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Update deepARG with minor changes for tools deployement #6763

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Feb 14, 2025
Merged

Update deepARG with minor changes for tools deployement #6763

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b63f3f4
typo changes
hugolefeuvre Feb 14, 2025
04b7d34
Update tools/deeparg/macros.xml
bgruening Feb 14, 2025
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8 changes: 4 additions & 4 deletions tools/deeparg/deeparg_predict.xml
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Expand Up @@ -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:

Expand All @@ -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"/>
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6 changes: 3 additions & 3 deletions tools/deeparg/deeparg_short_reads.xml
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Expand Up @@ -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>