Mercurial > repos > oinizan > frogs
changeset 11:ab9e3c8ab443 draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f1287ef131de1eb33c9d59c1b66312fe854a8c64-dirty
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--- a/affiliation_OTU.xml Thu May 12 11:40:39 2022 +0000 +++ b/affiliation_OTU.xml Fri May 13 15:33:27 2022 +0000 @@ -29,11 +29,11 @@ <options from_data_table="frogs_db"/> <validator type="no_options" message="A built-in database is not available"/> </param> - <param argument="--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)"/> + <param argument="--rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allows to perform it also with RDP classifier tool (default No)"/> <expand macro="taxonomic_ranks"/> <!-- 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)"/> + <param format="fasta" name="fasta_sequences" type="data" label="Sequence file" help="The sequences to affiliated (format: FASTA)"/> + <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="The abundance file (format: BIOM)"/> </inputs> <outputs> <data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation_abundance.biom" from_work_dir="affiliation.biom"/> @@ -57,7 +57,7 @@ What it does -Add taxonomic affiliation in abundance file. +this tool adds taxonomic affiliation in abundance file. .. class:: infomark page-header h2 @@ -84,11 +84,11 @@ The abundance file with affiliation (format `BIOM <http://biom-format.org/>`_). -**Summary file** (report.html): +**Report file** (report.html): This file presents the number of sequences affiliated by blast, and the number of multi-affiliation (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). - .. image:: static/images/FROGS_affiliation_summary.png + .. image:: FROGS_affiliation_summary.png :height: 975 :width: 867 @@ -100,7 +100,7 @@ .. class:: infomark page-header h2 -How it works +How it works ? .. csv-table:: :header: "Steps", "Description" @@ -119,13 +119,13 @@ * **Case 1: a sequencing of overlapping sequences i.e. 16S V3-V4 amplicon MiSeq sequencing** -.. image:: static/images/FROGS_affiliation_overlapped_percent_id.png +.. image:: FROGS_affiliation_overlapped_percent_id.png :height: 325 :width: 807 * **Case 2 : a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing** -.. image:: static/images/FROGS_affiliation_combined_percent_id.png +.. image:: FROGS_affiliation_combined_percent_id.png :height: 310 :width: 887 @@ -133,16 +133,18 @@ With the classical method of %id calculation, filtering on %id will systematically removed “FROGS combined” OTUs. So, we proposed to replace the classical %id by a %id computed on the sequenced bases only. -.. image:: static/images/FROGS_affiliation_percent_id_formula.png +.. image:: FROGS_affiliation_percent_id_formula.png :height: 36 :width: 637 For the precedent use cases we will obtain: * Case 1: 16S V3V4 overlapped sequence + % sequenced bases identity = 400 matches / 400 bp = 100% * Case 2: very large ITS1 “FROGS combined” shorter than the real sequence + % sequenced bases identity = (250 + 250 ) / (600 - 100) = 100% This calculation allows to return 100% of identity on sequenced bases for “FROGS combined” shorter or longer than reality in case of perfect sequencing, and a smaller percentage of identity in the case of small overlap repeat kept in FROGS combined sequence.
--- a/affiliation_filters.xml Thu May 12 11:40:39 2022 +0000 +++ b/affiliation_filters.xml Fri May 13 15:33:27 2022 +0000 @@ -53,7 +53,7 @@ </command> <inputs> <!-- Files --> - <param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: FASTA)"/> + <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="The sequence file to filter (format: FASTA)"/> <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)"/> <expand macro="taxonomic_ranks"/> <!-- It is used for optional output fasta --> @@ -156,11 +156,11 @@ What it does -Remove OTUs or hide taxonomical metadata according to one (or more criteria): +This tool removes OTUs or hides taxonomical metadata according to one or more criteria: - for RDP taxonomy : a minimal bootstrap threshold at a specific rank - - for Blast taxonomy : a minimal identity rate, coverage rate, or alignment length, or a maximal evalue, or the absence of full or partial taxon name. + - for blast taxonomy : a minimal identity rate, coverage rate, or alignment length, or a maximal evalue, or the absence of full or partial taxon name. .. class:: infomark page-header h2 @@ -201,23 +201,23 @@ The list of blast affiliations for multi-affiliated impacted OTU (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). -**Summary file** (report.html): +**Report file** (report.html): - A summary report HTML of impacted OTUs, taxonomies lost and details by samples (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). + A report HTML of impacted OTUs, lost taxonomies and details by samples (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). .. class:: infomark page-header h2 -How it works +How it works ? .. csv-table:: :header: "Steps", "description" :widths: 10, 150 :class: table table-striped - "1", "Compare all affiliations (RDP and all Blast hits) to each filtering criteria." - "2", "Update concensus Blast taxonomy if at least one blast criteria has an impact. When only part of the Blast affiliations are removed, the concensus Blast taxonomy is updated, and if it changes, the OTU is considered as *Modified*." - "3", "**In deleting mode**, OTU is removed either if the RDP bootstrap criteria is not respected or if none of the blast affiliation respect all the criteria . **In hidding mode**, RDP affiliation is hidden (removed) if the RDP bootstrap criteria is not respected, and independantly, blast affiliations are hidden (removed) if none of the blast affiliation respect all the criteria." - "4", "Write valid OTU into the filtered.biom file with potential Blast affiliation updated and impacting criteria annotations.All impacted/modified OTU with their original metadata are reported in the impacted.tsv file with its associated impacted.multihit.tsv file. Impacting status (OTU_deleted / Affiliation_masked / Blast_taxonomy_changed) and the list of impacting criteria are also reported in the impacted.tsv file." + "1", "Compare all affiliations (RDP and all blast hits) to each filtering criteria." + "2", "Update concensus blast taxonomy if at least one blast criteria has an impact. When only part of the blast affiliations are removed, the concensus blast taxonomy is updated, and if it changes, the OTU is considered as *Modified*." + "3", "**In deleting mode**, OTU is removed either if the RDP bootstrap criteria is not respected or if none of the blast affiliation respect all the criteria . **In hidding mode**, RDP affiliation is hidden if the RDP bootstrap criteria is not respected, and independantly, blast affiliations are hidden if none of the blast affiliation respect all the criteria." + "4", "Write valid OTU into the filtered.biom file with potential blast affiliation updated and impacting criteria annotations.All impacted/modified OTU with their original metadata are reported in the impacted.tsv file with its associated impacted.multihit.tsv file. Impacting status (OTU_deleted / Affiliation_masked / Blast_taxonomy_changed) and the list of impacting criteria are also reported in the impacted.tsv file." .. class:: infomark page-header h2 @@ -227,44 +227,44 @@ Imagine that you want to filter out affiliations with: - RDP bootstrap at the Species level less than 0.8 -- Blast %identity and %coverage less than 100 -- Blast taxonomies with "unknown species" +- blast %identity and %coverage less than 100 +- blast taxonomies with "unknown species" What will append in these different cases in deleting or hidding mode: - Cluster 1: -.. image:: static/images/FROGS_affiliation_filter1.png +.. image:: FROGS_affiliation_filter1.png The RDP taxonomy does not respect the RDP boostrap threshold, but all blast affiliation criteria are respected. In deleting mode, Cluster_1 will be removed. -In the summary.html, it will be considered as "Removed", and if the RDP taxonomy and/or the Blast taxonomy is/are not kept thanks to an other OTU, the RDP/Blast taxonomy(ies) will be considered as lost. +In the report.html, it will be considered as "Removed", and if the RDP taxonomy and/or the blast taxonomy is/are not kept thanks to an other OTU, the RDP/blast taxonomy(ies) will be considered as lost. In hidding mode, RDP taxonomy will be removed, blast taxonomy will remain