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changeset 12:613b7551f28b draft

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0c3aee486a7e9b369ad4c037c2f588236acad117-dirty
author oinizan
date Mon, 16 May 2022 14:19:09 +0000
parents ab9e3c8ab443
children 4dd70eba5941
files affiliation_filters.xml affiliation_postprocess.xml biom_to_stdBiom.xml biom_to_tsv.xml clustering.xml clusters_stat.xml demultiplex.xml frogsfunc_copynumbers.xml frogsfunc_functions.xml frogsfunc_pathways.xml frogsfunc_placeseqs.xml normalisation.xml otu_filters.xml phyloseq_alpha_diversity.xml phyloseq_beta_diversity.xml phyloseq_clustering.xml phyloseq_import_data.xml phyloseq_manova.xml phyloseq_structure.xml preprocess.xml remove_chimera.xml tsv_to_biom.xml
diffstat 22 files changed, 59 insertions(+), 56 deletions(-) [+]
line wrap: on
line diff
--- a/affiliation_filters.xml	Fri May 13 15:33:27 2022 +0000
+++ b/affiliation_filters.xml	Mon May 16 14:19:09 2022 +0000
@@ -99,8 +99,8 @@
         <data format="fasta" name="output_fasta" label="${tool.name}: affiFilter_sequences.fasta" from_work_dir="affiFilter_sequences.fasta">
             <filter> mode == 'delete'</filter>
         </data>
-        <data format="tabular" name="output_impacted" label="${tool.name}: impacted_OTU.tsv" from_work_dir="impacted.tsv"/>
-        <data format="tabular" name="output_multihit" label="${tool.name}: impacted_OTU.multi-affiliations.tsv" from_work_dir="impacted.multihit.tsv"/>
+        <data format="tsv" name="output_impacted" label="${tool.name}: impacted_OTU.tsv" from_work_dir="impacted.tsv"/>
+        <data format="tsv" name="output_multihit" label="${tool.name}: impacted_OTU.multi-affiliations.tsv" from_work_dir="impacted.multihit.tsv"/>
         <data format="html" name="output_summary" label="${tool.name}: report.html" from_work_dir="report.html"/>
     </outputs>
     <tests>
--- a/affiliation_postprocess.xml	Fri May 13 15:33:27 2022 +0000
+++ b/affiliation_postprocess.xml	Mon May 16 14:19:09 2022 +0000
@@ -1,5 +1,5 @@
 <tool id="FROGS_affiliation_postprocess" name="FROGS Affiliation postprocess" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">
-    <description>Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics</description>
+    <description>Aggregates OTUs based on alignment metrics</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -39,7 +39,7 @@
     <outputs>
         <data format="biom1" name="biom_out" label="${tool.name}: affiliation_abundance.biom" from_work_dir="affiliation.biom"/>
         <data format="fasta" name="fasta_out" label="${tool.name}: sequences.fasta" from_work_dir="sequences.fasta"/>
-        <data format="tabular" name="compo_out" label="${tool.name}: OTU_aggregation_composition.txt" from_work_dir="aggregation_composition.txt"/>
+        <data format="tsv" name="compo_out" label="${tool.name}: OTU_aggregation_composition.txt" from_work_dir="aggregation_composition.txt"/>
     </outputs>
     <tests>
         <test>
@@ -106,7 +106,7 @@
 
 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.
+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 shortest length. The aim is to resolve ambiguities due to potential inclusive sequences such as ITS.
 
 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.
--- a/biom_to_stdBiom.xml	Fri May 13 15:33:27 2022 +0000
+++ b/biom_to_stdBiom.xml	Mon May 16 14:19:09 2022 +0000
@@ -16,7 +16,7 @@
 	</inputs>
 	<outputs>
 		<data format="biom1" name="output_biom" label="${tool.name}: abundance.standard.biom" from_work_dir="abundance.biom"/>
-		<data format="tabular" name="output_blast_details" label="${tool.name}: all_blast_details.tsv" from_work_dir="blast_details.tsv" />
+		<data format="tsv" name="output_blast_details" label="${tool.name}: all_blast_details.tsv" from_work_dir="blast_details.tsv" />
 	</outputs>
 	<tests>
 		<test>
@@ -35,7 +35,7 @@
 
 Converts a BIOM generated by FROGS in generic BIOM.
 
