Add RDPclassifier

tools/FROGS_affiliation/FROGS_affiliation.rule.snakefile

@@ -15,7 +15,7 @@ rule <step_name>__FROGS_affiliation:
         taxfile = config["<step_name>__FROGS_affiliation_reference_fasta"]+"/train_set.fasta",
         yamlfile = config["<step_name>__FROGS_affiliation_reference_fasta"]+"/info.yaml",
         # taxonomic_ranks = "-t Domain Phylum Class Order Family Genus Species",
-        #rdp = "--rdp "+config["<step_name>__FROGS_affiliation_rdp"] if config["<step_name>__FROGS_affiliation_rdp"] else "",
+        rdp = " --rdp " if config["<step_name>__FROGS_affiliation_rdp"] else "",
     threads: 
         config["<step_name>__FROGS_affiliation_threads"],
     shell: """
@@ -39,5 +39,5 @@ rule <step_name>__FROGS_affiliation:
         {params.cmdStat} -i {output.abundance_file}  --tax-consensus-tag 'blast_taxonomy' --multiple-tag 'blast_affiliations' -o {params.outDir}/affiliations_stat.html ;
         echo \"2\t./{params.stepDir}/affiliations_stat.html\" >> {params.outDir}/text.generic.tsv
         """
-        # {params.rdp} \
+        
         #{params.taxonomic_ranks} \
\ No newline at end of file

tools/FROGS_affiliation/FROGS_affiliation.yaml

@@ -2,7 +2,7 @@
   id: FROGS_affiliation,
   name: FROGS affiliation,
   article: 10.1093/bib/bbab318,
-  website: "http://f  rogs.toulouse.inrae.fr/",
+  website: "http://frogs.toulouse.inrae.fr/",
   git: "https://github.com/geraldinepascal/FROGS",
   description: "Adding taxonomic affiliation in abundance file",
   version: "3.2.3",
@@ -42,7 +42,7 @@
               prefix: --rdp,
               type: checkbox,
               value: False,
-              label: "[NOT AVAILABLE] Also perform RDP assignation ?",
+              label: "Also perform RDP assignation ?",
             },
             {
               name: FROGS_affiliation_reference_fasta,
@@ -108,6 +108,18 @@
         # add to FROGS
         "ln -s /opt/biotools/FROGS-3.2.3/bin/EMBOSS-6.6.0/emboss/needleall /opt/biotools/FROGS-3.2.3/libexec/."
       ],
+      ant : ["apt-get install ant"],
+      RDPclasifier: [
+        "cd /opt/biotools/",
+        "git clone https://github.com/rdpstaff/RDPTools.git",
+        "cd RDPTools",
+        "git checkout 2.0.3",
+        "git submodule init",
+        "git submodule update",
+        "make",
+        # add to FROGS
+        "ln -s opt/biotools/RDPTools/classifier.jar /opt/biotools/FROGS-3.2.3/libexec/."
+      ],
     },
     data: [
     {