unchanged and Cluster_1 will be kept. -In the summary.html, it will be considered as "Hidden", and if the RDP taxonomy is not kept thanks to an other OTU, the RDP taxonomy will be considered as lost. +In the report.html, it will be considered as "Hidden", and if the RDP taxonomy is not kept thanks to an other OTU, the RDP taxonomy will be considered as lost. - Cluster 2: -.. image:: static/images/FROGS_affiliation_filter2.png +.. image:: FROGS_affiliation_filter2.png The RDP taxonomy respects the RDP boostrap threshold, but none of the blast affiliations respect all the blast criteria. In deleting mode, Cluster_1 will be removed. -In the summary.html, it will be considered as "Removed", and if the two blast taxonomies are not kept thanks to others OTUs, they will be considered as lost. In the same way, if there is no other OTU, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the summary.html. And idem for the RDP taxonomy. +In the report.html, it will be considered as "Removed", and if the two blast taxonomies are not kept thanks to others OTUs, they will be considered as lost. In the same way, if there is no other OTU, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the report.html. And idem for the RDP taxonomy. In hidding mode, RDP taxonomy will be remain unchanged, blast taxonomy will be removed and Cluster_2 will be kept. -In the summary.html, it will be considered as "Hidden", and if the two taxonomies are not kept thanks to others OTUs, they will be considered as lost. In the same way, if there is no other OTU, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the summary.html. +In the report.html, it will be considered as "Hidden", and if the two taxonomies are not kept thanks to others OTUs, they will be considered as lost. In the same way, if there is no other OTU, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the report.html. - Cluster 3: -.. image:: static/images/FROGS_affiliation_filter3.png +.. image:: FROGS_affiliation_filter3.png The RDP taxonomy respects the RDP boostrap threshold, and one of the two blast affiliations respect all the blast criteria. In both deleting and hidding mode, Cluster_1 will be kept. -In the summary.html, it will be considered as "Modified", as the RDP taxonomy will remain unchanged and the blast taxonomy will be updated. -If no other OTU is affiliated to the "unknown species" of the Fusobacterium genu, this species will be considered as lost. In the same way if no other OTU is affiliated to Fusobacterium genus but with an ambiguous species, 1 Multi-affilaition at the Species level will be considered as lost in the summary.html. +In the report.html, it will be considered as "Modified", as the RDP taxonomy will remain unchanged and the blast taxonomy will be updated. +If no other OTU is affiliated to the "unknown species" of the Fusobacterium genu, this species will be considered as lost. In the same way if no other OTU is affiliated to Fusobacterium genus but with an ambiguous species, 1 Multi-affilaition at the Species level will be considered as lost in the report.html. @HELP_CONTACT@
--- a/affiliation_postprocess.xml Thu May 12 11:40:39 2022 +0000 +++ b/affiliation_postprocess.xml Fri May 13 15:33:27 2022 +0000 @@ -19,7 +19,7 @@ </command> <inputs> <!-- Files --> - <param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: FASTA)."/> + <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="The sequence file to filter (format: FASTA)."/> <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)"/> <conditional name="is_HVL"> <param name="HVL_amplicon" type="boolean" label="Is this an amplicon hyper variable in length?" help="Multi-affiliation tag may be resolved by selecting the shortest amplicon reference. For this you need the reference fasta file of your targetted amplicon."/> @@ -62,7 +62,7 @@ What it does -Resolves multi-hit ambiguities if exact amplicon length are available and aggregrated OTUs sharing same taxonomy based on alignment metrics thresholds +This tool resolves multi-hit ambiguities if exact amplicon length are available and aggregrated OTUs sharing same taxonomy based on alignment metrics thresholds .. class:: infomark page-header h2 @@ -104,12 +104,12 @@ .. class:: infomark page-header h2 -How it works +How it works ? If a reference fasta file is provided, for each OTU with multiaffiliation, among the different possible affiliations, we only keep the affiliation of the sequence with the shorter length. The aim is to resolve ambiguities due to potential inclusive sequences such as ITS. -Second step is the OTUs aggregation that share the same taxonomy inferred on alignment metrics. -We start with the most abundant OTU. If an OTU shares at least one affiliation with another OTU with at least I% of identity and C% of alignment coverage, the OTUs are aggregated together : the different affiliations, are merged, blast concensus taxonomy is updated and abundance counts are summed. The seed of the most abundant OTU is kept. +Second step is the OTUs aggregation that shares the same taxonomy inferred on alignment metrics. +The process starts with the most abundant OTU. If an OTU shares at least one affiliation with another OTU with at least I% of identity and C% of alignment coverage, the OTUs are aggregated together : the different affiliations, are merged, blast concensus taxonomy is updated and abundance counts are summed. The seed of the most abundant OTU is kept. @HELP_CONTACT@
--- a/affiliations_stat.xml Thu May 12 11:40:39 2022 +0000 +++ b/affiliations_stat.xml Fri May 13 15:33:27 2022 +0000 @@ -31,7 +31,7 @@ </command> <inputs> <!-- Files --> - <param format="biom1" name="biom" type="data" label="Abundance file" help="OTUs abundances and affiliations (format: BIOM)"/> + <param format="biom1" name="biom" type="data" label="Abundance file" help="Abundances and affiliations (format: BIOM)"/> <!-- Parameters --> <expand macro="taxonomic_ranks"/> <param argument="--rarefaction-ranks" type="text" optional="false" value="Class Order Family Genus Species" @@ -115,33 +115,33 @@ Output -**Summary file** (summary.html): +**Report file** (report.html): OTUs taxonomies and affiliations metrics (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): - *-Taxonomy distribution*: display the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample + *-Taxonomy distribution*: displays the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample - .. image:: static/images/FROGS_affiliation_stat_taxonomies.png + .. image:: FROGS_affiliation_stat_taxonomies.png :height: 380 :width: 891 - .. image:: static/images/FROGS_affiliation_stat_rarefaction.png + .. image:: FROGS_affiliation_stat_rarefaction.png :height: 380 :width: 794 - .. image:: static/images/FROGS_affiliation_stat_sunburst.png + .. image:: FROGS_affiliation_stat_sunburst.png :height: 380 :width: 440 - -Bootstrap distribution: display for affiliation methods with bootstrap the bootstrap on each taxonomic rank + -Bootstrap distribution: displays for affiliation methods with bootstrap the bootstrap on each taxonomic rank - .. image:: static/images/FROGS_affiliation_stat_bootstrap.png + .. image:: FROGS_affiliation_stat_bootstrap.png :height: 380 :width: 867 - -Alignment distribution: display for affiliation methods with alignment the distribution of identity/covrage + -Alignment distribution: displays for affiliation methods with alignment the distribution of identity/coverage - .. image:: static/images/FROGS_affiliation_stat_alignment.png + .. image:: FROGS_affiliation_stat_alignment.png :height: 380 :width: 859
--- a/biom_to_stdBiom.xml Thu May 12 11:40:39 2022 +0000 +++ b/biom_to_stdBiom.xml Fri May 13 15:33:27 2022 +0000 @@ -60,7 +60,7 @@ .. class:: infomark page-header h2 -How it works +How it works ? FROGS BIOM to std BIOM extracts the blast alignment details in a second file, write a BIOM usable in every tools using BIOM and defined the consensus taxonomy provided by blast as main taxonomy.
--- a/biom_to_tsv.xml Thu May 12 11:40:39 2022 +0000 +++ b/biom_to_tsv.xml Fri May 13 15:33:27 2022 +0000 @@ -76,7 +76,7 @@ .. class:: infomark page-header h2 -How it works +How it works ? FROGS Biom to Tsv will search if any metadata are available, and the OTU sequence if fasta file is precised. Then it will extract the OTU name, sum the sample abundance, and extract the detailed abundance for each sample. Finally it will write all these fields separated by tabulation in the TSV file.