-The detailed blast affiliations can trigger problem with tools like Qiime. This tool extracts the blast details in a second file and writes a BIOM usable in every tools using BIOM.
+The detailed blast affiliations can trigger problems with tools like Qiime. This tool extracts the blast details in a second file and writes a BIOM usable in every tools using BIOM.
 
 .. class:: h3
 
--- a/biom_to_tsv.xml	Fri May 13 15:33:27 2022 +0000
+++ b/biom_to_tsv.xml	Mon May 16 14:19:09 2022 +0000
@@ -23,8 +23,8 @@
 		<param name="extract_multi_align" type="boolean" label="Extract multi-alignments" help="If you have used FROGS affiliation on your data, you can extract information about multiple alignements in a second TSV." checked="true"/>
 	</inputs>
 	<outputs>
-		<data format="tabular" name="tsv_file" label="${tool.name}: abundance.tsv" from_work_dir="abundance.tsv"/>
-		<data format="tabular" name="multi_affi_file" label="${tool.name}: multi-affiliations.tsv" from_work_dir="multi_hits.tsv" >
+		<data format="tsv" name="tsv_file" label="${tool.name}: abundance.tsv" from_work_dir="abundance.tsv"/>
+		<data format="tsv" name="multi_affi_file" label="${tool.name}: multi-affiliations.tsv" from_work_dir="multi_hits.tsv" >
 			<filter>extract_multi_align</filter>
 		</data>
 	</outputs>
@@ -78,7 +78,7 @@
 
 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.
+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.
 
 
 .. class:: infomark page-header h2
--- a/clustering.xml	Fri May 13 15:33:27 2022 +0000
+++ b/clustering.xml	Mon May 16 14:19:09 2022 +0000
@@ -26,7 +26,7 @@
     <inputs>
         <!-- Files -->
         <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The dereplicated sequences file (format: FASTA)" />
-        <param format="tabular" name="count_file" type="data" label="Count file" help="It contains the count by sample for each sequence (format: TSV)"/>
+        <param format="tabular,tsv" 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="The denoising step before a d3 clustering is no longer recommended since FROGS 3.2, but you can still choose it.">
@@ -46,7 +46,7 @@
     <outputs>
         <data format="fasta" name="seed_file" label="${tool.name}: seed_sequences.fasta" from_work_dir="seeds.fasta" />
         <data format="biom1" name="abundance_biom" label="${tool.name}: clustering_abundance.biom" from_work_dir="abundance.biom" />
-        <data format="tabular" name="swarms_composition" label="${tool.name}: swarms_composition.tsv" from_work_dir="swarms.tsv" />
+        <data format="tsv" name="swarms_composition" label="${tool.name}: swarms_composition.tsv" from_work_dir="swarms.tsv" />
     </outputs>
     <tests>
         <test>
--- a/clusters_stat.xml	Fri May 13 15:33:27 2022 +0000
+++ b/clusters_stat.xml	Mon May 16 14:19:09 2022 +0000
@@ -52,7 +52,7 @@
 
 **Report file** (report.html):
 
- *Cluster distribution* : describes the sizes distribution of all clusters thank to boxplot and tables
+ *Cluster distribution* : describes the sizes distribution of all clusters thanks to boxplots and tables
 
  .. image:: FROGS_cluster_stat_clusterDistrib1.png
     :height: 1180
--- a/demultiplex.xml	Fri May 13 15:33:27 2022 +0000
+++ b/demultiplex.xml	Mon May 16 14:19:09 2022 +0000
@@ -21,7 +21,7 @@
 	</command>
 	<inputs>
 		<!-- Input file -->
-		<param format="tabular" argument="--input_barcode" type="data" label="Barcode file" help="This file describes barcodes and samples (one line by sample tabulated separated from barcode sequence(s)). See Help section" />
+		<param format="tabular,tsv" argument="--input_barcode" type="data" label="Barcode file" help="This file describes barcodes and samples (one line by sample tabulated separated from barcode sequence(s)). See Help section" />
 
 		<conditional name="fastq_input">
 	      	<param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single-end data">
@@ -47,7 +47,7 @@
 	<outputs>
 		<data name="demultiplexed_archive" format="tar" label="${tool.name}: demultiplexed.tar.gz" from_work_dir="demultiplexed.tar.gz"/>
 		<data name="undemultiplexed_archive" format="tar" label="${tool.name}: undemultiplexed.tar.gz" from_work_dir="undemultiplexed.tar.gz"/>
-		<data name="summary" format="tabular" label="${tool.name}: report" from_work_dir="report.tsv"/>
+		<data name="summary" format="tsv" label="${tool.name}: report" from_work_dir="report.tsv"/>
 	</outputs>
     <tests>
         <test>
--- a/frogsfunc_copynumbers.xml	Fri May 13 15:33:27 2022 +0000
+++ b/frogsfunc_copynumbers.xml	Mon May 16 14:19:09 2022 +0000
@@ -16,7 +16,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
 <tool id="FROGSFUNC_step2_copynumbers" name="FROGSFUNC_step2_copynumbers" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-	<description>Hidden-state prediction of gene families/functions. This script predicts the missing genome for each OTU sequence, i.e. it predicts the copy number of functions (and 16S/ITS/18S copy number) for each OTU sequence. </description>
+	<description>Predicts number of marker and function copy number in each OTU. </description>
 
 	<macros>
         <import>macros.xml</import>
@@ -46,9 +46,8 @@
 	</command> 
 	<inputs>
 	    <!-- Input files -->
-        <param argument="--input-biom" format="biom1" name="input_biom" type="data" label="Biom file" help="The abundance file to analyse i.e. FROGSFUNC_step1_placeseqs tool output file (frogsfunc_placeseqs.biom)." optional="false" />
-	    <param argument="--tree" format="nhx" name="input_tree" type="data" label="Tree file" help="The file contains the tree information from FROGSFUNC_step1_placeseqs tool (frogsfunc_placeseqs_tree.nwk)."	optional="false" />
-
+        <param argument="--input-biom" format="biom1" name="input_biom" type="data" label="Biom file" help="The abundance file to analyse i.e. FROGSFUNC_step1_placeseqs tool output file (frogsfunc_placeseqs.biom)." optional="false"/>
+	    <param argument="--tree" format="nhx" name="input_tree" type="data" label="Tree file" help="The file contains the tree information from FROGSFUNC_step1_placeseqs tool (frogsfunc_placeseqs_tree.nwk)." optional="false"/>
 	   	<!-- Parameters-->
 	    <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio">
             <options from_data_table="frogs_picrust2_marker_table">
@@ -69,7 +68,6 @@
  		<validator type="expression" message="'EC' is the default database used by PICRUSt2. 'EC' or 'KO' must be at least selected. Other tables are optionnal">"EC" in value or "KO" in value</validator>               
             </options>
         </param>
-
 		<param argument="--hsp-method" name="hsp_method" type="select" label="HSP method" help='Hidden-state prediction method to use: maximum parsimony (mp), empirical probabilities (emp_prob), continuous traits prediction using subtree averaging (subtree_average), continuous traits prediction with phylogentic independent contrast (pic), continuous traits reconstruction using squared-change parsimony (scp) (default: mp).' multiple="false" display="radio">
             <option value="mp">mp</option>
             <option value="emp_prob">emp_prob</option>
@@ -80,8 +78,8 @@
 	</inputs>
 	<outputs>
         <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
-		<data format="tabular" name="out_function" label="${tool.name}: frogsfunc_copynumbers_predicted_functions.tsv" from_work_dir="frogsfunc_copynumbers_predicted_functions.tsv"/>
-		<data format="tabular" name="out_marker" label="${tool.name}: frogsfunc_copynumbers_marker.tsv" from_work_dir="${category}_marker.tsv"/> 
+		<data format="tsv" name="out_function" label="${tool.name}: frogsfunc_copynumbers_predicted_functions.tsv" from_work_dir="frogsfunc_copynumbers_predicted_functions.tsv"/>
+		<data format="tsv" name="out_marker" label="${tool.name}: frogsfunc_copynumbers_marker.tsv" from_work_dir="${category}_marker.tsv"/> 
 	</outputs>
 
