Mercurial > repos > oinizan > frogs_3_1_0
changeset 2:fcc5cf5a34dd draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 1acf18f0a4c28a9f4e870c04e3a5ec7ca78c8efa-dirty
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--- a/README.md Fri Dec 21 08:40:50 2018 -0500 +++ b/README.md Tue Jan 08 08:36:26 2019 -0500 @@ -1,8 +1,10 @@ - <img src="static/frogs_images/FROGS_logo.png" width="20%" style="display: block; margin: auto;"/> <img src="galaxy_project_logo_square.png" width="20%" style="display: block; margin: auto;"/> + <img src="static/images/frogs_images/FROGS_logo.png" width="20%" style="display: block; margin: auto;"/> <img src="galaxy_project_logo_square.png" width="20%" style="display: block; margin: auto;"/> -[](https://github.com/geraldinepascal/FROGS-wrappers/releases) +Visit our web site : http://frogs.toulouse.inra.fr/ + +[](https://github.com/geraldinepascal/FROGS-wrappers/releases)[<img src="https://www.podcastscience.fm/wp-content/uploads/2017/12/deezer.png" width="5%" style="display: block; margin: auto;"/>](https://www.deezer.com/fr/playlist/5233843102?utm_source=deezer&utm_content=playlist-5233843102&utm_term=18632989_1545296531&utm_medium=web) @@ -16,11 +18,16 @@ * [Installing FROGS\-wrappers](#installing-frogs-wrappers) * [Simplest way](#simplest-way) - * [From source](#from-source) + * [From sources](#from-sources) * [Prerequisites](#prerequisites) - * [FROGS\-wrapper installation](#frogs-wrapper-installation) - * [Use PEAR as reads merge software in preprocess](#use-pear-as-reads-merge-software-in-preprocess) + * [FROGS\-wrappers installation](#frogs-wrappers-installation) +* [Use PEAR as reads merge software in preprocess](#use-pear-as-reads-merge-software-in-preprocess) * [Upload and configure the databanks](#upload-and-configure-the-databanks) +* [Galaxy configuration](#galaxy-configuration) + * [Setup Galaxy environment variables](#setup-galaxy-environment-variables) + * [Install python packages inside virtual env](#install-python-packages-inside-virtual-env) + * [Avoid FROGS HTML report sanitization](#avoid-FROGS-HTML-report-sanitization) + * [Set memory and parallelisation settings](#set-memory-and-parallelisation-settings) * [License](#license) * [Copyright](#copyright) * [Citation](#citation) @@ -30,30 +37,66 @@ ## Simplest way -FROGS is available in the Toolshed : [release 2.0.0](https://toolshed.g2.bx.psu.edu/repository?repository_id=525e78406276b403&changeset_revision=76c750c5f0d1) +FROGS is available on the Toolshed : https://toolshed.g2.bx.psu.edu/repository?repository_id=525e78406276b403&changeset_revision=76c750c5f0d1 It will install FROGS thanks to [conda](https://anaconda.org/bioconda/frogs), download all these XML tools and well configure them in your Galaxy. -## From source +The 22 FROGS tools will be in random order in your tools panel. We propose to control that order by modifying the `integrated_tool_panel.xml `. + +We suppose that you installed FROGS in a spécific section named `FROGS` (update the FROGS version if necessary). + +``` +<section id="FROGS" name="FROGS" version=""> + + <label text="OTUs reconstruction" id="FROGS_OTU" /> + + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_demultiplex/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_preprocess/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_clustering/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_remove_chimera/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_filters/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_itsx/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_affiliation_OTU/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_affiliation_postprocess/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_normalisation/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_Tree/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_clusters_stat/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_affiliations_stat/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_biom_to_stdBiom/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_biom_to_tsv/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_tsv_to_biom/3.1" /> + + <label