--- a/clustering.xml Thu May 12 11:40:39 2022 +0000 +++ b/clustering.xml Fri May 13 15:33:27 2022 +0000 @@ -29,13 +29,13 @@ <param format="tabular" name="count_file" type="data" label="Count file" help="It contains the count by sample for each sequence (format: TSV)"/> <!-- Parameters --> <conditional name="FROGS_guidelines"> - <param name="guidelines_version" type="select" label="FROGS guidelines version" help="Denoising step prior to a d3 clustering is no more recommended since FROGS 3.2, but you can still choose it."> + <param name="guidelines_version" type="select" label="FROGS guidelines version" help="The denoising step before a d3 clustering is no longer recommended since FROGS 3.2, but you can still choose it."> <option value="3.2" selected="true">New guidelines from version 3.2</option> <option value="3.1">First guidelines until 3.1</option> </param> <when value="3.2"> <param argument="--distance" type="integer" label="Aggregation distance clustering" help="Maximum number of differences between sequences in each aggregation swarm step. (recommended d=1)" value="1" min="1" max="15" optional="false" /> - <param argument="--fastidious" type="boolean" checked="true" truevalue="--fastidious" falsevalue="" label="Refine OTU clustering" help="Clustering will be performed with the swarm --fastidious option, which is recommended and only usable in association with a distance of 1 (default and recommended: Yes)" /> + <param argument="--fastidious" type="boolean" checked="true" truevalue="--fastidious" falsevalue="" label="Refine OTU clustering" help="Clustering will be performed with the swarm --fastidious option. It is recommended and only usable in association with a distance of 1 (default and recommended: Yes)" /> </when> <when value="3.1"> <param argument="--distance" type="integer" value="3" min="1" max="15" optional="false" label="Aggregation distance clustering" help="Maximum number of differences between sequences in each aggregation swarm step" /> @@ -150,19 +150,19 @@ **Swarm focus** -Swarm use an iterative growth process and the use of sequence abundance values to delineate OTUs. +Swarm uses an iterative growth process and the use of sequence abundance values to delineate OTUs. -.. image:: static/images/FROGS_cluster_swarm.png +.. image:: FROGS_cluster_swarm.png :height: 223 :width: 666 -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". +In each growth 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". -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. +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. -On the other hand, the fastidious option of swarm allow to aggregate small and rare cluster into bigger one if they share sequence with at most 2*d distance. In this case d is restricted to 1 so, cluster distance will be 2. (image extracted from `Swarm github <https://github.com/torognes/swarm>`_) +On the other hand, the fastidious option of swarm allows to aggregate small and rare clusters into bigger one if they share sequence with at most 2*d distance. In this cases, d is restricted to 1 so, cluster distance will be 2. (image extracted from `Swarm github <https://github.com/torognes/swarm>`_) -.. image:: static/images/FROGS_cluster_fastidious.png +.. image:: FROGS_cluster_fastidious.png :height: 319 :width: 681
--- a/clusters_stat.xml Thu May 12 11:40:39 2022 +0000 +++ b/clusters_stat.xml Fri May 13 15:33:27 2022 +0000 @@ -50,25 +50,25 @@ Output -**Summary file** (summary.html): +**Report file** (report.html): - *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables + *Cluster distribution* : describes the sizes distribution of all clusters thank to boxplot and tables - .. image:: static/images/FROGS_cluster_stat_clusterDistrib1.png + .. image:: FROGS_cluster_stat_clusterDistrib1.png :height: 1180 :width: 900 - *Sequences distributions* : describes the sequences distribution among clusters + *Sequence distribution* : describes the sequences distribution among clusters - .. image:: static/images/FROGS_cluster_stat_seq_dist.png + .. image:: FROGS_cluster_stat_seq_dist.png - *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering <http://en.wikipedia.org/wiki/Hierarchical_clustering>`_ on samples abundance profile (distance method = `braycurtis <http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis>`_, linkage method = average) + *Sample distribution* : describes clusters distribution among samples and gives an `hierarchical clustering <http://en.wikipedia.org/wiki/Hierarchical_clustering>`_ on samples abundance profile (distance method = `braycurtis <http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis>`_, linkage method = average) - .. image:: static/images/FROGS_cluster_stat_sample_dist1.png + .. image:: FROGS_cluster_stat_sample_dist1.png :height: 400 :width: 700 - .. image:: static/images/FROGS_cluster_stat_sample_dist2.png + .. image:: FROGS_cluster_stat_sample_dist2.png :height: 350 :width: 610 @@ -76,7 +76,7 @@ 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. +This is a very usefull tool to see the evolution of the OTUs. Do not hesitate to run this tool after each FROGS step beginning at the clustering step.
--- a/demultiplex.xml Thu May 12 11:40:39 2022 +0000 +++ b/demultiplex.xml Fri May 13 15:33:27 2022 +0000 @@ -131,13 +131,13 @@ Example of barcode file: Here the sample is multiplexed by both fragment ends. - .. image:: static/images/FROGS_demultiplex_barcode.png + .. image:: FROGS_demultiplex_barcode.png :height: 60 :width: 316 .. class:: infomark page-header h2 -How it works +How it works ? 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.
--- a/deseq2_preprocess.xml Thu May 12 11:40:39 2022 +0000 +++ b/deseq2_preprocess.xml Fri May 13 15:33:27 2022 +0000 @@ -20,7 +20,7 @@ <!-- Files --> <param format="rdata" name="data" type="data" label="Phyloseq object " help="This is the result of FROGSSTAT Phyloseq Import Data with normalise option set to NO (DESeq2 is more powerful on unnormalised counts) (format RData)"/> <!-- Parameters --> - <param name="var1" type="text" label="Experimental variable" help="The factor suspected to have an effect on OTUs' abundances. Ex: Treatment, etc."> + <param name="var1" type="text" label="Experimental variable" help="The factor suspected to have an effect on OTU abundances. Ex: Treatment, etc."> <expand macro="sanitizer_validator"/> </param> <conditional name="multiple"> @@ -58,7 +58,7 @@ What it does -Launch Rscript to compute differential abundance analysis using `DESeq2 <https://bioconductor.org/packages/release/bioc/html/DESeq2.html>`_ on a `Phyloseq <https://joey711.github.io/phyloseq/>`_ object. +This tool launches Rscript to compute differential abundance analysis using `DESeq2 <https://bioconductor.org/packages/release/bioc/html/DESeq2.html>`_ on a `Phyloseq <https://joey711.github.io/phyloseq/>`_ object. .. class:: infomark page-header h2 @@ -86,7 +86,7 @@ .. class:: infomark page-header h2 -How it works +How it works ? The DESeq function performs a default analysis through the steps: @@ -99,10 +99,10 @@ You must precise at least on variable on which the differential abundances will be compared. -You may precise a confounding factor, by adding an other variable and precise the relation between the two variables: +You may precise a confounding factor, by adding an other variable and you may precise the relation between the two variables: -- + for independant variables -- * for interacting variables +- for independant variables +- for interacting variables @HELP_CONTACT@
