22\n+125\t22\n+126\t22\n+127\t22\n+128\t22\n+129\t22\n+130\t22\n+131\t22\n+132\t22\n+133\t22\n+134\t22\n+135\t22\n+136\t22\n+137\t22\n+138\t22\n+139\t22\n+140\t22\n+141\t22\n+142\t22\n+143\t22\n+144\t22\n+145\t22\n+146\t22\n+147\t22\n+148\t22\n+149\t23\n+150\t23\n+151\t23\n+152\t24\n+153\t24\n+154\t24\n+155\t24\n+156\t24\n+157\t24\n+158\t24\n+159\t24\n+160\t25\n+161\t27\n+162\t27\n+163\t27\n+164\t27\n+165\t27\n+166\t27\n+167\t27\n+168\t27\n+169\t27\n+170\t28\n+171\t28\n+172\t28\n+173\t28\n+174\t28\n+175\t28\n+176\t28\n+177\t29\n+178\t29\n+179\t29\n+180\t29\n+181\t29\n+182\t30\n+183\t33\n+184\t35\n+185\t35\n+186\t35\n+187\t35\n+188\t35\n+189\t43\n+190\t43\n+191\t53\n+192\t53\n+193\t53\n+194\t53\n+195\t53\n+196\t53\n+197\t53\n+198\t53\n+199\t53\n+200\t53\n+201\t53\n+202\t53\n+203\t53\n+204\t53\n+205\t53\n+206\t53\n+207\t53\n+208\t53\n+209\t53\n+210\t53\n+211\t53\n+212\t53\n+213\t53\n+214\t53\n+215\t54\n+216\t54\n+217\t54\n+218\t54\n+219\t54\n+220\t54\n+221\t84\n+222\t88\n+223\t88\n+224\t90\n+225\t90\n+226\t90\n+227\t90\n+228\t90\n+229\t90\n+230\t90\n+231\t90\n+232\t90\n+233\t90\n+234\t90\n+235\t90\n+236\t90\n+237\t90\n+238\t90\n+239\t90\n+240\t90\n+241\t90\n+242\t90\n+243\t90\n+244\t90\n+245\t90\n+246\t90\n+247\t90\n+248\t92\n+249\t92\n+250\t93\n+251\t95\n+252\t95\n+253\t95\n+254\t95\n+255\t96\n+256\t96\n+257\t96\n+258\t96\n+259\t96\n+260\t96\n+261\t96\n+262\t96\n+263\t96\n+264\t96\n+265\t96\n+266\t96\n+267\t96\n+268\t96\n+269\t96\n+270\t96\n+271\t97\n+272\t97\n+273\t97\n+274\t97\n+275\t98\n+276\t98\n+277\t98\n+278\t98\n+279\t98\n+280\t98\n+281\t98\n+282\t98\n+283\t98\n+284\t98\n+285\t98\n+286\t98\n+287\t98\n+288\t98\n+289\t98\n+290\t98\n+291\t98\n+292\t98\n+293\t98\n+294\t98\n+295\t98\n+296\t98\n+297\t98\n+298\t98\n+299\t98\n+300\t98\n+301\t98\n+302\t98\n+303\t98\n+304\t98\n+305\t98\n+306\t98\n+307\t98\n+308\t98\n+309\t98\n+310\t98\n+311\t98\n+312\t98\n+313\t98\n+314\t98\n+315\t99\n+316\t99\n+317\t99\n+318\t99\n+319\t100\n+320\t100\n+321\t101\n+322\t101\n+323\t101\n+324\t101\n+325\t101\n+326\t101\n+327\t101\n+328\t101\n+329\t101\n+330\t101\n+331\t101\n+332\t101\n+333\t101\n+334\t101\n+335\t101\n+336\t101\n+337\t101\n+338\t101\n+339\t101\n+340\t101\n+341\t101\n+342\t101\n+343\t101\n+344\t101\n+345\t101\n+346\t101\n+347\t101\n+348\t101\n+349\t101\n+350\t101\n+351\t102\n+352\t102\n+353\t102\n+354\t102\n+355\t102\n+356\t107\n+357\t107\n+358\t107\n+359\t107\n+360\t107\n+361\t107\n+362\t107\n+363\t107\n+364\t107\n+365\t107\n+366\t107\n+367\t107\n+368\t107\n+369\t107\n+370\t107\n+371\t107\n+372\t107\n+373\t107\n+374\t107\n+375\t108\n+376\t108\n+377\t108\n+378\t108\n+379\t108\n+380\t108\n+381\t108\n+382\t108\n+383\t108\n+384\t108\n+385\t108\n+386\t109\n+387\t109\n+388\t109\n+389\t109\n+390\t110\n+391\t110\n+392\t110\n+393\t110\n+394\t110\n+395\t110\n+396\t110\n+397\t110\n+398\t112\n+399\t123\n+400\t123\n+401\t123\n+402\t123\n+403\t123\n+404\t123\n+405\t123\n+406\t125\n+407\t125\n+408\t125\n+409\t126\n+410\t126\n+411\t126\n+412\t126\n+413\t126\n+414\t127\n+415\t128\n+416\t128\n+417\t129\n+418\t132\n+419\t132\n+420\t132\n+421\t132\n+422\t132\n+423\t132\n+424\t132\n+425\t132\n+426\t132\n+427\t132\n+428\t132\n+429\t132\n+430\t132\n+431\t132\n+432\t132\n+433\t132\n+434\t133\n+435\t133\n+436\t134\n+437\t134\n+438\t136\n+439\t136\n+440\t136\n+441\t136\n+442\t138\n+443\t138\n+444\t162\n+445\t162\n+446\t162\n+447\t162\n+448\t162\n+449\t162\n+450\t162\n+451\t162\n+452\t162\n+453\t162\n+454\t162\n+455\t162\n+456\t163\n+457\t163\n+458\t163\n+459\t163\n+460\t165\n+461\t165\n+462\t165\n+463\t165\n+464\t166\n+465\t166\n+466\t166\n+467\t166\n+468\t166\n+469\t166\n+470\t166\n+471\t166\n+472\t166\n+473\t166\n+474\t166\n+475\t166\n+476\t166\n+477\t166\n+478\t168\n+479\t168\n+480\t169\n+481\t169\n+482\t169\n+483\t169\n+484\t169\n+485\t169\n+486\t169'..b'9\t42307\n+65230\t4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b
