Some change

rules/Analysis/MGMT.rules

@@ -537,22 +537,20 @@ rule ANALYSIS_KRONA_PLOT_MG:
         "%s/benchmarks/ANALYSIS_KRONA_PLOT.json" % AN_OUT
     input:
         "%s/MG.prokkaID2ec.txt" % AN_OUT,
-#        "%s/ec2pwy.txt" % U_OUT,
-#        "%s/pwy2hierarchy.txt" % U_OUT,
+        "%s/ec2pwy.txt" % U_OUT,
+        "%s/pwy2hierarchy.txt" % U_OUT,
         "%s/MG.gene_depth.avg" % AN_OUT,
         "%s/MG.gene.len" % AN_OUT
     output:
-#        "%s/results/MG.gene_kegg_krona.txt" % AN_OUT,
-#        "%s/results/MG.gene_kegg_krona.html" % AN_OUT
-        "%s/krona.done" % AN_OUT
+        "%s/results/MG.gene_kegg_krona.txt" % AN_OUT,
+        "%s/results/MG.gene_kegg_krona.html" % AN_OUT
     shell:
         """
         echo "[x] PLOT KRONA `date +"%Y/%m/%d %H:%M:%S"`" >> {log}
         echo {input}
         echo {output[0]}
-        touch {output[0]}
+        python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -H {input[1]} -m {input[2]} -c {input[3]} -L {input[4]} -o {output[0]}
+        ktImportText -o {output[1]} {output[0]}
         """
-#        python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[4]} -o {output[0]}
-#        ktImportText -o {output[1]} {output[0]}
 
 #rule ANALYSIS_KRONA_PLOT_MT: