Merge pull request #6763 from hugolefeuvre/update_deeparg

Update deepARG with minor changes for tools deployement

tools/deeparg/deeparg_predict.xml

@@ -99,14 +99,14 @@
         </test>
     </tests>
     <help>
-DeepARG Predict is a computational tool designed to classify and annotate antibiotic resistance genes (ARGs) from nucleotide or protein sequences.
+DeepARG Predict is a computational tool designed to classify and annotate antibiotic resistance genes (ARGs) from nucleotide or protein sequences
 
-It takes as input a **fasta nucleotide or protein file** containing short (SS model) or long (LS model) sequences.
+It takes as input a **fasta nucleotide or protein file** containing short (SS model) or long (LS model) sequences
 
 DeepARG output
 ---------------
 
-DeepARG generates two main files: .ARG that contains the sequences with a probability sup or = --prob (0.8 default) and .potential.ARG with sequences containing a probability inf to --prob (0.8 default). The .potential.ARG file can still contain ARG-like sequences, howevere, it is necessary inspect its sequences.
+DeepARG generates two main files: .ARG that contains the sequences with a probability sup or = --prob (0.8 default) and .potential.ARG with sequences containing a probability inf to --prob (0.8 default). The .potential.ARG file can still contain ARG-like sequences, howevere, it is necessary inspect its sequences
 
 The output format for both files consists of the following fields:
 
@@ -123,7 +123,7 @@ The output format for both files consists of the following fields:
 * ALIGNMENT_BESTHIT_EVALUE
 * COUNTS
 
-If you want to annotate paired-end short read sequencing data use the DeepARG Short Reads tool.
+If you want to annotate paired-end short read sequencing data use the DeepARG Short Reads tool
 
     </help>
     <expand macro="citations"/>

tools/deeparg/deeparg_short_reads.xml

@@ -136,11 +136,11 @@
         </test>
     </tests>
     <help>
-The DeepARG Short Reads Pipeline is a specialized tool for detecting antibiotic resistance genes (ARGs) directly from **paired-end short read sequencing data**.
+The DeepARG Short Reads Pipeline is a specialized tool for detecting antibiotic resistance genes (ARGs) directly from **paired-end short read sequencing data**
 
-It provides detailed output files summarizing ARG detection, merged results, subtype and type classifications, potential ARGs, and all detected hits.
+It provides detailed output files summarizing ARG detection, merged results, subtype and type classifications, potential ARGs, and all detected hits
 
-If you want to annotate ARGs from assembled contigs, use the DeepARG Predict tool.
+If you want to annotate ARGs from assembled contigs, use the DeepARG Predict tool
     </help>
     <expand macro="citations"/>
 </tool>