Mercurial > repos > oinizan > frogs_2_0_0
changeset 20:6d15880bd05f draft
planemo upload commit feaf3a90fd5f2fc9a9571ecb7166acd92fade57a-dirty
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--- a/affiliation_OTU.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/affiliation_OTU.xml Tue Oct 23 11:17:08 2018 -0400 @@ -67,7 +67,7 @@ <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110 @@ -107,7 +107,7 @@ 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_path}/images/tools/frogs/FROGS_affiliation_summary.png + .. image:: static/images/FROGS_affiliation_summary.png :height: 800 :width: 600
--- a/affiliations_stat.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/affiliations_stat.xml Tue Oct 23 11:17:08 2018 -0400 @@ -94,7 +94,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/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_path}/images/tools/frogs/FROGS_affiliation_stat_taxonomies.png + .. image:: static/images/FROGS_affiliation_stat_taxonomies.png :height: 380 :width: 650 - .. image:: ${static_path}/images/tools/frogs/FROGS_affiliation_stat_rarefaction.png + .. image:: static/images/FROGS_affiliation_stat_rarefaction.png :height: 380 :width: 550 - .. image:: ${static_path}/images/tools/frogs/FROGS_affiliation_stat_sunburst.png + .. image:: static/images/FROGS_affiliation_stat_sunburst.png :height: 380 :width: 430 -Bootstrap distribution: display for affiliation methods with bootstrap the bootstrap on each taxonomic rank - .. image:: ${static_path}/images/tools/frogs/FROGS_affiliation_stat_bootstrap.png + .. image:: static/images/FROGS_affiliation_stat_bootstrap.png :height: 380 :width: 650 -Alignment distribution: display for affiliation methods with alignment the distribution of identity/covrage - .. image:: ${static_path}/images/tools/frogs/FROGS_affiliation_stat_alignment.png + .. image:: static/images/FROGS_affiliation_stat_alignment.png :height: 380 :width: 650
--- a/biom_to_stdBiom.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/biom_to_stdBiom.xml Tue Oct 23 11:17:08 2018 -0400 @@ -47,7 +47,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110
--- a/biom_to_tsv.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/biom_to_tsv.xml Tue Oct 23 11:17:08 2018 -0400 @@ -59,7 +59,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110
--- a/clustering.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/clustering.xml Tue Oct 23 11:17:08 2018 -0400 @@ -66,7 +66,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110 @@ -142,7 +142,7 @@ Swarm use an iterative growth process and the use of sequence abundance values to delineate OTUs. -.. image:: ${static_path}/images/tools/frogs/FROGS_cluster_swarm.png +.. image:: static/images/FROGS_cluster_swarm.png :height: 223 :width: 666
--- a/clusters_stat.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/clusters_stat.xml Tue Oct 23 11:17:08 2018 -0400 @@ -43,7 +43,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/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_path}/images/tools/frogs/FROGS_cluster_stat_clusterDistrib1.png + .. image:: static/images/FROGS_cluster_stat_clusterDistrib1.png :height: 426 :width: 520 - .. image:: ${static_path}/images/tools/frogs/FROGS_cluster_stat_clusterDistrib2.png + .. image:: static/images/FROGS_cluster_stat_clusterDistrib2.png :height: 300 :width: 460 *Sequences distributions* : describes the sequences distribution among clusters - .. image:: ${static_path}/images/tools/frogs/FROGS_cluster_stat_seq_dist.png + .. image:: static/images/FROGS_cluster_stat_seq_dist.png :height: 326 :width: 473 *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering <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_path}/images/tools/frogs/FROGS_cluster_stat_sample_dist1.png + .. image:: static/images/FROGS_cluster_stat_sample_dist1.png :height: 400 :width: 700 - .. image:: ${static_path}/images/tools/frogs/FROGS_cluster_stat_sample_dist2.png + .. image:: static/images/FROGS_cluster_stat_sample_dist2.png :height: 350 :width: 610
--- a/demultiplex.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/demultiplex.xml Tue Oct 23 11:17:08 2018 -0400 @@ -147,7 +147,7 @@ Example of barcode file: Here the sample is multiplexed by both fragment ends. -.. image:: ${static_path}/images/tools/frogs/demultiplex_barcode.png +.. image:: static/images/demultiplex_barcode.png :height: 18 :width: 286 @@ -166,7 +166,7 @@ Example of fastq read corresponding to the previous barcode file -.. image:: ${static_path}/images/tools/frogs/demultiplex_fastq_ex.png +.. image:: static/images/demultiplex_fastq_ex.png :height: 57 :width: 420
--- a/filters.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/filters.xml Tue Oct 23 11:17:08 2018 -0400 @@ -161,7 +161,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110