text="OTUs structure and composition analysis" id="FROGSSTAT_Phyloseq" /> + + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Import_Data/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Composition_Visualisation/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Alpha_Diversity/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Beta_Diversity/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Sample_Clustering/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Structure_Visualisation/3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.1" /> +</section> +``` + + + +## From sources #### Prerequisites You should start by installing [FROGS](https://github.com/geraldinepascal/FROGS) (remember, FROGS is now installable via [conda](https://anaconda.org/bioconda/frogs) ) -FROGS python programs need to be available in your path, if installing from source, you need to add `<FROGS_PATH>/app` directory in the Galaxy PATH environment variable. (see [environment-setup-file parameter](https://docs.galaxyproject.org/en/latest/admin/config.html#environment-setup-file) ) - -#### FROGS-wrapper installation +#### FROGS-wrappers installation 1. <u>Download wrapper</u> - Download the last released versions of FROGS-wrapper - Available at https://github.com/geraldinepascal/FROGS-wrappers/releases + Download the last released versions of FROGS-wrappers: https://github.com/geraldinepascal/FROGS-wrappers/releases Uncompress and unarchive the release in your ` <Galaxy_Dir>/tools` directory (replace the) link to the new directory like this - ` ln -s <Galaxy_Dir>/tools/FROGS-wrapper-<Release_Number> <Galaxy_Dir>/tools/FROGS` + ` ln -s <Galaxy_Dir>/tools/FROGS-wrappers-<Release_Number> <Galaxy_Dir>/tools/FROGS` 2. <u>Add tools in galaxy</u> @@ -71,12 +114,12 @@ <tool file="FROGS/affiliation_OTU.xml" /> <tool file="FROGS/affiliation_postprocess.xml" /> <tool file="FROGS/normalisation.xml" /> + <tool file="FROGS/tree.xml" /> <tool file="FROGS/clusters_stat.xml" /> <tool file="FROGS/affiliations_stat.xml" /> <tool file="FROGS/biom_to_stdBiom.xml" /> <tool file="FROGS/biom_to_tsv.xml" /> <tool file="FROGS/tsv_to_biom.xml" /> - <tool file="FROGS/tree.xml" /> <label text="OTUs structure and composition analysis" id="FROGSSTAT_Phyloseq" /> <tool file="FROGS/r_import_data.xml" /> <tool file="FROGS/r_composition.xml" /> @@ -87,17 +130,132 @@ <tool file="FROGS/r_manova.xml" /> </section> ``` - If you used previous version of FROGS, you must removed `app` direcotry path. + NB: If you used previous version of FROGS, you must removed `app` direcotry name in the paths names. 3. <u>Add images</u> - **Deal with images ??** + Add the FROGS-wrappers images in `<Galaxy_Dir>/static/images` directory + + `cp -r <Galaxy_Dir>/tools/FROGS/static/images/frogs_images/ <Galaxy_Dir>/static/images/.` + + +# Use PEAR as reads merge software in preprocess +[PEAR](https://cme.h-its.org/exelixis/web/software/pear/) is one of the most effective software for read pair merging, but as its licence is not free for private use, we can not distribute it in FROGS. +If you work in an academic lab on a private Galaxy server, or if you have payed your licence you can use PEAR in FROGS preprocess. +For that, you need to: + +* have PEAR in your PATH or in the FROGS libexec directory + +* add PEAR in the FROGS preprocess Galaxy wrapper (<FROGS_DIR>/tools/preprocess/preprocess.xml): + + :warning: there is two places where the list merge_software is defined, add pear in both of them! + + add pear value in the list of `merge_software` +``` + <conditional name="merge_software_type"> + <param name="merge_software" type="select" label="Merge software" help="Select the software to merge paired-end reads."> + <option value="vsearch" selected="true">Vsearch</option> + <option value="flash">Flash</option> + <option value="pear">PEAR</option> + </param> + <when value="flash"> + <param name="expected_amplicon_size" type="integer" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons." value="" /> + </when> + </conditional> +``` -4. <u>Set memory and parallelisation settings</u> +:warning: remember, there is two places where the list merge_software is defined, add pear in both of them! + +# Upload and configure the databanks + +Databanks are defined in `loc` files and `loc` files are defined in Galaxy datatable. + +* Manual installation : + + * datatables : `<Galaxy_Dir>/config/tool_data_table_conf.xml` , example : `<Galaxy_Dir>/tools/FROGS/tool_data_table_conf.xml.sample` + + Add FROGS-wrappers datatables in the Galaxy datatables, but replace `{__HERE__}` by `tools/FROGS`. + + * loc files example : `<Galaxy_Dir>/tools/FROGS/tool-data/` + + Copy and rename them as indicated in the tool_data_table. + + Then add entry as indicated in each loc files. + +* Toolshed installation : + + * datatables : `<Galaxy_Dir>/config/shed_tool_data_table_conf.xml` (nothing to modify, FROGS datatables should automatically be added) + * loc files to filled in : `tool-data/toolshed.g2.bx.psu.edu/repos/frogs/frogs_<VERSION>/<RANDOM>/` + + + +We provide some databanks for each of these 3 data tables, you simply need to download them and add them in the corresponding `loc` files. + +- Assignation databank for affiliation_OTU tool + + URL : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation - If you have more than one CPU, it is recommended to increase the number of CPUs used by tools. + loc file :`frogs_db.loc` + +- Contaminant databank for filter tool + + URL : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants + + loc file : `phiX_db.loc` + +- Hyper variable in length amplicon databank for affiliation_postprocess tool + + URL : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL + + loc file : `HVL.loc` + + +# Galaxy configuration + +## setup Galaxy environment variables + +FROGS python programs need to be available in the PATH, if installing from source or via conda, you need to add `<FROGS_PATH>/app` directory in the Galaxy PATH environment variable. (see [environment-setup-file parameter](https://docs.galaxyproject.org/en/latest/admin/config.html#environment-setup-file) ) + +## Install python packages inside virtual env + +Galaxy runs in a specific virtual env. To allow FROGS clusters stat to access to the python scipy library, you need to (re)install it inside the Galaxy virtual env +``` +cd <Galaxy_Dir> +source .venv/bin/activate +pip install scipy +deactivate +``` - All CPUs must be on the same computer/node. +## Avoid FROGS HTML report sanitization + +By default Galaxy sanitizes HTML outputs to prevent XSS attacks. +FROGS outputs, for almost all tools, report in HTML format. To allow their visualization inside Galaxy, we need to avoid the Galaxy sanitization. +You need to uncomment `sanitize_whitelist_file` line in `<Galaxy_Dir>/config/galaxy.ini`, create the corresponding `<Galaxy_Dir>/config/sanitize_whitelist.txt` file if not already done, and add the following lines in it. +``` +FROGSSTAT_Phyloseq_Alpha_Diversity +FROGSSTAT_Phyloseq_Beta_Diversity +FROGSSTAT_Phyloseq_Composition_Visualisation +FROGSSTAT_Phyloseq_Import_Data +FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance +FROGSSTAT_Phyloseq_Sample_Clustering +FROGSSTAT_Phyloseq_Structure_Visualisation +FROGS_Tree +FROGS_affiliation_OTU +FROGS_affiliations_stat +FROGS_clustering +FROGS_clusters_stat +FROGS_filters +FROGS_itsx +FROGS_normalisation +FROGS_preprocess +FROGS_remove_chimera +``` + +## Set memory and parallelisation settings + +If you have more than one CPU, it is recommended to increase the number of CPUs used by tools. + +All CPUs must be on the same computer/node. * Specifications @@ -159,61 +317,6 @@ </tools> ``` -## Use PEAR as reads merge software in preprocess -[PEAR](https://cme.h-its.org/exelixis/web/software/pear/) is one of the most effective software for read pair merging, but as its licence is not free for private use, we can not distribute it in FROGS. -If you work in an academic lab on a private Galaxy server, or if you have payed your licence you can use PEAR in FROGS preprocess. -For that you need to: - -* have PEAR in your PATH or in the FROGS libexec directory - -* add PEAR in the FROGS preprocess Galaxy wrapper (<FROGS_DIR>/tools/preprocess/preprocess.xml): - - :warning: there is two places where the list merge_software is defined, add pear in both of them! - - add pear value in the list of `merge_software` -``` - <conditional name="merge_software_type"> - <param name="merge_software" type="select" label="Merge software" help="Select the software to merge paired-end reads."> - <option value="vsearch" selected="true">Vsearch</option> - <option value="flash">Flash</option> - <option value="pear">PEAR</option> - </param> - <when value="flash"> - <param name="expected_amplicon_size" type="integer" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons." value="" /> - </when> - </conditional> -``` - -:warning: remember, there is two places where the list merge_software is defined, add pear in both of them! - -# Upload and configure the databanks - -3 tools use external databanks. Theses databanks are defined in `loc` files and `loc` files are defined in Galaxy datatable. - -**Deal with data-table???** - -We provide some databanks for each of them, you simply need to download them and add them in the corresponding `loc` files. - -- Assignation databank for affiliation_OTU tool - - URL : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation - - `loc` file example : `<FROGS-wrapper_Dir>/tool-data/frogs_db.loc.sample` - -- Contaminant databank for filter tool - - URL : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants - - `loc` file example : `<FROGS-wrapper_Dir>/tool-data/phiX_db.loc.sample` - -- Hyper variable in length amplicon databank for affiliation_postprocess tool - - URL : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL - - `loc` file example : `<FROGS-wrapper_Dir>/tool-data/HVL.loc.sample` - - - # License GNU GPL v3
--- a/RELEASE_NOTE.md Fri Dec 21 08:40:50 2018 -0500 +++ b/RELEASE_NOTE.md Tue Jan 08 08:36:26 2019 -0500 @@ -1,4 +1,4 @@ -# v3.1 [DEV] +# v3.1 [2018-01-08] This release corresponds to the FROGS 3.1.0 release. @@ -10,11 +10,11 @@ * ### Modifications: - - use tool data table intead of simply loc files for filter, affiliation_OTU and affiliation_postprocess - - tree do no longer support Pynast alignment thanks to a template file + - use tool data table instead of simple loc files for filters, affiliation_OTU and affiliation_postprocess + - Tree do no longer support Pynast alignment thanks to a template file # v2.0.0 [2018-12-11] First package. -This release corresponds to the FROGS 2.0.0 release \ No newline at end of file +This release corresponds to the FROGS 2.0.0 release
--- a/affiliation_OTU.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/affiliation_OTU.xml Tue Jan 08 08:36:26 2019 -0500 @@ -69,7 +69,7 @@ <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -109,7 +109,7 @@ 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/frogs_images/FROGS_affiliation_summary.png + .. image:: static/images/frogs_images/FROGS_affiliation_summary.png :height: 800 :width: 600 @@ -141,13 +141,13 @@ * **Case 1: a sequencing of overlapping sequences i.e. 16S V3-V4 amplicon MiSeq sequencing** -.. image:: static/frogs_images/FROGS_affiliation_overlapped_percent_id.png +.. image:: static/images/frogs_images/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/frogs_images/FROGS_affiliation_combined_percent_id.png +.. image:: static/images/frogs_images/FROGS_affiliation_combined_percent_id.png :height: 310 :width: 887 @@ -155,7 +155,7 @@ 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/frogs_images/FROGS_affiliation_percent_id_formula.png +.. image:: static/images/frogs_images/FROGS_affiliation_percent_id_formula.png :height: 36 :width: 637
--- a/affiliation_postprocess.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/affiliation_postprocess.xml Tue Jan 08 08:36:26 2019 -0500 @@ -76,7 +76,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110
--- a/affiliations_stat.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/affiliations_stat.xml Tue Jan 08 08:36:26 2019 -0500 @@ -94,7 +94,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -130,27 +130,27 @@ *-Taxonomy distribution*: display the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample - .. image:: static/frogs_images/FROGS_affiliation_stat_taxonomies.png + .. image:: static/images/frogs_images/FROGS_affiliation_stat_taxonomies.png :height: 380 :width: 650 - .. image:: static/frogs_images/FROGS_affiliation_stat_rarefaction.png + .. image:: static/images/frogs_images/FROGS_affiliation_stat_rarefaction.png :height: 380 :width: 550 - .. image:: static/frogs_images/FROGS_affiliation_stat_sunburst.png + .. image:: static/images/frogs_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/frogs_images/FROGS_affiliation_stat_bootstrap.png + .. image:: static/images/frogs_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/frogs_images/FROGS_affiliation_stat_alignment.png + .. image:: static/images/frogs_images/FROGS_affiliation_stat_alignment.png :height: 380 :width: 650
--- a/biom_to_stdBiom.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/biom_to_stdBiom.xml Tue Jan 08 08:36:26 2019 -0500 @@ -47,7 +47,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110
--- a/biom_to_tsv.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/biom_to_tsv.xml Tue Jan 08 08:36:26 2019 -0500 @@ -59,7 +59,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110
--- a/clustering.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/clustering.xml Tue Jan 08 08:36:26 2019 -0500 @@ -65,7 +65,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -141,7 +141,7 @@ Swarm use an iterative growth process and the use of sequence abundance values to delineate OTUs. -.. image:: static/frogs_images/FROGS_cluster_swarm.png +.. image:: static/images/frogs_images/FROGS_cluster_swarm.png :height: 223 :width: 666
--- a/clusters_stat.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/clusters_stat.xml Tue Jan 08 08:36:26 2019 -0500 @@ -43,7 +43,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -79,27 +79,27 @@ *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables - .. image:: static/frogs_images/FROGS_cluster_stat_clusterDistrib1.png + .. image:: static/images/frogs_images/FROGS_cluster_stat_clusterDistrib1.png :height: 426 :width: 520 - .. image:: static/frogs_images/FROGS_cluster_stat_clusterDistrib2.png + .. image:: static/images/frogs_images/FROGS_cluster_stat_clusterDistrib2.png :height: 300 :width: 460 *Sequences distributions* : describes the sequences distribution among clusters - .. image:: static/frogs_images/FROGS_cluster_stat_seq_dist.png + .. image:: static/images/frogs_images/FROGS_cluster_stat_seq_dist.png :height: 326 :width: 473 *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering <http://en.wikipedia.org/wiki/Hierarchical_clustering>`_ on samples abundance profile (distance method = `braycurtis <http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis>`_, linkage method = average) - .. image:: static/frogs_images/FROGS_cluster_stat_sample_dist1.png + .. image:: static/images/frogs_images/FROGS_cluster_stat_sample_dist1.png :height: 400 :width: 700 - .. image:: static/frogs_images/FROGS_cluster_stat_sample_dist2.png + .. image:: static/images/frogs_images/FROGS_cluster_stat_sample_dist2.png :height: 350 :width: 610
--- a/demultiplex.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/demultiplex.xml Tue Jan 08 08:36:26 2019 -0500 @@ -147,7 +147,7 @@ Example of barcode file: Here the sample is multiplexed by both fragment ends. -.. image:: static/frogs_images/demultiplex_barcode.png +.. image:: static/images/frogs_images/demultiplex_barcode.png :height: 18 :width: 286 @@ -166,7 +166,7 @@ Example of fastq read corresponding to the previous barcode file -.. image:: static/frogs_images/demultiplex_fastq_ex.png +.. image:: static/images/frogs_images/demultiplex_fastq_ex.png :height: 57 :width: 420
--- a/filters.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/filters.xml Tue Jan 08 08:36:26 2019 -0500 @@ -173,7 +173,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110
--- a/itsx.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/itsx.xml Tue Jan 08 08:36:26 2019 -0500 @@ -64,7 +64,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110
--- a/normalisation.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/normalisation.xml Tue Jan 08 08:36:26 2019 -0500 @@ -53,7 +53,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110
--- a/preprocess.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/preprocess.xml Tue Jan 08 08:36:26 2019 -0500 @@ -275,7 +275,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -337,13 +337,13 @@ This file reports the number of remaining sequences after each filter (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). - .. image:: static/frogs_images/FROGS_preprocess_summary_v3.png + .. image:: static/images/frogs_images/FROGS_preprocess_summary_v3.png :height: 850 :width: 831 It also presents the length distribution of the remaining full amplicon sequences. - .. image:: static/frogs_images/FROGS_preprocess_lengthsSamples_v3.png + .. image:: static/images/frogs_images/FROGS_preprocess_lengthsSamples_v3.png :height: 379 :width: 364 @@ -372,13 +372,13 @@ - **Case of a sequencing of overlapping sequences: case of 16S V3-V4 amplicon MiSeq sequencing** -.. image:: static/frogs_images/FROGS_preprocess_overlapped_sequence.png +.. image:: static/images/frogs_images/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/frogs_images/FROGS_preprocess_combined_sequence1.png +.. image:: static/images/frogs_images/FROGS_preprocess_combined_sequence1.png :height: 279 :width: 797 @@ -394,7 +394,7 @@ 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 600 bp. -.. image:: static/frogs_images/FROGS_preprocess_combined_sequence2.png +.. image:: static/images/frogs_images/FROGS_preprocess_combined_sequence2.png :height: 357 :width: 798 @@ -429,11 +429,11 @@ The two following images show two examples of perfect values fors sizes parameters. - .. image:: static/frogs_images/FROGS_preprocess_ampliconSize_unimodal_v3.png + .. image:: static/images/frogs_images/FROGS_preprocess_ampliconSize_unimodal_v3.png :height: 415 :width: 676 - .. image:: static/frogs_images/FROGS_preprocess_ampliconSize_multimodal_v3.png + .. image:: static/images/frogs_images/FROGS_preprocess_ampliconSize_multimodal_v3.png :height: 415 :width: 676
--- a/r_alpha_diversity.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/r_alpha_diversity.xml Tue Jan 08 08:36:26 2019 -0500 @@ -64,7 +64,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -92,22 +92,22 @@ **Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): the review of richness plots and rarefaction curves. -.. image:: static/frogs_images/phyloseq_plot_richness.png +.. image:: static/images/frogs_images/phyloseq_plot_richness.png :height: 400 :width: 525 -.. image:: static/frogs_images/phyloseq_plot_richness_box.png +.. image:: static/images/frogs_images/phyloseq_plot_richness_box.png :height: 400 :width: 499 -.. image:: static/frogs_images/phyloseq_rarefaction_curves.png +.. image:: static/images/frogs_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/frogs_images/phyloseq_alpha_diversity_table.png +.. image:: static/images/frogs_images/phyloseq_alpha_diversity_table.png .. class:: infomark page-header h2
--- a/r_beta_diversity.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/r_beta_diversity.xml Tue Jan 08 08:36:26 2019 -0500 @@ -80,7 +80,7 @@ <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -116,7 +116,7 @@ The review of beta diversity with heatmap plots: -.. image:: static/frogs_images/phyloseq_beta_diversity.png +.. image:: static/images/frogs_images/phyloseq_beta_diversity.png :height: 609 :width: 800 @@ -124,7 +124,7 @@ **beta diversity matrix** (format tabular): The distance matrix of beta diversity. - .. image:: static/frogs_images/phyloseq_beta_diversity_matrix.png + .. image:: static/images/frogs_images/phyloseq_beta_diversity_matrix.png .. class:: infomark page-header h2
--- a/r_clustering.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/r_clustering.xml Tue Jan 08 08:36:26 2019 -0500 @@ -63,7 +63,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -98,7 +98,7 @@ .. container:: row - .. image:: static/frogs_images/phyloseq_clustering_ward.png + .. image:: static/images/frogs_images/phyloseq_clustering_ward.png :height: 576 :width: 768
