update version in xml to 3.2.3.1, README and RELEASE_NOTE

README.md

@@ -6,7 +6,7 @@
 
 Visit our web site : http://frogs.toulouse.inrae.fr/
 
-[![Release](https://img.shields.io/badge/release-3.2.3-blue.svg)![Date](https://img.shields.io/badge/date-Jun%202021-red.svg)](https://github.com/geraldinepascal/FROGS-wrappers/releases)[<img src="https://www.podcastscience.fm/wp-content/uploads/2017/12/deezer.png" width="5%" style="display: block; margin: auto;"/>](https://www.deezer.com/fr/playlist/5233843102?utm_source=deezer&utm_content=playlist-5233843102&utm_term=18632989_1545296531&utm_medium=web)
+[![Release](https://img.shields.io/badge/release-3.2.3.1-blue.svg)![Date](https://img.shields.io/badge/date-Jun%202021-red.svg)](https://github.com/geraldinepascal/FROGS-wrappers/releases)[<img src="https://www.podcastscience.fm/wp-content/uploads/2017/12/deezer.png" width="5%" style="display: block; margin: auto;"/>](https://www.deezer.com/fr/playlist/5233843102?utm_source=deezer&utm_content=playlist-5233843102&utm_term=18632989_1545296531&utm_medium=web)
 
 
 
@@ -50,41 +50,41 @@ The 25 FROGS tools will be in random order in your tools panel. We propose to co
 We suppose that you installed FROGS in a specific section named `FROGS`. 
 
 ```
-<section id="FROGS" name="FROGS" version="">
-
-    <label id="FROGS_OTU_toolshed_3.2.3" text="OTUs reconstruction" version="" />
-
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_demultiplex/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clustering/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.3" />    
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_postprocess/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_stdBiom/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_tsv/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_tsv_to_biom/3.2.3" />
-
-    <label id="FROGSSTAT_Phyloseq_toolshed_3.2.3" text="OTUs structure and composition analysis" version="" />
+<section id="FROGS_3.2.3.1" name="FROGS" version="">
+
+    <label id="FROGS_OTU_toolshed_3.2.3.1" text="OTUs reconstruction" version="" />
+
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_demultiplex/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clustering/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.3.1" />    
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_postprocess/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_stdBiom/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_tsv/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_tsv_to_biom/3.2.3.1" />
+
+    <label id="FROGSSTAT_Phyloseq_toolshed_3.2.3.1" text="OTUs structure and composition analysis" version="" />
     
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Import_Data/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Composition_Visualisation/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Alpha_Diversity/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Beta_Diversity/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Sample_Clustering/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Structure_Visualisation/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.2.3" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Import_Data/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Composition_Visualisation/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Alpha_Diversity/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Beta_Diversity/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Sample_Clustering/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Structure_Visualisation/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.2.3.1" />
     
-    <label id="FROGSSTAT_DESeq_toolshed_3.2.3" text="Differential abundance analysis" version="" />
+    <label id="FROGSSTAT_DESeq_toolshed_3.2.3.1" text="Differential abundance analysis" version="" />
     
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Preprocess/3.2.3" />
-    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Visualisation/3.2.3" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Preprocess/3.2.3.1" />
+    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Visualisation/3.2.3.1" />
 </section>
 ```
 

RELEASE_NOTE.md

@@ -1,3 +1,13 @@
+# v3.2.3.1 [2021-06]
+
+This version still refers to FROGS_3.2.3 suit.
+
+## Modifications:
+
+* DESeq2 visualisation : correctly use the reference modality (in the tool conf pannel) as the expected modality2 in the deseq2_visualisation.py command line. Results were correct in the previous version but the reference condition was not the one precised by the user.
+
+
+
 # v3.2.3 [2021-06]
 
 ## Modifications:

affiliation_OTU.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="3.2.3">
+<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="3.2.3.">
   <description>Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</description>
   <requirements>
         <requirement type="package" version="3.2.3">frogs</requirement>

affiliation_filters.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_affiliation_filters" name="FROGS Affiliation Filters" version="3.2.3">
+<tool id="FROGS_affiliation_filters" name="FROGS Affiliation Filters" version="3.2.3.1">
 	<description>Filters OTUs on several affiliation criteria.</description>
         <requirements>
             <requirement type="package" version="3.2.3">frogs</requirement>

affiliation_postprocess.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_affiliation_postprocess" name="FROGS Affiliation postprocess" version="3.2.3">
+<tool id="FROGS_affiliation_postprocess" name="FROGS Affiliation postprocess" version="3.2.3.1">
 	<description>Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics</description>
  	<requirements>
     	<requirement type="package" version="3.2.3">frogs</requirement>

affiliations_stat.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="3.2.3">
+<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="3.2.3.1">
 	<description>Process some metrics on taxonomies.</description>
         <requirements>
                 <requirement type="package" version="3.2.3">frogs</requirement>

biom_to_stdBiom.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="3.2.3">
+<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="3.2.3.1">
 	<description>Converts a FROGS BIOM in fully compatible BIOM.</description>
         <requirements>
             <requirement type="package" version="3.2.3">frogs</requirement>

biom_to_tsv.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_biom_to_tsv" name="FROGS BIOM to TSV" version="3.2.3">
+<tool id="FROGS_biom_to_tsv" name="FROGS BIOM to TSV" version="3.2.3.1">
 	<description>Converts a BIOM file in TSV file.</description>
         <requirements>
             <requirement type="package" version="3.2.3">frogs</requirement>

clustering.xml

@@ -15,7 +15,7 @@
 # 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_clustering" name="FROGS Clustering swarm" version="3.2.3">
+<tool id="FROGS_clustering" name="FROGS Clustering swarm" version="3.2.3.1">
     <description>Single-linkage clustering on sequences</description>
         <requirements>
                 <requirement type="package" version="3.2.3">frogs</requirement>

