Add Frogs biom 2 tsv

tools/FROGS_biom_to_tsv/FROGS_biom_to_tsv.rule.snakefile

+rule <step_name>__FROGS_biom_to_tsv:
+    input:
+        **<step_name>__FROGS_biom_to_tsv_inputs(),
+    output:
+        abundance_file = config["results_dir"]+'/'+config["<step_name>__FROGS_biom_to_tsv_output_dir"]+'/tax_affiliation.tsv',
+    log: config["results_dir"]+'/logs/' + config["<step_name>__FROGS_biom_to_tsv_output_dir"] + '/FROGS_biom_to_tsv_log.txt',
+    params:
+        command = config["<step_name>__FROGS_biom_to_tsv_command"],
+        outDir = config["results_dir"]+'/'+config["<step_name>__FROGS_biom_to_tsv_output_dir"],
+    shell: """
+        {params.command} -b {input.biom} -t {output.abundance_file}
+        """
\ No newline at end of file

tools/FROGS_biom_to_tsv/FROGS_biom_to_tsv.yaml

+{
+  id: FROGS_biom_to_tsv,
+  name: FROGS biom2tsv,
+  article: 10.1093/bib/bbab318,
+  website: "http://frogs.toulouse.inrae.fr/",
+  git: "https://github.com/geraldinepascal/FROGS",
+  description: "Adding taxonomic affiliation in abundance file",
+  version: "3.2.3",
+  documentation: "http://frogs.toulouse.inrae.fr/html/commands_utax.html",
+  multiqc: "custom",
+  commands:
+    [
+      {
+        name: FROGS_biom_to_tsv,
+        command: "/opt/biotools/FROGS-3.2.3/app/biom_to_tsv.py",
+        category: "FROGS",
+        output_dir: FROGS_biom_to_tsv,
+        inputs: 
+          [
+            #{ name: fasta, type: "fasta_file", description: "the sequences in fasta format"},
+            { name: biom, type: "biom", description: "the abundance of each OTU in each sample"}
+          ],
+        outputs:
+          [
+            { name: "abundance_file", file: "tax_affiliation.tsv", type: "tsv", description: "output file with the abundance and metadata (tsv)"},
+          ],
+        options:
+          [
+           
+          ],
+      },
+    ],
+  install:
+    {
+      perl: [
+        "sudo apt-get install python3 perl" # deja installé
+      ],
+      frogs: [
+        "cd /opt/biotools",
+        "wget https://github.com/geraldinepascal/FROGS/archive/v3.2.3.tar.gz",
+        "tar -zxvf v3.2.3.tar.gz",
+        "cd FROGS-3.2.3",
+        "mkdir bin"
+      ],
+      scipy: [
+        "apt-get install python3-scipy" # demande confirmation
+      ],
+    },
+  citations:  {
+    frogs: [
+      " Maria Bernard, Olivier Rué, Mahendra Mariadassou and Géraldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093/bib/bbab318 "
+    ]
+  }
+}