--- a/normalisation.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/normalisation.xml Tue Oct 23 11:17:08 2018 -0400 @@ -53,7 +53,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110
--- a/preprocess.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/preprocess.xml Tue Oct 23 11:17:08 2018 -0400 @@ -232,7 +232,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110 @@ -295,13 +295,13 @@ This file reports the number of remaining sequences after each filter (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). - .. image:: ${static_path}/images/tools/frogs/FROGS_preprocess_summary.png + .. image:: static/images/FROGS_preprocess_summary.png :height: 355 :width: 676 It also presents the length distribution of the remaining sequences. - .. image:: ${static_path}/images/tools/frogs/FROGS_preprocess_lengthsSamples.png + .. image:: static/images/FROGS_preprocess_lengthsSamples.png :height: 350 :width: 676 @@ -349,11 +349,11 @@ The two following images show two examples of perfect values fors sizes parameters. - .. image:: ${static_path}/images/tools/frogs/FROGS_preprocess_ampliconSize_unimodal.png + .. image:: static/images/FROGS_preprocess_ampliconSize_unimodal.png :height: 415 :width: 676 - .. image:: ${static_path}/images/tools/frogs/FROGS_preprocess_ampliconSize_multimodal.png + .. image:: static/images/FROGS_preprocess_ampliconSize_multimodal.png :height: 415 :width: 676
--- a/r_alpha_diversity.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/r_alpha_diversity.xml Tue Oct 23 11:17:08 2018 -0400 @@ -64,7 +64,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/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_path}/images/tools/frogs/phyloseq_plot_richness.png +.. image:: static/images/phyloseq_plot_richness.png :height: 400 :width: 525 -.. image:: ${static_path}/images/tools/frogs/phyloseq_plot_richness_box.png +.. image:: static/images/phyloseq_plot_richness_box.png :height: 400 :width: 499 -.. image:: ${static_path}/images/tools/frogs/phyloseq_rarefaction_curves.png +.. image:: static/images/phyloseq_rarefaction_curves.png :height: 400 :width: 498 **Alpha diversity table** (alpha_diversity.tsv): The data file containing table of alpha diversity indices. -.. image:: ${static_path}/images/tools/frogs/phyloseq_alpha_diversity_table.png +.. image:: static/images/phyloseq_alpha_diversity_table.png .. class:: infomark page-header h2
--- a/r_beta_diversity.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/r_beta_diversity.xml Tue Oct 23 11:17:08 2018 -0400 @@ -80,7 +80,7 @@ <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110 @@ -116,7 +116,7 @@ The review of beta diversity with heatmap plots: -.. image:: ${static_path}/images/tools/frogs/phyloseq_beta_diversity.png +.. image:: static/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_path}/images/tools/frogs/phyloseq_beta_diversity_matrix.png + .. image:: static/images/phyloseq_beta_diversity_matrix.png .. class:: infomark page-header h2
--- a/r_clustering.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/r_clustering.xml Tue Oct 23 11:17:08 2018 -0400 @@ -63,7 +63,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110 @@ -98,7 +98,7 @@ .. container:: row - .. image:: ${static_path}/images/tools/frogs/phyloseq_clustering_ward.png + .. image:: static/images/phyloseq_clustering_ward.png :height: 576 :width: 768
--- a/r_composition.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/r_composition.xml Tue Oct 23 11:17:08 2018 -0400 @@ -76,7 +76,7 @@ </test> </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/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_path}/images/tools/frogs/phyloseq_bar_plot.png + .. image:: static/images/phyloseq_bar_plot.png :height: 646 :width: 800 @@ -124,7 +124,7 @@ - Number of the most abundant taxa to keep: 5 - .. image:: ${static_path}/images/tools/frogs/phyloseq_composition_plot.png + .. image:: static/images/phyloseq_composition_plot.png :height: 644 :width: 800
--- a/r_import_data.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/r_import_data.xml Tue Oct 23 11:17:08 2018 -0400 @@ -67,7 +67,7 @@ <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/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_path}/images/tools/frogs/biomfile.png + .. image:: static/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_path}/images/tools/frogs/nwk_treefile.png + .. image:: static/images/nwk_treefile.png **Sample file**: The file contains the conditions of experiment with sample ID in the first column: - .. image:: ${static_path}/images/tools/frogs/phyloseq_samplefile.png + .. image:: static/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_path}/images/tools/frogs/phyloseq_import_data_html.png + .. image:: static/images/phyloseq_import_data_html.png **Data file** (format rdata): The informations of data in one phyloseq object.