 	<tests>
--- a/frogsfunc_functions.xml	Fri May 13 15:33:27 2022 +0000
+++ b/frogsfunc_functions.xml	Mon May 16 14:19:09 2022 +0000
@@ -16,7 +16,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
 <tool id="FROGSFUNC_step3_functions" name="FROGSFUNC_step3_functions" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>Predicting of functions weighted by the relative abundance of OTUs in the community. Inferring the metagenomes of the communities.</description>
+    <description>Calculates functions abundances in each sample.</description>
 
     <macros>
         <import>macros.xml</import>
@@ -43,18 +43,18 @@
     <inputs>
         <!-- Input files -->
         <param argument="--input-biom" format="biom1" name="input_biom" type="data" label="Biom file" help="The abundance file i.e. FROGSFUNC_step1_placeseqs tool output file (frogsfunc_placeseqs.biom)." optional="false"/>
-        <param argument='--function' format="tabular" type="data" label="Function file" help="Copy number table of functions present in the predicted genome for each OTU i.e. FROGSFUNC_step2_copynumbers tool output file (frogsfunc_copynumbers_predicted_functions.tsv)." optional="false"/>
-        <param argument='--marker' format="tabular" type="data" label="Marker file" help="Table of predicted marker copy number i.e. FROGSFUNC_step2_copynumbers output (frogsfunc_copynumbers_marker.tsv)." optional="false"/>
+        <param argument='--function' format="tsv" type="data" label="Function file" help="Copy number table of functions present in the predicted genome for each OTU i.e. FROGSFUNC_step2_copynumbers tool output file (frogsfunc_copynumbers_predicted_functions.tsv)." optional="false"/>
+        <param argument='--marker' format="tsv" type="data" label="Marker file" help="Table of predicted marker copy number i.e. FROGSFUNC_step2_copynumbers output (frogsfunc_copynumbers_marker.tsv)." optional="false"/>
         
         <!-- Parameters-->
         <param argument="--max-nsti" name="max_nsti" type="float" label="NSTI cut-off" help="Any sequence with an NSTI above this threshold will be out. (default: 2)" value="2" min="0" optional="false" /> 
     </inputs>
     <outputs>
         <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
-        <data format="tabular" name="seqtab" label="${tool.name}: frogsfunc_functions_marker_norm.tsv" from_work_dir="frogsfunc_functions_marker_norm.tsv.tsv"/> 
-        <data format="tabular" name="weighted" label="${tool.name}: frogsfunc_functions_weighted_nsti.tsv" from_work_dir="frogsfunc_functions_weighted_nsti.tsv"/> 
-        <data format="tabular" name="excluded" label="${tool.name}: frogsfunc_functions_excluded.tsv" from_work_dir="frogsfunc_functions_excluded.tsv"/>
-        <data format="tabular" name="function_abund" label="${tool.name}:   frogsfunc_functions_unstrat.tsv" from_work_dir=" frogsfunc_functions_unstrat.tsv"/> 
+        <data format="tsv" name="seqtab" label="${tool.name}: frogsfunc_functions_marker_norm.tsv" from_work_dir="frogsfunc_functions_marker_norm.tsv.tsv"/> 
+        <data format="tsv" name="weighted" label="${tool.name}: frogsfunc_functions_weighted_nsti.tsv" from_work_dir="frogsfunc_functions_weighted_nsti.tsv"/> 
+        <data format="tsv" name="excluded" label="${tool.name}: frogsfunc_functions_excluded.tsv" from_work_dir="frogsfunc_functions_excluded.tsv"/>
+        <data format="tsv" name="function_abund" label="${tool.name}:   frogsfunc_functions_unstrat.tsv" from_work_dir=" frogsfunc_functions_unstrat.tsv"/> 
     </outputs>
 
 
--- a/frogsfunc_pathways.xml	Fri May 13 15:33:27 2022 +0000
+++ b/frogsfunc_pathways.xml	Mon May 16 14:19:09 2022 +0000
@@ -16,7 +16,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
 <tool id="FROGSFUNC_step4_pathways" name="FROGSFUNC_step4_pathways" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-	<description>Inference of pathway-level abundances. </description>
+	<description>Calculates pathway abundances in each sample. </description>
 