--- a/deseq2_visualisation.xml Thu May 12 11:40:39 2022 +0000 +++ b/deseq2_visualisation.xml Fri May 13 15:33:27 2022 +0000 @@ -24,9 +24,9 @@ <param format="rdata" argument="--phyloseqData" type="data" label="Phyloseq object (format: RData)" help="This is the result of FROGS Phyloseq Import Data, used in FROGSSTAT DESeq2 Preprocess tool" /> <param format="rdata" argument="--dds" type="data" label="DESeq2 object (format: RData)" help="This is the result of FROGSSTAT DESeq2 Preprocess tool"/> <!-- Parameters --> - <param argument="var" type="text" value="" label="Experimental variable" help="The factor suspected to have an effect on OTUs' abundances (one of the variables used in FROGS DESeq2 Preprocess tool). Ex : Treatment"/> + <param argument="var" type="text" value="" label="Experimental variable" help="The suspected factor to have an effect on OTU abundances (one of the variables used in FROGS DESeq2 Preprocess tool). Ex : Treatment"/> <conditional name="varType"> - <param type="select" name="vartType_selected" label="Is your Variable quantitative or qualitative?" help="If qualitative, choose 2 conditions to compare"> + <param type="select" name="vartType_selected" label="Is your variable quantitative or qualitative?" help="If qualitative, choose 2 conditions to compare"> <option value="qual">Qualitative</option> <option value="quant">Quantitative</option> </param> @@ -40,7 +40,7 @@ </when> <when value="quant"/> </conditional> - <param argument="--padj" type="float" value="0.05" label="Adjusted p-value threshold" help="Threshold used for statistical significance of the differentially abundant OTUs analysis"/> + <param argument="--padj" type="float" value="0.05" label="Adjusted p-value threshold" help="Threshold used for statistical significance of the differentially abundant OTU analysis"/> </inputs> <outputs> <data format="html" name="html" label="${tool.name}: report.nb.html" from_work_dir="report.nb.html"/> @@ -108,39 +108,39 @@ * Table containing the differentially abundant OTUs. - .. image:: static/images/FROGS_DESeq2_html_table.png + .. image:: FROGS_DESeq2_html_table.png :height: 216 :width: 789 * Pie Chart, MA plot and Volcano plot - .. image:: static/images/FROGS_DESeq2_html_pieChart.png + .. image:: FROGS_DESeq2_html_pieChart.png :height: 576 :width: 768 - .. image:: static/images/FROGS_DESeq2_html_MA_plot.png + .. image:: FROGS_DESeq2_html_MA_plot.png :height: 480 :width: 672 - .. image:: static/images/FROGS_DESeq2_html_Volcano_plot.png + .. image:: FROGS_DESeq2_html_Volcano_plot.png :height: 506 :width: 633 * Heatmap plot corresponding to the differentially abundant OTUs. - .. image:: static/images/FROGS_DESeq2_html_heatmap_plot.png + .. image:: FROGS_DESeq2_html_heatmap_plot.png :height: 576 :width: 768 .. class:: infomark page-header h2 -How it works +How it works ? -Based on the variable you precise to construct the model in FROGSSTAT DESeq2 Preprocess, this tool will construct table and graphs to visualise différentially abundant OTU between condition of the selected variables. +Based on the variable you precise to construct the model in FROGSSTAT DESeq2 Preprocess, this tool will construct table and graphs to visualise differentially abundant OTU between condition of the selected variables. -You may first precise the variable used to construct the model during the FROGSSTAT DESeq Preprocess step. If you precised variable with a confounding factor (a second variale), you may choose between one of the variables, but remember that you will see the result of this variable corrected by the confounding factor (and reversely) not just the selected variable itself. +You may first precise the variable used to construct the model during the FROGSSTAT DESeq Preprocess step. If you precised variable with a confounding factor (a second variable), you may choose between one of the variables, but remember that you will see the result of this variable corrected by the confounding factor (and reversely) not just the selected variable itself. -If the variable is qualitative (ex: variable Treatment is define by two conditions : treatment1, treatment2, control), you must specify 2 conditions to compare (e.g. treatment1 vs treatment2 or treatment1 vs control, ...). +If the variable is qualitative (ex: variable treatment is define by two conditions : treatment1, treatment2, control), you must specify 2 conditions to compare (e.g. treatment1 vs treatment2 or treatment1 vs control, ...). @HELP_CONTACT@
--- a/frogsfunc_copynumbers.xml Thu May 12 11:40:39 2022 +0000 +++ b/frogsfunc_copynumbers.xml Fri May 13 15:33:27 2022 +0000 @@ -166,6 +166,8 @@ **Report file**: .. image:: FROGS_frogsfunc_copynumbers_nsti.png + :height: 350 + :width: 639 Nearest Sequenced Taxon Index (NSTI) is the phylogenetic distance between the OTU and the nearest sequenced reference genome. This metric can be used to identify OTUs that are highly distant from all reference sequences but the predictions for these sequences are less reliable. The higher the NSTI score, the less the affiliations are relevant. Any OTUs with a NSTI value higher than 2 are typically either from uncharacterized phyla or off-target sequences.
--- a/frogsfunc_pathways.xml Thu May 12 11:40:39 2022 +0000 +++ b/frogsfunc_pathways.xml Fri May 13 15:33:27 2022 +0000 @@ -125,7 +125,7 @@ If this option is set, the pathway abundances file (frogsfunc_functions_unstrat.tsv) is normalized: values are divided by sum of columns, then multiplied by 10^6 (Count Per Million values). -.. image:: icon_warning_sml.gif +.. class:: warningmark This normalization allows to compare the samples between them. But to perform more precise statistical analysis, some tools as **DESeq2 need the non-normalized abundance table** to perform the normalization by themselves. So be careful which table to use for further analysis.
--- a/frogsfunc_placeseqs.xml Thu May 12 11:40:39 2022 +0000 +++ b/frogsfunc_placeseqs.xml Fri May 13 15:33:27 2022 +0000 @@ -131,7 +131,7 @@ EPA-NG or SEPP. SEPP is a low-memory alternative to EPA-ng for placing sequences. -.. image:: icon_warning_sml.gif +.. class:: warningmark So, if the tool crashes with EPA-ng, try again with SEPP. @@ -165,7 +165,7 @@ The report file describes which OTUs are contained or not in the phylogenetic tree. Note that PICRUSt2 uses its own reference tree to affiliate OTUs/ASVs from reference sequences. The report file indicates for each OTU/ASV which is the closest PICRUSt2 reference sequence, and compares it to the original FROGS taxonomy. Clicking on the sequence ID gives you more information about it (`JGI database <https://img.jgi.doe.gov/>`_). -.. image:: static/images/FROGS_frogsfunc_placeseqs_piecharts.png +.. image:: FROGS_frogsfunc_placeseqs_piecharts.png :height: 290 :width: 676 @@ -173,7 +173,7 @@ The pie charts describe the proportion of number of OTUs/ASVs excluded and the proportion of total sequences excluded for the following steps. OTUs/ASVs are excluded if the total length of the input sequence aligned against reference sequence is less than the specified " Minimum alignment length " threshold parameter. -.. image:: static/images/FROGS_frogsfunc_placeseqs_table_JGI.png +.. image:: FROGS_frogsfunc_placeseqs_table_JGI.png :height: 580 :width: 1220 @@ -197,7 +197,7 @@ * **Comment** : " identical taxonomy " if the FROGS and PICRUSt2 taxonomic affiliations are identical. " identical sequence " if the OTU sequence is strictly the same as the reference sequence. -.. image:: static/images/FROGS_frogsfunc_placeseqs_closest_explained.png +.. image:: FROGS_frogsfunc_placeseqs_closest_explained.png Closest reference sequence (from JGI database) from one cluster sequence.
--- a/itsx.xml Thu May 12 11:40:39 2022 +0000 +++ b/itsx.xml Fri May 13 15:33:27 2022 +0000 @@ -21,14 +21,14 @@ </command> <inputs> <!-- Files --> - <param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: FASTA)." /> + <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="The sequence file to filter (format: FASTA)." /> <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)" /> - <param argument="--region" type="select" label="ITS region" help="Which fungal ITS region is targeted: either ITS1 or ITS2"> + <param argument="--region" type="select" label="ITS region" help="Which fungal ITS region is targeted: either ITS1 or ITS2 ?"> <option value="ITS1">ITS1</option> <option value="ITS2">ITS2</option> </param> <param argument="--check-its-only" name="trim_sequence" type="boolean" checked="false" truevalue="" falsevalue="--check-its-only" label="Trim conserved sequence (SSU, 5.8S, LSU) ?" help="If Yes, only part of the sequences with ITS signature will be kept, SSU, LSU or 5.8S regions will be trimmed (default : No)" /> - <param argument="--organism-groups" type="select" multiple="true" display="checkboxes" label="Choose pertinent organisms to scan?" help="Save a lot of time by checking pertinent organism group model to scan"> + <param argument="--organism-groups" type="select" multiple="true" display="checkboxes" label="Choose pertinent organisms to scan:" help="Save a lot of time by checking pertinent organism group model to scan"> <option value="F" selected="true">Fungi</option> <option value="A">Alveolata</option> <option value="B">Bryophyta</option> @@ -78,7 +78,7 @@ What it does -Identify (and optionnaly extract) the highly variable ITS1 and ITS2 subregions from ITS sequences. +This tool identifies (and optionnaly extract) the highly variable ITS1 and ITS2 subregions from ITS sequences. .. class:: infomark page-header h2 @@ -126,14 +126,14 @@ The sequence file with discarded sequences. -**Summary file** (report.html): +**Report file** (report.html): This file presents the summary of process (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). .. class:: infomark page-header h2 -How it works +How it works ? .. csv-table:: :header: "Steps", "Description" @@ -142,7 +142,7 @@ "1", "Predicts positions of the ribosomal genes in the sequences (`ITSx <http://microbiology.se/software/itsx/>`_)." "2", "Removes the sequences without prediction of the targeted ITS region (ITS1 or ITS2)." - "3", "(optional) trim conserved region." + "3", "(optional) trims conserved region."
--- a/macros.xml Thu May 12 11:40:39 2022 +0000 +++ b/macros.xml Fri May 13 15:33:27 2022 +0000 @@ -30,7 +30,7 @@ <xml name="taxonomic_ranks"> <param argument="--taxonomic-ranks" type="text" optional="false" value="Domain Phylum Class Order Family Genus Species" - label="Taxonomic ranks" help="The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space"> + label="Taxonomic ranks" help="The ordered taxonomic rank levels stored in BIOM. Each rank is separated by one space"> <sanitizer invalid_char=""> <valid initial="string.letters"> <add value=" " />
--- a/normalisation.xml Thu May 12 11:40:39 2022 +0000 +++ b/normalisation.xml Fri May 13 15:33:27 2022 +0000 @@ -16,7 +16,7 @@ # along with this program. If not, see <http://www.gnu.org/licenses/>. --> <tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>Normalise OTUs abundance.</description> + <description>Normalise OTU abundance.</description> <macros> <import>macros.xml</import> @@ -109,7 +109,7 @@ - **Sampling by the number of sequences of the smallest sample** : Automatically detects the number of reads of the smallest sample, and selects this number for all other samples. - **Select number of reads** : Manually select a number of reads. -.. image:: static/images/icon_warning_sml.gif +.. class:: warningmark If the **remove samples** option is enabled, samples whose total number of sequences is lower than the specified number will be removed inside the abundance table. If the option is disabled, the samples will be kept in the analysis but with a number of sequences lower than the specified number (the total number of the sample). @@ -120,7 +120,7 @@ **Sequence file** (normalised_seed.fasta): - The normalised sequences file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + The normalised sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). **Abundance file** (normalised_abundance.biom):
--- a/otu_filters.xml Thu May 12 11:40:39 2022 +0000 +++ b/otu_filters.xml Fri May 13 15:33:27 2022 +0000 @@ -107,7 +107,7 @@ <option value="count">as count</option> </param> <when value="proportion"> - <param name="min_abundance_proportion" argument="--min_abundance" type="float" optional="true" label="Minimum proportion of sequences abundancy to keep OTU" help='Fill the field only if you want this treatment. Example: 0.00005, recommended by Bokulich et al 2013, to keep OTU with at least 0.005% of all sequences)'> + <param name="min_abundance_proportion" argument="--min_abundance" type="float" optional="true" label="Minimum proportion of sequences abundancy to keep OTU" help='Fill the field only if you want this treatment. Example: 0.00005, recommended by Bokulich et al 2013, to keep OTU with at least 0.005% of all sequences'> <validator type="in_range" min="0" exclude_min="true" max="1" exclude_max="true" message="Abundance proportion threshold need to be strictly greater than 0 and less than 1, otherwise you will not remove anything or remove everything." /> </param> </when> @@ -171,7 +171,7 @@ What it does -Filter the OTUs of an abundance table according to: +Filter the OTUs in an abundance table according to: -The abundance and the occurence of OTUs: presence in samples, OTU size and maximum number of OTUs. @@ -209,6 +209,8 @@ The file must consist of only 2 columns, separated by a tab or a space. The first column contains the exact names of the samples (exactly those contained in the biom file) and the second column contains the name of the group to which they belong. Please note that group names must not contain accents, spaces or special characters. +.. class:: h3 + Outputs **Sequence file** (sequences.fasta): @@ -231,7 +233,7 @@ .. class:: infomark page-header h2 -How it works +How it works? @@ -247,7 +249,7 @@ :widths: 5, 150 :class: table table-striped - "1", "Except the filter to select the n most abundant OTUs, all the selected filters are run independently. For each filters a list of the OTUs to remove is generated. Concerning contaminant research, OTU are added to the previous list if it aligns on a contaminant reference sequence with 80% identity and 80% coverage" + "1", "Except the filter to select the n most abundant OTUs, all the selected filters are run independently. For each filters a list of the OTUs to remove is generated. Concerning contaminant research, OTUs are added to the previous list if it aligns on a contaminant reference sequence with 80% of identity and 80% of coverage" "2", "All the OTUs tagged to remove by at least one filter are removed." "3", "If the filter to select the N most abundant OTUs is filled it is applied." @@ -265,8 +267,7 @@ -To keep the filters that are present in half of the replicates, fill the **Minimum prevalence method** field with **replicate identification** option, with a minimum prevalence of "0.5". -static/images/FROGS_otu_filter_replicates_file.png - +.. image:: FROGS_otu_filter_replicates_file.png In this example, if we want to keep the OTUs/ASVs that are present in at least 50% of the samples, we set the threshold at 0.5. The process will therefore keep the OTUs/ASVs present in at least @@ -277,9 +278,9 @@ and all OTUs/ASVs in sample9 since it is the only representative of the "low" condition. --To display the 20 biggest OTU, fill the corresponding field with "20". +-To display the 20 biggest OTUs, fill the corresponding field with "20". --To filter on abundance, we advise you to specify 0.005%. It seems to be the optimal threshold (`Bokulich *et al*, 2013 <http://www.nature.com/nmeth/journal/v10/n1/abs/nmeth.2276.html>`_ ). +-To filter on abundance, we advise you to specify 0.005% i.e. 0.00005. It seems to be the optimal threshold (`Bokulich *et al*, 2013 <http://www.nature.com/nmeth/journal/v10/n1/abs/nmeth.2276.html>`_ ). @HELP_CONTACT@
