add a simple OTU abundance count output

tools/FROGS_biom_to_tsv/FROGS_biom_to_tsv.rule.snakefile

@@ -3,10 +3,12 @@ rule <step_name>__FROGS_biom_to_tsv:
         **<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',
+        lulu_abundance_file = config["results_dir"]+'/'+config["<step_name>__FROGS_biom_to_tsv_output_dir"]+'/simple_OTU_abundance.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}
+        {params.command} -b {input.biom} -t {output.abundance_file} ;
+        cut -f10,12- -d$'\t'  {output.abundance_file} > {output.lulu_abundance_file}
         """
\ No newline at end of file

tools/FROGS_biom_to_tsv/FROGS_biom_to_tsv.yaml

@@ -23,6 +23,8 @@
         outputs:
           [
             { name: "abundance_file", file: "tax_affiliation.tsv", type: "tsv", description: "output file with the abundance and metadata (tsv)"},
+            { name: "lulu_abundance_file", file: "simple_OTU_abundance.tsv", type: "tsv", description: "OTU abundance with samples as columns and OTUs as rows (for lulu)"},
+
           ],
         options:
           [