   <macros>
         <import>macros.xml</import>
@@ -45,7 +45,7 @@
 	</command> 
 	<inputs>
         <!-- Input files -->       
-        <param argument="--input-file" format="tabular" name="input_file" type="data" label="Function abundance file" help="TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table)." optional="false"/>
+        <param argument="--input-file" format="tsv" name="input_file" type="data" label="Function abundance file" help="TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table)." optional="false"/>
 
         <!-- References -->
 	      <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio">
@@ -70,7 +70,7 @@
         </inputs>
 	<outputs>
 		<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
-		 <data format="tabular" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/> 
+		 <data format="tsv" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/> 
 	</outputs>
 
   <tests>
--- a/frogsfunc_placeseqs.xml	Fri May 13 15:33:27 2022 +0000
+++ b/frogsfunc_placeseqs.xml	Mon May 16 14:19:09 2022 +0000
@@ -16,7 +16,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 -->
 <tool id="FROGSFUNC_step1_placeseqs" name="FROGSFUNC_step1_placeseqs" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-	<description>Place studies sequences (i.e. OTUs) into a reference tree.</description>
+	<description>Places the OTUs into a reference phylogenetic tree.</description>
 
     <macros>
         <import>macros.xml</import>
@@ -70,9 +70,9 @@
 	<outputs>
 		<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
 		<data format="nhx" name="out_tree" label="${tool.name}: frogsfunc_placeseqs_tree.nwk" from_work_dir="frogsfunc_placeseqs_tree.nwk"/>
-		<data format="tabular" name="excluded" label="${tool.name}: frogsfunc_placeseqs_excluded.tsv" from_work_dir="frogsfunc_placeseqs_excluded.tsv"/> 
+		<data format="tsv" name="excluded" label="${tool.name}: frogsfunc_placeseqs_excluded.tsv" from_work_dir="frogsfunc_placeseqs_excluded.tsv"/> 
 		<data format="fasta" name="insert_fasta" label="${tool.name}: frogsfunc_placeseqs.fasta" from_work_dir="frogsfunc_placeseqs.fasta"/>
-		<data format="tabular" name="closests_ref" label="${tool.name}: frogsfunc_placeseqs_closests_ref_sequences.txt" from_work_dir="frogsfunc_placeseqs_closests_ref_sequences.txt"/>
+		<data format="tsv" name="closests_ref" label="${tool.name}: frogsfunc_placeseqs_closests_ref_sequences.txt" from_work_dir="frogsfunc_placeseqs_closests_ref_sequences.txt"/>
 		<data format="biom1" name="insert_biom" label="${tool.name}: frogsfunc_placeseqs.biom" from_work_dir="frogsfunc_placeseqs.biom"/> 
 	</outputs>
 
--- a/normalisation.xml	Fri May 13 15:33:27 2022 +0000
+++ b/normalisation.xml	Mon May 16 14:19:09 2022 +0000
@@ -51,7 +51,7 @@
 		<conditional name="sampling_method">
 			<param name="sampling_by_min" type="select" label="Sampling method" help='Sampling by the number of sequences of the smallest sample, or select a number manually' display='radio'>
             	<option value="yes" selected="true">Sampling by the number of sequences of the smallest sample</option>
-            	<option value="no">Select a number of reads</option>
+            	<option value="no">Select a number of sequences</option>
 			</param>
 		<when value="no">
 			<param name="num_reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
@@ -106,12 +106,15 @@
 
 Sequence normalisation method :
 
- - **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.
+ - **Sampling by the number of sequences of the smallest sample** : Automatically detects the number of sequences of the smallest sample, and selects this number for all other samples.
+ - **Select number of sequences** : Manually select a number of sequences.
+
+With this number, a random draw of sequences is made and once normalisation is complete, each sample will contain the specified number of sequences.
 
 .. 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).
 
 .. class:: h3
--- a/otu_filters.xml	Fri May 13 15:33:27 2022 +0000
+++ b/otu_filters.xml	Mon May 16 14:19:09 2022 +0000
@@ -81,7 +81,7 @@
 	</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="choice_prevalence_method">
@@ -95,7 +95,7 @@
 				</param>
 			</when>
 			<when value="replicate">
-				<param name="replicate_file" type="data" format="txt" optional="True" label="File of replicated sample names" help="Replicate file to link each sample to its group (cf. Help section)." />
+				<param name="replicate_file" type="data" format="tsv" optional="True" label="File of replicated sample names" help="Replicate file to link each sample to its group (cf. Help section)." />
 				<param name="min_replicate_presence" type="float" min="0" max="1" optional="true" label="Minimum prevalence" size="5" help="Fill the field only if you want this treatment. Keep OTU present in at least this proportion of replicates in at least one group (must be a proportion between 0 and 1).">
 				</param>
 			</when>
@@ -141,7 +141,7 @@
 	<outputs>
 		<data format="biom1" name="output_biom" label="${tool.name}: otuFilter_abundance.biom" from_work_dir="otuFilter_abundance.biom" />
 		<data format="fasta" name="output_fasta" label="${tool.name}: otuFilter_sequences.fasta" from_work_dir="otuFilter_sequences.fasta" />
-		<data format="tabular" name="output_excluded" label="${tool.name}: excluded.tsv" from_work_dir="excluded.tsv" />
+		<data format="tsv" name="output_excluded" label="${tool.name}: excluded.tsv" from_work_dir="excluded.tsv" />
 		<data format="html" name="output_summary" label="${tool.name}: report.html" from_work_dir="report.html" />
 	</outputs>
 	<tests>
@@ -206,7 +206,8 @@
 
 If not all samples are present in the "File of replicated sample names", they will not be affected by this filter step and will be kept in the abundance table.
 
-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.
+The file must consist of only 2 columns, separated by a tabulation. 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
--- a/phyloseq_alpha_diversity.xml	Fri May 13 15:33:27 2022 +0000
+++ b/phyloseq_alpha_diversity.xml	Mon May 16 14:19:09 2022 +0000
@@ -30,7 +30,7 @@
         </param>
 	</inputs>
 	<outputs>
-		<data format="tabular" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/>
+		<data format="tsv" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/>
 		<data format="html" name="html" label="${tool.name}: alpha_diversity.nb.html" from_work_dir="alpha_diversity.nb.html"/>
 	</outputs>
     <tests>
--- a/phyloseq_beta_diversity.xml	Fri May 13 15:33:27 2022 +0000
+++ b/phyloseq_beta_diversity.xml	Mon May 16 14:19:09 2022 +0000
@@ -43,7 +43,7 @@
     </inputs>
     <outputs>
         <data format="html" name="html" label="${tool.name}: beta_diversity.nb.html" from_work_dir="beta_diversity.nb.html">
-            <discover_datasets pattern="__designation__" ext="tabular" directory="BetaMatrix" visible="true"/>
+            <discover_datasets pattern="__designation__" ext="tsv" directory="BetaMatrix" visible="true"/>
         </data>
     </outputs>
     <tests>
--- a/phyloseq_clustering.xml	Fri May 13 15:33:27 2022 +0000
+++ b/phyloseq_clustering.xml	Mon May 16 14:19:09 2022 +0000
@@ -14,7 +14,7 @@
     <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="This file is the result of FROGS Phyloseq Beta Diversity tool."/>
+        <param argument="--distance-matrix" format="tsv" 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.">
             <expand macro="sanitizer_validator"/>
--- a/phyloseq_import_data.xml	Fri May 13 15:33:27 2022 +0000
+++ b/phyloseq_import_data.xml	Mon May 16 14:19:09 2022 +0000
@@ -32,7 +32,7 @@
     </inputs>
     <outputs>
         <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/>
-        <data format="html" name="html" label="${tool.name}: summary.nb.html" from_work_dir="summary.nb.html"/>
+        <data format="html" name="html" label="${tool.name}: report.nb.html" from_work_dir="report.nb.html"/>
     </outputs>
     <tests>
         <test>
--- a/phyloseq_manova.xml	Fri May 13 15:33:27 2022 +0000
+++ b/phyloseq_manova.xml	Mon May 16 14:19:09 2022 +0000
@@ -14,7 +14,7 @@
     <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="This file is the result of FROGS Phyloseq Beta Diversity tool"/>
+        <param argument="--distance-matrix" format="tsv" 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">
             <expand macro="sanitizer_validator"/>
--- a/phyloseq_structure.xml	Fri May 13 15:33:27 2022 +0000
+++ b/phyloseq_structure.xml	Mon May 16 14:19:09 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="This file is the result of FROGS Phyloseq Beta Diversity tool"/>
+        <param argument="--distance-matrix" format="tsv" 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"/>
--- a/preprocess.xml	Fri May 13 15:33:27 2022 +0000
+++ b/preprocess.xml	Mon May 16 14:19:09 2022 +0000
@@ -233,7 +233,7 @@
     </inputs>
     <outputs>
         <data format="fasta" name="dereplicated_file" label="${tool.name}: dereplicated.fasta" from_work_dir="dereplicated.fasta" />
-        <data format="tabular" name="count_file" label="${tool.name}: count.tsv" from_work_dir="count.tsv" />
+        <data format="tsv" name="count_file" label="${tool.name}: count.tsv" from_work_dir="count.tsv" />
         <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
     </outputs>
     <tests>
@@ -340,7 +340,7 @@
    :Files: One sequence file by sample (format `FASTQ &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_)
    :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 upstream 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 upstream part from this tag (_R1 and _R2) will be consider as sample name.
 