--- a/phyloseq_alpha_diversity.xml Thu May 12 11:40:39 2022 +0000 +++ b/phyloseq_alpha_diversity.xml Fri May 13 15:33:27 2022 +0000 @@ -80,22 +80,22 @@ **Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): the review of richness plots and rarefaction curves. -.. image:: static/images/FROGS_Phyloseq_plot_richness.png +.. image:: FROGS_Phyloseq_plot_richness.png :height: 400 :width: 525 -.. image:: static/images/FROGS_Phyloseq_plot_richness_box.png +.. image:: FROGS_Phyloseq_plot_richness_box.png :height: 400 :width: 499 -.. image:: static/images/FROGS_Phyloseq_rarefaction_curves.png +.. image:: FROGS_Phyloseq_rarefaction_curves.png :height: 400 :width: 498 **Alpha diversity table** (alpha_diversity.tsv): The data file containing table of alpha diversity indices. -.. image:: static/images/FROGS_Phyloseq_alpha_diversity_table.png +.. image:: FROGS_Phyloseq_alpha_diversity_table.png .. class:: infomark page-header h2
--- a/phyloseq_beta_diversity.xml Thu May 12 11:40:39 2022 +0000 +++ b/phyloseq_beta_diversity.xml Fri May 13 15:33:27 2022 +0000 @@ -94,7 +94,7 @@ The review of beta diversity with heatmap plots: -.. image:: static/images/FROGS_Phyloseq_beta_diversity.png +.. image:: FROGS_Phyloseq_beta_diversity.png :height: 609 :width: 800 @@ -102,7 +102,7 @@ **beta diversity matrix** (format tabular): The distance matrix of beta diversity. - .. image:: static/images/FROGS_Phyloseq_beta_diversity_matrix.png + .. image:: FROGS_Phyloseq_beta_diversity_matrix.png .. class:: infomark page-header h2
--- a/phyloseq_clustering.xml Thu May 12 11:40:39 2022 +0000 +++ b/phyloseq_clustering.xml Fri May 13 15:33:27 2022 +0000 @@ -76,7 +76,7 @@ .. container:: row - .. image:: static/images/FROGS_Phyloseq_clustering_ward.png + .. image:: FROGS_Phyloseq_clustering_ward.png :height: 576 :width: 768
--- a/phyloseq_composition.xml Thu May 12 11:40:39 2022 +0000 +++ b/phyloseq_composition.xml Fri May 13 15:33:27 2022 +0000 @@ -92,7 +92,7 @@ Bar plot of OTUs is colored with aggregated taxonomic level *i.e* "Phylum" : - .. image:: static/images/FROGS_Phyloseq_bar_plot.png + .. image:: FROGS_Phyloseq_bar_plot.png :height: 646 :width: 800 @@ -109,7 +109,7 @@ - Number of the most abundant taxa to keep: 9 - .. image:: static/images/FROGS_Phyloseq_composition_plot.png + .. image:: FROGS_Phyloseq_composition_plot.png :height: 644 :width: 800
--- a/phyloseq_import_data.xml Thu May 12 11:40:39 2022 +0000 +++ b/phyloseq_import_data.xml Fri May 13 15:33:27 2022 +0000 @@ -21,11 +21,11 @@ <inputs> <!-- Files --> <param format="biom1" argument="--biomfile" type="data" label="Abundance biom file with taxonomical metadata (format: BIOM)" help="The file contains the OTU informations "/> - <param format="tabular,tsv" argument="--samplefile" type="data" label="Sample file (format: TSV)" help="The file contains the samples informations."/> - <param format="nhx" argument="--treefile" type="data" optional="true" label="Tree file (format: Newick)" help="The file contains the tree informations (optional)"/> + <param format="tabular,tsv" argument="--samplefile" type="data" label="Sample file (format: TSV)" help="The file contains the samples information."/> + <param format="nhx" argument="--treefile" type="data" optional="true" label="Tree file (format: Newick)" help="The file contains the tree information (optional)"/> <!-- Parameters --> <param argument="--ranks" type="text" value="Kingdom Phylum Class Order Family Genus Species" - label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space"> + label="Names of taxonomic levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space"> <expand macro="sanitizer_validator"/> </param> <param argument="--normalisation" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before statistical analysis (default : No)"/> @@ -84,7 +84,7 @@ The OTU biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). The example of biom file: - .. image:: static/images/FROGS_Phyloseq_biomfile.png + .. image:: FROGS_Phyloseq_biomfile.png :height: 30 :width: 733 @@ -92,12 +92,12 @@ Newick file (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_) is the result of FROGS Tree: - .. image:: static/images/FROGS_nwk_treefile.png + .. image:: FROGS_nwk_treefile.png **Sample file**: The file contains the conditions of experiment with sample ID in the first column: - .. image:: static/images/FROGS_Phyloseq_samplefile.png + .. image:: FROGS_Phyloseq_samplefile.png :height: 115 :width: 369 @@ -107,9 +107,9 @@ **Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. - .. image:: static/images/FROGS_Phyloseq_import_data_html.png + .. image:: FROGS_Phyloseq_import_data_html.png -**Data file** (format rdata): The informations of data in one phyloseq object. +**Data file** (format rdata): The information of data in one phyloseq object. .. class:: infomark page-header h2
--- a/phyloseq_manova.xml Thu May 12 11:40:39 2022 +0000 +++ b/phyloseq_manova.xml Fri May 13 15:33:27 2022 +0000 @@ -63,7 +63,7 @@ **html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The review of Manova test. -.. image:: static/images/FROGS_Phyloseq_manova.png +.. image:: FROGS_Phyloseq_manova.png .. class:: infomark page-header h2
--- a/phyloseq_structure.xml Thu May 12 11:40:39 2022 +0000 +++ b/phyloseq_structure.xml Fri May 13 15:33:27 2022 +0000 @@ -17,7 +17,7 @@ <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."/> - <param argument="--distance-matrix" format="tabular" type="data" label="The beta diversity distance matrix file" help="These file is the result of FROGS Phyloseq Beta Diversity tool"/> + <param argument="--distance-matrix" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool"/> <!-- Parameters --> <param argument="--varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" > <expand macro="sanitizer_validator"/> @@ -65,7 +65,7 @@ Input **data file** (format rdata): -The informations of data in one phyloseq object. +The information of data in one phyloseq object. This file is the result of "FROGS Phyloseq Import Data tool". **distance file** (format tabular): @@ -80,7 +80,7 @@ The review of data structure with an ordination plot and with an heatmap plot: -.. image:: static/images/FROGS_Phyloseq_plot_sample_ellipse.png +.. image:: FROGS_Phyloseq_plot_sample_ellipse.png :height: 343 :width: 450 @@ -90,7 +90,7 @@ These percentages will be computed for MDS/PCoA and DPCoA ordination methods as a percentage of explained beta diversity variation. For NMDS there is not simple equivalent notion. -.. image:: static/images/FROGS_Phyloseq_plot_heatmap_red.png +.. image:: FROGS_Phyloseq_plot_heatmap_red.png :height: 343 :width: 450