diff -r 000000000000 -r 76c750c5f0d1 tool-data/frogs_db.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/frogs_db.loc.sample Thu Oct 25 05:01:13 2018 -0400
b
@@ -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>
+#
+#db.fasta db.fasta db.fasta ${__HERE__}/test-data/db.fasta
+#db.fasta db.fasta db.fasta /root/mydisk/FROGS-wrappers/test-data/db.fasta
+db.fasta db.fasta /root/mydisk/FROGS-wrappers/test-data/db.fasta
b
diff -r 000000000000 -r 76c750c5f0d1 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of frogs database files -->
+    <table name="frogs_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/tool-data/frogs_db.loc" />
+    </table>
+</tables>
b
diff -r 000000000000 -r 76c750c5f0d1 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of frogs database files -->
+    <table name="frogs_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/frogs_db.loc" />
+    </table>
+</tables>
b
diff -r 000000000000 -r 76c750c5f0d1 tree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tree.xml Thu Oct 25 05:01:13 2018 -0400
b
@@ -0,0 +1,137 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_Tree" name="FROGS Tree" version="1.0.0">
+ <description>Reconstruction of phylogenetic tree </description>
+  <requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+ <command>tree.py 
+                                            --input-otu $input_otu
+                                              #if $template.fileTemplate
+                                            --template-pynast ${template.template_pynast}
+                                              #end if
+                                            --biomfile $biomfile
+                                            --nb-cpus $nb_cpus
+                                            --out-tree $out_tree
+                                            --html $html
+ </command>
+    <inputs>
+ <!-- Files -->
+ <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+ <conditional name="template">
+ <param name="fileTemplate" type="boolean" label="Do you have the template alignment file ?" help="If yes, precise the template multi-alignment file." optional="false" />
+ <when value="false"></when>           
+ <when value="true">
+ <param format="fasta" name="template_pynast" type="data" label="Template alignment file" help="Template multi-alignment file (format: fasta)." optional="false" />
+ </when>
+ </conditional>
+        <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
+         <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <!-- Parameter -->
+        <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" />
+     </inputs>
+ <outputs>
+ <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/>
+         <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="input_otu" value="references/04-filters.fasta"/>
+ <conditional name="template">
+ <param name="fileTemplate" value="false"/>
+ </conditional>
+ <param name="biomfile" value="references/04-affiliation.biom"/>
+ <output name="out_tree" value="references/10b-tree.nwk"/>
+ </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 `PyNAST &lt;http://biocore.github.io/pynast/&gt;`_ (if you have an alignment template file) or with `Mafft &lt;http://mafft.cbrc.jp/alignment/software&gt;`_ (if you have not an aligned template file).