 .. class:: h3
 
@@ -348,7 +348,7 @@
 
 **Sequence file** (dereplicated.fasta):
 
- Only one file with all samples sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_). 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.
+ Only one file with all samples sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_). 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 sequences if you want to keep them.
 
 **Count file** (count.tsv):
 
@@ -392,6 +392,7 @@
 Keeping or not un-merged paired reads
 
 .. 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
--- a/remove_chimera.xml	Fri May 13 15:33:27 2022 +0000
+++ b/remove_chimera.xml	Mon May 16 14:19:09 2022 +0000
@@ -31,7 +31,7 @@
                 <param format="biom1" name="abundance_biom" type="data" label="Abundance file (format: BIOM)" help="It contains the count by sample for each sequence."  />
             </when>
             <when value="count">
-                <param format="tabular" name="abundance_count" type="data" label="Count file (format: TSV)" help="It contains the count by sample for each sequence (see below)."  />
+                <param format="tabular,tsv" name="abundance_count" type="data" label="Count file (format: TSV)" help="It contains the count by sample for each sequence (see below)."  />
             </when>
         </conditional>
     </inputs>
@@ -40,7 +40,7 @@
         <data format="biom1" name="out_abundance_biom" label="${tool.name}: non_chimera_abundance.biom" from_work_dir="non_chimera_abundance.biom">
             <filter>abundance_type['abundance_type_selected'] == "biom"</filter>
         </data>
-        <data format="tabular" name="out_abundance_count" label="${tool.name}: non_chimera_abundance.tsv" from_work_dir="non_chimera_abundance.tsv">
+        <data format="tsv" name="out_abundance_count" label="${tool.name}: non_chimera_abundance.tsv" from_work_dir="non_chimera_abundance.tsv">
             <filter>abundance_type['abundance_type_selected'] == "count"</filter>
         </data>
         <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
@@ -135,7 +135,7 @@
    :widths: 10, 90
    :class: table table-striped
 
-   "1", "Split input data by sample (classicaly the PCR is realised by sample)."
+   "1", "Split input data by sample (classicaly the PCR is performed by sample)."
    "2", "Find chimera in each sample (`vsearch &lt;https://github.com/torognes/vsearch&gt;`_)."
    "3", "Remove the sequences identify as chimera in all samples where they are present."
 
--- a/tsv_to_biom.xml	Fri May 13 15:33:27 2022 +0000
+++ b/tsv_to_biom.xml	Mon May 16 14:19:09 2022 +0000
@@ -17,8 +17,8 @@
     </command>
     <inputs>
         <!-- Files -->
-        <param format="tabular" name="tsv_file" type="data" label="Abundance TSV File" help="Your FROGS abundance TSV file. Take care to keep original column names." />
-        <param format="tabular" name="multi_affi_file" type="data" label="Multi_affiliation TSV File" help="TSV file describing multi_affiliation blast results." optional="true" />
+        <param format="tabular,tsv" 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,tsv" 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>