--- a/r_manova.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/r_manova.xml Tue Oct 23 11:17:08 2018 -0400 @@ -62,7 +62,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/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_path}/images/tools/frogs/phyloseq_manova.png +.. image:: static/images/phyloseq_manova.png .. class:: infomark page-header h2
--- a/r_structure.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/r_structure.xml Tue Oct 23 11:17:08 2018 -0400 @@ -70,7 +70,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/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_path}/images/tools/frogs/phyloseq_plot_sample_ellipse.png +.. image:: static/images/phyloseq_plot_sample_ellipse.png :height: 343 :width: 450 -.. image:: ${static_path}/images/tools/frogs/phyloseq_plot_heatmap_red.png +.. image:: static/images/phyloseq_plot_heatmap_red.png :height: 343 :width: 450
--- a/remove_chimera.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/remove_chimera.xml Tue Oct 23 11:17:08 2018 -0400 @@ -80,7 +80,7 @@ </tests> <help> -.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tree.new Tue Oct 23 11:17:08 2018 -0400 @@ -0,0 +1,137 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_Tree" name="FROGS Tree" version="1.0.0"> + <description>Reconstruction of phylogenetic tree </description> + <requirements> + <requirement type="package" version="2.0.1">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>tree.py + --input-otu $input_otu + #if $template.fileTemplate + --template-pynast ${template.template_pynast} + #end if + --biomfile $biomfile + --nb-cpus $nb_cpus + --out-tree $out_tree + --html $html + </command> + <inputs> + <!-- Files --> + <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <conditional name="template"> + <param name="fileTemplate" type="boolean" label="Do you have the template alignment file ?" help="If yes, precise the template multi-alignment file." optional="false" /> + <when value="false"></when> + <when value="true"> + <param format="fasta" name="template_pynast" type="data" label="Template alignment file" help="Template multi-alignment file (format: fasta)." optional="false" /> + </when> + </conditional> + <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameter --> + <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" /> + </inputs> + <outputs> + <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/> + <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/> + </outputs> + <tests> + <test> + <param name="input_otu" value="references/04-filters.fasta"/> + <conditional name="template"> + <param name="fileTemplate" value="false"/> + </conditional> + <param name="biomfile" value="references/04-affiliation.biom"/> + <output name="out_tree" value="references/10b-tree.nwk"/> + </test> + </tests> + <help> +.. image:: static/images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Creation of a multiple alignment of OTUs with `PyNAST <http://biocore.github.io/pynast/>`_ (if you have an alignment template file) or with `Mafft <http://mafft.cbrc.jp/alignment/software>`_ (if you have not an aligned template file). +And creation of a phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**OTUs fasta file**: + +The OTUs sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). +Careful: FROGS Tree works only with less than 10 000 sequences! + + .. image:: static/images/frogs_tree_otufile.png + +**(optional) Template alignment file**: + +A pre-aligned database of sequences (the “template” sequence) (format `multiple alignement <https://en.wikipedia.org/wiki/Multiple_sequence_alignment>`_). + + .. image:: static/images/frogs_tree_templatefile.png + +**OTUs biom file**: + +The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). +This file can be obtained in particular with the FROGS pipeline. + +.. class:: h3 + +Outputs + +**Newick file** (tree.nwk): + +The phylogenetic tree in Newick format (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_). + + .. image:: static/images/nwk_treefile.png + +**Html file** (summary.html): + +The summary file describing which OTUs are contained or not in the phylogenetic tree (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + </help> + <citations> + <citation type="doi">10.7287/peerj.preprints.386v1</citation> + </citations> +</tool>
--- a/tree.xml Tue Oct 23 10:48:57 2018 -0400 +++ b/tree.xml Tue Oct 23 11:17:08 2018 -0400 @@ -67,7 +67,7 @@ </test> </tests> <help> -.. image:: img/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110 @@ -91,13 +91,13 @@ 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_path}/images/tools/frogs/frogs_tree_otufile.png + .. image:: static/images/frogs_tree_otufile.png **(optional) Template alignment file**: A pre-aligned database of sequences (the “template” sequence) (format `multiple alignement <https://en.wikipedia.org/wiki/Multiple_sequence_alignment>`_). - .. image:: ${static_path}/images/tools/frogs/frogs_tree_templatefile.png + .. image:: static/images/frogs_tree_templatefile.png **OTUs biom file**: @@ -112,7 +112,7 @@ The phylogenetic tree in Newick format (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_). - .. image:: ${static_path}/images/tools/frogs/nwk_treefile.png + .. image:: static/images/nwk_treefile.png **Html file** (summary.html):