clusters_stat.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_clusters_stat" name="FROGS Clusters stat" version="3.2.3">
+<tool id="FROGS_clusters_stat" name="FROGS Clusters stat" version="3.2.3.1">
 	<description>Process some metrics on clusters.</description>
         <requirements>
                 <requirement type="package" version="3.2.3">frogs</requirement>

demultiplex.xml

@@ -15,7 +15,7 @@
 # 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_demultiplex" name="FROGS Demultiplex reads" version="3.2.3">
+<tool id="FROGS_demultiplex" name="FROGS Demultiplex reads" version="3.2.3.1">
 	<description>Attribute reads to samples in function of inner barcode.</description>
         <requirements>
             <requirement type="binary">perl</requirement>

deseq2_preprocess.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool name="FROGSSTAT DESeq2 Preprocess" id="FROGSSTAT_DESeq2_Preprocess" version="3.2.3">
+<tool name="FROGSSTAT DESeq2 Preprocess" id="FROGSSTAT_DESeq2_Preprocess" version="3.2.3.1">
   <description>import a Phyloseq object and prepare it for DESeq2 differential abundance analysis </description>
   <requirements>
       <requirement type="package" version="3.2.3">frogs</requirement>

deseq2_visualisation.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool name="FROGSTAT Deseq2 Visualisation" id="FROGSSTAT_DESeq2_Visualisation" version="3.2.3">
+<tool name="FROGSTAT Deseq2 Visualisation" id="FROGSSTAT_DESeq2_Visualisation" version="3.2.3.1">
     <description>to extract and visualise differentially abundant OTUs</description>
     <requirements>
         <requirement type="package" version="3.2.3">frogs</requirement>

itsx.xml

@@ -15,7 +15,7 @@
 # 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_itsx" name="FROGS ITSx" version="3.2.3">
+<tool id="FROGS_itsx" name="FROGS ITSx" version="3.2.3.1">
 	<description>Extract the highly variable ITS1 and ITS2 subregions from ITS sequences.</description>
     <requirements>
         <requirement type="package" version="3.2.3">frogs</requirement>

normalisation.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="3.2.3">
+<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="3.2.3.1">
         <description>Normalise OTUs abundance.</description>
         <requirements>
                 <requirement type="package" version="3.2.3">frogs</requirement>

otu_filters.xml

@@ -15,7 +15,7 @@
 # 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_OTU_filters" name="FROGS OTU Filters" version="3.2.3">
+<tool id="FROGS_OTU_filters" name="FROGS OTU Filters" version="3.2.3.1">
 	<description>Filters OTUs on several criteria.</description>
         <requirements>
                 <requirement type="package" version="3.2.3">frogs</requirement>

phyloseq_alpha_diversity.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.2.3">
+<tool name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.2.3.1">
 	<description>with richness plot</description>
         <requirements>
             <requirement type="package" version="3.2.">frogs</requirement>

phyloseq_beta_diversity.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool name="FROGSSTAT Phyloseq Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="3.2.3">
+<tool name="FROGSSTAT Phyloseq Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="3.2.3.1">
 	<description>distance matrix</description>
         <requirements>
             <requirement type="package" version="3.2.3">frogs</requirement>

phyloseq_clustering.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="3.2.3">
+<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="3.2.3.1">
 	<description>of samples using different linkage methods</description>
         <requirements>
             <requirement type="package" version="3.2.3">frogs</requirement>

phyloseq_composition.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="3.2.3">
+<tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="3.2.3.1">
     <description>with bar plot and composition plot</description>
     <requirements>
         <requirement type="package" version="3.2.3">frogs</requirement>

phyloseq_import_data.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.2.3">
+<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.2.3.1">
     <description>from 3 files: biomfile, samplefile, treefile </description>
         <requirements>
             <requirement type="package" version="3.2.3">frogs</requirement>

phyloseq_manova.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="3.2.3">
+<tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="3.2.3.1">
         <description>perform Multivariate Analysis of Variance (MANOVA)</description>
         <requirements>
             <requirement type="package" version="3.2.3">frogs</requirement>

phyloseq_structure.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool name="FROGSSTAT Phyloseq Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="3.2.3">
+<tool name="FROGSSTAT Phyloseq Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="3.2.3.1">
 	<description>with heatmap plot and ordination plot</description>
     <requirements>
         <requirement type="package" version="3.2.3">frogs</requirement>

preprocess.xml

@@ -15,7 +15,7 @@
 # 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_preprocess" name="FROGS Pre-process" version="3.2.3">
+<tool id="FROGS_preprocess" name="FROGS Pre-process" version="3.2.3.1">
 	<description>merging, denoising and dereplication.</description>
         <requirements>
                 <requirement type="package" version="3.2.3">frogs</requirement>

remove_chimera.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="3.2.3">
+<tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="3.2.3.1">
 	<description>Remove PCR chimera in each sample.</description>
         <requirements>
             <requirement type="package" version="3.2.3">frogs</requirement>

tree.xml

@@ -15,7 +15,7 @@
 # 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="3.2.3">
+<tool id="FROGS_Tree" name="FROGS Tree" version="3.2.3.1">
     <description>Reconstruction of phylogenetic tree </description>
     <requirements>
         <requirement type="package" version="3.2.3">frogs</requirement>

tsv_to_biom.xml

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="3.2.3">
+<tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="3.2.3.1">
 	<description>Converts a TSV file in a BIOM file.</description>
         <requirements>
             <requirement type="package" version="3.2.3">frogs</requirement>