--- a/r_composition.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/r_composition.xml Tue Jan 08 08:36:26 2019 -0500 @@ -76,7 +76,7 @@ </test> </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -107,7 +107,7 @@ Bar plot of OTUs is colored with aggregated taxonomic level *i.e* "Phylum" : - .. image:: static/frogs_images/phyloseq_bar_plot.png + .. image:: static/images/frogs_images/phyloseq_bar_plot.png :height: 646 :width: 800 @@ -124,7 +124,7 @@ - Number of the most abundant taxa to keep: 5 - .. image:: static/frogs_images/phyloseq_composition_plot.png + .. image:: static/images/frogs_images/phyloseq_composition_plot.png :height: 644 :width: 800
--- a/r_import_data.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/r_import_data.xml Tue Jan 08 08:36:26 2019 -0500 @@ -67,7 +67,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -91,7 +91,7 @@ This file is the result of FROGS BIOM to std BIOM. The example of biom file: - .. image:: static/frogs_images/biomfile.png + .. image:: static/images/frogs_images/biomfile.png :height: 30 :width: 733 @@ -99,12 +99,12 @@ Newick file (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_) is the result of FROGS Tree: - .. image:: static/frogs_images/nwk_treefile.png + .. image:: static/images/frogs_images/nwk_treefile.png **Sample file**: The file contains the conditions of experiment with sample ID in the first column: - .. image:: static/frogs_images/phyloseq_samplefile.png + .. image:: static/images/frogs_images/phyloseq_samplefile.png :height: 115 :width: 369 @@ -114,7 +114,7 @@ **Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. - .. image:: static/frogs_images/phyloseq_import_data_html.png + .. image:: static/images/frogs_images/phyloseq_import_data_html.png **Data file** (format rdata): The informations of data in one phyloseq object.
--- a/r_manova.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/r_manova.xml Tue Jan 08 08:36:26 2019 -0500 @@ -62,7 +62,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -94,7 +94,7 @@ **html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The review of Manova test. -.. image:: static/frogs_images/phyloseq_manova.png +.. image:: static/images/frogs_images/phyloseq_manova.png .. class:: infomark page-header h2
--- a/r_structure.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/r_structure.xml Tue Jan 08 08:36:26 2019 -0500 @@ -70,7 +70,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -104,11 +104,11 @@ The review of data structure with an ordination plot and with an heatmap plot: -.. image:: static/frogs_images/phyloseq_plot_sample_ellipse.png +.. image:: static/images/frogs_images/phyloseq_plot_sample_ellipse.png :height: 343 :width: 450 -.. image:: static/frogs_images/phyloseq_plot_heatmap_red.png +.. image:: static/images/frogs_images/phyloseq_plot_heatmap_red.png :height: 343 :width: 450
--- a/remove_chimera.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/remove_chimera.xml Tue Jan 08 08:36:26 2019 -0500 @@ -75,7 +75,7 @@ </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110
--- a/tool-data/HVL_db.loc.sample Fri Dec 21 08:40:50 2018 -0500 +++ b/tool-data/HVL_db.loc.sample Tue Jan 08 08:36:26 2019 -0500 @@ -18,8 +18,7 @@ #inclusive amplicon sequence by selecting the smallest reference among multihit #You will need to create or download exact amplicon sequence reference fasta file #download link : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL_reference -#Finally you will need to create HVL_db.loc file similar to this one in your galaxy -#tool-data directory.The HVL_db.loc file has this format (longer white space characters are +#Finally you will need to create HVL_db.loc file similar to this one.The HVL_db.loc file has this format (longer white space characters are #TAB characters): # #<unique_database_name> <name> <file_path> @@ -29,4 +28,4 @@ #in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta #then the HVL_db.loc entry would look like this: # -#UNITE 7.1 ITS1 UNITE 7.1 ITS1 /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta +#UNITE_7.1_ITS1 UNITE 7.1 ITS1 <FROGS-wrappers>/test-data/databases/HVL_db_data/Unite_extract_ITS1.fasta