--- a/preprocess.xml Thu May 12 11:40:39 2022 +0000 +++ b/preprocess.xml Fri May 13 15:33:27 2022 +0000 @@ -340,7 +340,7 @@ :Files: One sequence file by sample (format `FASTQ <https://en.wikipedia.org/wiki/FASTA_format>`_) :Example: splA.fastq.gz, splB.fastq.gz -Remark: In an archive if you use R1 and R2 files their names must end with *_R1* and *_R2*. The part upstram from this tag (_R1 and _R2) will be consider as sample name. +Remark: In an archive, if you use R1 and R2 files, their names must end with *_R1* and *_R2*. The part upstream from this tag (_R1 and _R2) will be consider as sample name. .. class:: h3 @@ -348,29 +348,29 @@ **Sequence file** (dereplicated.fasta): - Only one file with all samples sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). These sequences are dereplicated: strictly identical sequence are represented only once, the initial count by sample is kept in count file (see bellowà) and the total count is added in the sequence header. A "FROGS_combined" suffix will be added to un-merged pair sequence if you want to keep them. + Only one file with all samples sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). These sequences are dereplicated: strictly identical sequences are represented only once, the initial count by sample is kept in count file (see bellow) and the total count is added in the sequence header. A "FROGS_combined" suffix will be added to un-merged pair sequence if you want to keep them. **Count file** (count.tsv): This file contains the count of all unique sequences in each sample (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). -**Summary file** (report.html): +**Report file** (report.html): This file reports the number of remaining sequences after each filter (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). Depending of the tool configuration there will be more or less filtering steps so more or less bars in the barplot. - .. image:: static/images/FROGS_preprocess_summary_v3.png + .. image:: FROGS_preprocess_summary_v3.png :height: 850 :width: 831 It also presents the length distribution of the full amplicon sequences after merging step and after filtering steps. - .. image:: static/images/FROGS_preprocess_lengthsSamples_v3.png + .. image:: FROGS_preprocess_lengthsSamples_v3.png :height: 379 :width: 364 .. class:: infomark page-header h2 -How it works +How it works ? .. csv-table:: :header: "Steps", "Illumina", "454" @@ -378,8 +378,8 @@ :class: table table-striped "1", "For un-merged data: Merges R1 and R2 with a maximum of M% mismatch in the overlaped region(`VSEARCH <https://github.com/torognes/vsearch/>`_ or `FLASH <http://ccb.jhu.edu/software/FLASH/>`_ or optionnaly `PEAR <https://sco.h-its.org/exelixis/web/software/pear/>`_) with a minimum of 10 bp in the overlap region. Resulting un-merged reads may optionnaly be artificially combined by adding 100 N between the reads", "/" - "2", "If sequencing protocol is the illumina standard protocol : Removes sequences where the two primers are not present and removes primers in the remaining sequence (`cutadapt <http://cutadapt.readthedocs.org/en/latest/guide.html>`_). The primer search accepts 10% of differences", "Removes sequences where the two primers are not present, removes primers sequence from amplicon sequence and reverse complement the sequences on strand - (`cutadapt <http://cutadapt.readthedocs.org/en/latest/guide.html>`_). The primer search accepts 10% of differences" - "3", "Filters sequences with ambiguous nucleotides and for merged sequences filters on their length which must be range between 'Minimum amplicon size - primer length' and 'Maximum amplicon size - primer length'", "Removes sequences with at least one homopolymer with more than seven nucleotides and with a distance of less than or equal to 10 nucleo-tides between two poor quality positions, i.e. with a Phred quality score lesser than 10" + "2", "If sequencing protocol is the illumina standard protocol: Removes sequences where the two primers are not present and removes primers in the remaining sequence (`cutadapt <http://cutadapt.readthedocs.org/en/latest/guide.html>`_). The primer search accepts 10% of differences", "Removes sequences where the two primers are not present, removes primers sequence from amplicon sequence and reverse complement the sequences on strand - (`cutadapt <http://cutadapt.readthedocs.org/en/latest/guide.html>`_). The primer search accepts 10% of differences" + "3", "Filters sequences with ambiguous nucleotides and for merged sequences filters on their length which must be range between 'Minimum amplicon size - primer length' and 'Maximum amplicon size - primer length'", "Removes sequences with at least one homopolymer with more than seven nucleotides and with a distance of less than or equal to 10 nucleotides between two poor quality positions, i.e. with a Phred quality score lesser than 10" "4", "Dereplicates sequences", "Dereplicates sequences" @@ -391,7 +391,8 @@ Keeping or not un-merged paired reads -This option is usefull when and only when, targeted amplicon is longer than the sequencing technology can provide (ITS amplicon for example). In other case, carefully, you will only keep noise in your analysis. +.. class:: warningmark +This option is usefull when and only when, **targeted amplicon is longer than the sequencing technology** can provide (ITS amplicons, V1-V4 region of 16S for example). In other case, carefully, you will only keep noise in your analysis. .. class:: h3 @@ -399,13 +400,13 @@ - **Case of a sequencing of overlapping sequences: case of 16S V3-V4 amplicon MiSeq sequencing** -.. image:: static/images/FROGS_preprocess_overlapped_sequence.png +.. image:: FROGS_preprocess_overlapped_sequence.png :height: 261 :width: 531 - **Case of a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing** -.. image:: static/images/FROGS_preprocess_combined_sequence1.png +.. image:: FROGS_preprocess_combined_sequence1.png :height: 279 :width: 797 @@ -413,7 +414,7 @@ **“FROGS combined” warning points** -Reads pair are not merged because: +Read pairs are not merged because: - the real amplicon length is greater than de number of base sequences (490 bp for MiSeq 2x250bp, remember of the minimum 10 bp overlap) - the overlapped region is smaller than 10 (fixed parameter in FROGS). @@ -421,7 +422,7 @@ Thus, “FROGS combined” sequences are artificial and present particular features especially on size. Imagine a MiSeq sequencing of 2x250pb with sequences that cannot overlap, the resulting “FROGS combined” sequences length will be fixed to 600 bp. -.. image:: static/images/FROGS_preprocess_combined_sequence2.png +.. image:: FROGS_preprocess_combined_sequence2.png :height: 357 :width: 798 @@ -429,7 +430,7 @@ Primers parameters -The (`Kozich et al. 2013 <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/>`_ ) protocol uses custom sequencing primers which are also the PCR primers. In this case the reads do not contain the PCR primers. +The (`Kozich et al. 2013 <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/>`_ ) protocol uses custom sequencing primers that are also the PCR primers. In this case, the reads do not contain the PCR primers. In case of Illumina standard protocol, the primers must be provided in 5' to 3' orientation. @@ -445,19 +446,19 @@ .. class:: h3 -FLASH : Amplicons sizes parameters +FLASH : Amplicon size parameters .. class:: infomark - We now recommend to use PEAR if availbale (only for accademic user) or Vsearch. + We now recommend to use PEAR if availbale (only for accademic user) or Vsearch. PEAR is available only in command line. - The two following images show two examples of perfect values fors sizes parameters. + The two following images show two examples of perfect values for sizes parameters. - .. image:: static/images/FROGS_preprocess_ampliconSize_unimodal_v3.png + .. image:: FROGS_preprocess_ampliconSize_unimodal_v3.png :height: 415 :width: 676 - .. image:: static/images/FROGS_preprocess_ampliconSize_multimodal_v3.png + .. image:: FROGS_preprocess_ampliconSize_multimodal_v3.png :height: 415 :width: 676
--- a/remove_chimera.xml Thu May 12 11:40:39 2022 +0000 +++ b/remove_chimera.xml Fri May 13 15:33:27 2022 +0000 @@ -65,7 +65,7 @@ What it does -Remove chimeric sequences by sample. +This tool removes chimeric sequences by sample. .. class:: infomark page-header h2 @@ -121,14 +121,14 @@ The abundance file with only non-chimera (format the same of the abundance input). -**Summary file** (report.html): +**Report file** (report.html): This file presents the number of removed elements (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). .. class:: infomark page-header h2 -How it works +How it works ? .. csv-table:: :header: "Steps", "Description"
