Update blockdiag.rst

docs/source/blockdiag.rst

@@ -1,14 +1,54 @@
 .. blockdiag::
 
   diagram {
-
-   Chromosomes [stacked];
-   "MPI enabled" [shape = diamond];
-   MGEScan [shape = roundedbox];
-   nonLTR -> "Protein Translation by bioperl" -> "Signals of APE by hmmer" -> 'E-values from 12 clades by hmmer' -> 'Searching path of  
-   states' -> 'classification by hmmer (post processing)';
-   "Signals of APE by hmmer" -> 'E-values from 12 clades by hmmer' [folded];
-   LTR -> "TRF" -> "Finding pairs of maximal exact  repeats by modified GAME" -> 'Identifying putative LTRs - emboss matcher to find 
-   similarity' -> 'analysis of RT domains / Scanning ORFs by hmmer, emboss transeq' -> 'Deleting fragments';
-   "Finding pairs of maximal exact  repeats by modified GAME" -> 'Identifying putative LTRs - emboss matcher to find similarity' [folded]    ;
+
+  orientation = portrait
+
+   Chromosomes [shape = flowchart.input, stacked];
+   nonLTR [ numbered = MPI ];
+   LTR [ numbered = MPI ];
+
+   Chromosomes -> MGEScan -> nonLTR -> "Translation \n to Protein" -> "Signals of APE" -> 'E-values \n from 12 clades' -> 'Searching  \n Path of States' -> 'Classification \n (post processing)' -> 'Results \n(gff3)';
+   "Translation \n to Protein" -> 'Signals of RT' -> 'E-values \n from 12 clades';
+
+   group { 
+   label = 'HMMER';
+   color='#E6E6E6';
+   "Signals of APE";
+   "Signals of RT";
+   'E-values \n from 12 clades';
+   }
+
+   group { 
+   label = 'C program';
+   color='#E6E6E6';
+   'Searching \n Path of States';
+   }
+
+   group { 
+   label = 'HMMER';
+   color='#E6E6E6';
+   'Classification \n (post processing)' ;
+   }
+
+   Chromosomes -> MGEScan -> LTR -> "Tandem Repeat Finder\n(TRF)" -> "Finding pairs \nof Maximal Exact \nrepeats" -> 'Identifying \nputative LTRs' -> 'Analysis of RT \n/ Scanning ORFs' -> 'Deleting fragments' ->  'Results \n(gff3)';
+
+   group {
+   label = 'GAME';
+   color='#E6E6E6';
+   "Finding pairs \nof Maximal Exact \nrepeats";
+   }
+
+   group {
+   label = 'EMBOSS';
+   color='#E6E6E6';
+   'Identifying \nputative LTRs';
+
+   }
+
+   group {
+   label = ' HMMER, EMBOSS';
+   color='#E6E6E6';
+   'Analysis of RT \n/ Scanning ORFs';
+   }
    }