+And creation of a phylogenetic tree with `FastTree &lt;http://www.microbesonline.org/fasttree/&gt;`_.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**OTUs fasta file**:
+
+The OTUs sequence file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+Careful: FROGS Tree works only with less than 10 000 sequences!

+ .. image:: static/images/frogs_tree_otufile.png
+
+**(optional) Template alignment file**:
+
+A pre-aligned database of sequences (the “template” sequence) (format `multiple alignement &lt;https://en.wikipedia.org/wiki/Multiple_sequence_alignment&gt;`_).
+
+ .. image:: static/images/frogs_tree_templatefile.png 
+     
+**OTUs biom file**:
+
+The OTUs biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
+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 `nxh &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_).
+
+ .. image:: static/images/nwk_treefile.png
+
+**Html file** (summary.html):
+   
+The summary file describing which OTUs are contained or not in the phylogenetic tree (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
+
+.. class:: infomark page-header h2
+   
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+
+ </help>
+ <citations>
+ <citation type="doi">10.7287/peerj.preprints.386v1</citation>
+ </citations>
+</tool>
b
diff -r 000000000000 -r 76c750c5f0d1 tsv_to_biom.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tsv_to_biom.xml Thu Oct 25 05:01:13 2018 -0400
[
@@ -0,0 +1,145 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2016 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="2.0.0">
+ <description>Converts a TSV file in a BIOM file.</description>
+        <requirements>
+                <requirement type="package" version="2.0.1">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 $sequence_file
+               #end if
+ </command>
+ <inputs>
+ <!-- Files -->
+ <param format="tabular" name="tsv_file" type="data" label="Abundance TSV File" help="Your FROGS abundance TSV file. Take care to keep original column names." optional="false"/>
+ <param format="tabular" name="multi_affi_file" type="data" label="Multi_hits TSV File" help="TSV file describing multi_hit blast results." optional="true" />
+ <!-- Parameters -->
+ <param name="extract_fasta" type="boolean" label="Extract seeds in FASTA file" help="If there is a 'seed_sequence' column in your TSV table, you can extract seed sequences in a separated FASTA file." />
+ </inputs>
+ <outputs>
+ <data format="biom1" name="biom_file" label="${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/07-biom2tsv.tsv" />
+ <param name="multi_affi_file" value="references/07-biom2tsv.multi" />
+ <param name="extract_fasta" value="true"/>
+ <output name="biom_file" file="references/09-tsv2biom.biom" compare="sim_size" delta="0"/>
+ <output name="sequence_file" file="references/09-tsv2biom.fasta" />
+ </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 &lt;http://biom-format.org/&gt;`_).
+
+**Sequence file [optional]**:
+
+ By checking the "Extract seed FASTA file" option, the sequences will be extract from TSV to create a file in `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_ 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@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+ </help>
+        <citations>
+                <citation type="doi">10.1093/bioinformatics/btx791</citation>
+                <citation type="doi">10.1128/AEM.01043-13</citation>
+                <citation type="doi">10.14806/ej.17.1.200</citation>
+                <citation type="doi">10.1093/bioinformatics/btr507</citation>
+        </citations>
+
+</tool>