--- a/tool-data/frogs_HVL_db.loc.sample Thu May 12 11:40:39 2022 +0000 +++ b/tool-data/frogs_HVL_db.loc.sample Fri May 13 15:33:27 2022 +0000 @@ -31,7 +31,14 @@ #in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta #then the HVL_db.loc entry would look like this: # +# +# # EXAMPLE FOR TEST : -#Unite_extract_ITS1_test Unite_extract_ITS1_test ${__HERE__}/HVL_db_data/Unite_extract_ITS1.fasta -#UNITE_7.1_ITS1 UNITE 7.1 ITS1 <PATH_TO>/Unite_s_7.1_20112016_ITS1.fasta -#UNITE_7.1_ITS2 UNITE 7.1 ITS2 <PATH_TO>/Unite_s_7.1_20112016_ITS2.fasta +#Unite_extract_ITS1_test Unite_extract_ITS1_test <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/test-data/databases/HVL_db_data/Unite_extract_ITS1.fasta +# +# +# +# PRODUCTION FILES, with FROGS toolsheds path to adapt (Galaxy_dir and XXXXXX) +# +#UNITE_7.1_ITS1 UNITE 7.1 ITS1 <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/tool-data/databases/frogs_HVL_db_data/Unite_s_7.1_20112016_ITS1.fasta +#UNITE_7.1_ITS2 UNITE 7.1 ITS2 <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/tool-data/databases/frogs_HVL_db_data/Unite_s_7.1_20112016_ITS2.fasta
--- a/tool-data/frogs_contaminant_db.loc.sample Thu May 12 11:40:39 2022 +0000 +++ b/tool-data/frogs_contaminant_db.loc.sample Fri May 13 15:33:27 2022 +0000 @@ -31,6 +31,7 @@ #then the phiX_db.loc entry would look like this: # # +# # EXAMPLE FOR TEST : #phiX_test phiX_test ${__HERE__}/contaminant_db/phi.fa # @@ -42,5 +43,10 @@ #-rw-rwxr-- 1 gpascal FROGS 88 16 sept. 2015 phi.fa.nin #-rw-rwxr-- 1 gpascal FROGS 1348 16 sept. 2015 phi.fa.nsq # -#phiX phiX tool-data/contaminant_db/phi.fa -#Arabido_TAIR10_Chl_Mito Arabidopsis TAIR10 Chloroplast and mitochondria tool-data/contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa +# +# +# +# PRODUCTION FILES, with FROGS toolsheds path to adapt (Galaxy_dir and XXXXXX) +# +#phiX phiX <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/tool-data/databases/tool-data/contaminant_db/phi.fa +#Arabido_TAIR10_Chl_Mito Arabidopsis TAIR10 Chloroplast and mitochondria <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/tool-data/databases/tool-data/contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa
--- a/tool-data/frogs_db.loc.sample Thu May 12 11:40:39 2022 +0000 +++ b/tool-data/frogs_db.loc.sample Fri May 13 15:33:27 2022 +0000 @@ -18,7 +18,9 @@ #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 +# a datamanager is available to deal with these databases : https://toolshed.g2.bx.psu.edu/view/frogs/data_manager_frogs/7403d6c4f510 +# +# databases formatted and shared by FROGS team are available here : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation # #Finally you will need to create frogs_db.loc file similar to this one. #The frogs_db.loc file has this format (longer white space characters are @@ -51,4 +53,5 @@ # #<value> <name> <file_path> # -#ITS_test ITS1 extract <FROGS-wrappers>/test-data/databases/frogs_db_data/ITS1.rdp.fasta +# FOR TESTING +#ITS_test ITS1 extract <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/test-data/databases/frogs_db_data/ITS1.rdp.fasta
--- a/tool-data/frogs_picrust2_marker_table.loc.sample Thu May 12 11:40:39 2022 +0000 +++ b/tool-data/frogs_picrust2_marker_table.loc.sample Fri May 13 15:33:27 2022 +0000 @@ -18,20 +18,23 @@ #the copy number of gene families present in the predicted genome for OTU, # given a tree and a set of known trait values (FROGS_frogsfunc_placeseqs). # -#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult -#PICRUSt2 documentation to find out where they are located in your environment. -# -#If you are not comfortable with picrust2 command lines, just create .loc files -#with EXAMPLE FOR TEST files remembering to replace <Galaxy_dir> with the real path. -# -#The indicated path is the one if you do not change the default galaxy config of conda directory. +#PICRUSt2 files are present in the arborescence of PICRUSt2. # #<marker_gene> <db> <picrust2_input_marker> <picrust2_input_function> # -#With 16S data, PICRUSt2 only takes the dname of the database as input (for exemple EC). -#With ITS and 18S data, you have to specify the path of marke gene counts files. +# For 16S data (see the 6 first lines), PICRUSt2 only takes the dname of the database as input (for exemple EC). +# With ITS and 18S data, you have to specify the path of marker gene counts files. +# +# +# Bellow you will find out how to implement this loc file. # -# EXAMPLE FOR TEST : +# The indicated path is the one if you do not change the default galaxy config of conda directory. +# Just adapt path by replacing <Galaxy_dir> with the real path and eventually the picrust version. +# +# If you are not using this default conda behavior, please consult PICRUSt2 documentation to find out where they are located in your environment. +# +# +# #16S EC EC EC #16S KO KO KO #16S PFAM PFAM PFAM
--- a/tree.xml Thu May 12 11:40:39 2022 +0000 +++ b/tree.xml Fri May 13 15:33:27 2022 +0000 @@ -20,8 +20,8 @@ </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!"/> - <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: BIOM)"/> + <param format="fasta" name="input_otu" type="data" label="Sequence file" help="Sequence file (format: FASTA). Warning: FROGS Tree does not work on more than 10000 sequences!"/> + <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance file (format: BIOM)"/> </inputs> <outputs> <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk" /> @@ -52,8 +52,8 @@ What it does -Creation of a multiple alignment of OTUs with `Mafft <http://mafft.cbrc.jp/alignment/software>`_. -And creation of a rooted phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_ and `Phangorn R package <https://cran.r-project.org/web/packages/phangorn/index.html>`_. +This tool creates a multiple alignment of OTUs with `Mafft <http://mafft.cbrc.jp/alignment/software>`_. +And creates a rooted phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_ and `Phangorn R package <https://cran.r-project.org/web/packages/phangorn/index.html>`_. .. class:: infomark page-header h2 @@ -63,14 +63,14 @@ Input -**OTUs fasta file**: +**Fasta file**: -The OTUs sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). +The OTU sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). Careful: FROGS Tree works only with less than 10 000 sequences! - .. image:: static/images/FROGS_tree_otufile.png + .. image:: FROGS_tree_otufile.png -**OTUs biom file**: +**Biom file**: The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). This file can be obtained in particular with the FROGS pipeline. @@ -83,11 +83,11 @@ The phylogenetic tree in Newick format (format `nwk or nhx <https://en.wikipedia.org/wiki/Newick_format>`_). - .. image:: static/images/FROGS_nwk_treefile.png + .. image:: FROGS_nwk_treefile.png -**Html file** (summary.html): +**Report file** (report.html): -The summary file describing which OTUs are contained or not in the phylogenetic tree. +The report file describing which OTUs are contained or not in the phylogenetic tree. .. class:: infomark page-header h2
--- a/tsv_to_biom.xml Thu May 12 11:40:39 2022 +0000 +++ b/tsv_to_biom.xml Fri May 13 15:33:27 2022 +0000 @@ -18,7 +18,7 @@ <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." /> - <param format="tabular" name="multi_affi_file" type="data" label="Multi_hits TSV File" help="TSV file describing multi_hit blast results." optional="true" /> + <param format="tabular" name="multi_affi_file" type="data" label="Multi_affiliation TSV File" help="TSV file describing multi_affiliation 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> @@ -58,7 +58,7 @@ **Multiple affiliation file**: -The file that stores the multiple blast hits. +The file that stores the multiple blast affiliations. .. class:: h3 @@ -76,13 +76,13 @@ .. class:: infomark page-header h2 -How it works +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. +If blast_taxonomy is included in metadata and if blast_subject is equal to "multi-subject", it parses multi_affiliation TSV file. Then it extracts the list of blast_affiliations that contains the non ambiguous blast_taxonomy. @@ -96,9 +96,9 @@ * -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. + * -take care to choose a taxonomy available in your multi_affiliation TSV file + * -if you delete lines of the multi_affiliation 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_affiliation TSV file.