--- a/tool-data/frogs_db.loc.sample Fri Dec 21 08:40:50 2018 -0500 +++ b/tool-data/frogs_db.loc.sample Tue Jan 08 08:36:26 2019 -0500 @@ -18,18 +18,18 @@ #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 +#Finally you will need to create frogs_db.loc file similar to this one. +#The frogs_db.loc file has this format (longer white space characters are #TAB characters): # -#<unique_database_name> <file_path> +#<unique_database_name> <printed_database_name> <file_path> # -#First column will be the visible name in galaxy. +#Second column will be the visible name in galaxy. #So, for example, if you had 16S silva 128 indexed stored in #/galaxy_databanks/16S/silva_128/ #then the frogs_db.loc entry would look like this: # -#silva 128 16S /galaxy_databanks/16S/silva_128/silva_128_16S.fasta +#silva_128_16S silva 128 16S /galaxy_databanks/16S/silva_128/silva_128_16S.fasta # #and your /galaxy_databanks/16S/silva_128/ directory #would contain index files: @@ -47,6 +47,6 @@ #-rw-r--r-- 1 mbernard FROGS 964048 5 déc. 16:57 wordConditionalProbIndexArr.txt # # -#<name> <name> <file_path> +#<value> <name> <file_path> # -#db.fasta db.fasta /root/mydisk/FROGS-wrappers/test-data/db.fasta +#ITS_test ITS1 extract <FROGS-wrappers>/test-data/databases/frogs_db_data/ITS1.rdp.fasta
--- a/tool-data/phiX_db.loc.sample Fri Dec 21 08:40:50 2018 -0500 +++ b/tool-data/phiX_db.loc.sample Tue Jan 08 08:36:26 2019 -0500 @@ -16,14 +16,13 @@ # #This is a sample file that enables tools FROGS_filters to identify phix contaminant. You will #need to create or download Blast+ index. #download link : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants -#Finally you will need to create phiX_db.loc file similar to this one in your galaxy -#tool-data directory.The phiX_db.loc file has this format (longer white space characters are +#Finally you will need to create phiX_db.loc file similar to this one.The phiX_db.loc file has this format (longer white space characters are #TAB characters): # -#<contaminant_name> <name> <file_path> +#<unique_database_name> <printed_database_name> <file_path> # -#First column will be the visible name in galaxy. -#So, for example, if you had phix indexed stored in +#Second column will be the visible name in galaxy. +#So, for example, if you had phix Blast+ indexed stored in #/galaxy_databanks/phiX/ #then the phiX_db.loc entry would look like this: # @@ -37,4 +36,6 @@ #-rw-rwxr-- 1 gpascal FROGS 88 16 sept. 2015 phi.fa.nin #-rw-rwxr-- 1 gpascal FROGS 1348 16 sept. 2015 phi.fa.nsq # - +#<value> <name> <file_path> +# +#phiX phiX <FROGS-wrappers>/test-data/databases/phiX_db_data/phi.fa
--- a/tree.xml Fri Dec 21 08:40:50 2018 -0500 +++ b/tree.xml Tue Jan 08 08:36:26 2019 -0500 @@ -55,15 +55,14 @@ <has_text_matching expression="FROGS\sTree" /> <has_text_matching expression="abundance_removed.*:\s0" /> <has_text_matching expression="abundance_kept.*:\s175968" /> + <has_text_matching expression="otu_removed.*:\s0" /> <has_text_matching expression="otu_kept.*:\s142" /> - <has_text_matching expression="number_otu_all.*:\s142" /> - <has_text_matching expression="number_abundance_all.*:\s175968" /> </assert_contents> </output> </test> </tests> <help> -.. image:: static/frogs_images/FROGS_logo.png +.. image:: static/images/frogs_images/FROGS_logo.png :height: 144 :width: 110 @@ -87,7 +86,7 @@ The OTUs sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). Careful: FROGS Tree works only with less than 10 000 sequences! - .. image:: static/frogs_images/frogs_tree_otufile.png + .. image:: static/images/frogs_images/frogs_tree_otufile.png **OTUs biom file**: @@ -102,7 +101,7 @@ The phylogenetic tree in Newick format (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_). - .. image:: static/frogs_images/nwk_treefile.png + .. image:: static/images/frogs_images/nwk_treefile.png **Html file** (summary.html):