docs: update tutorial about integration with Chewie-NS to separate commands to run from the expected output.

Author: rfm-targa

CHEWBBACA/docs/user/tutorials/chewieNS_step_by_step.rst

@@ -83,6 +83,8 @@ To upload the schema included in the *Streptococcus agalactiae* dataset, you can
 
     $ chewBBACA.py LoadSchema -i sagalactiae_schema/ -sp 1 -sn tut -lp tut --df sagalactiae_description.md --a sagalactiae_annotations.tsv --ns tutorial
 
+::
+
     ==========================
       chewBBACA - LoadSchema
     ==========================
@@ -171,6 +173,8 @@ To download the schema you have uploaded, please run the following command:
 
     $ chewBBACA.py DownloadSchema -sp 1 -sc 1 -o sagalactiae_ns --ns tutorial
 
+::
+
     ==============================
       chewBBACA - DownloadSchema
     ==============================
@@ -207,6 +211,8 @@ To perform allele call and determine the allelic profiles of the genomes in the
 
     $ chewBBACA.py AlleleCall -i sagalactiae_genomes/subset1/ -g sagalactiae_ns/Streptococcus_agalactiae_tut/ -o subset1_results 
 
+::
+
     ==========================
       chewBBACA - AlleleCall
     ==========================
@@ -372,6 +378,8 @@ Running the ``SyncSchema`` process is fairly simple. To retrieve new alleles add
 
     $ chewBBACA.py SyncSchema -sc sagalactiae_ns/Streptococcus_agalactiae_tut/ --submit
 
+::
+
     ==========================
       chewBBACA - SyncSchema
     ==========================
@@ -446,6 +454,8 @@ A sample command would be:
 
     $ chewBBACA.py DownloadSchema -sp 1 -sc 1 -o sagalactiae_snapshot --ns tutorial --d "2020-08-07T22:47:52"
 
+::
+
     ==============================
       chewBBACA - DownloadSchema
     ==============================
@@ -486,6 +496,8 @@ We will perform allele call with the genomes in subset2 to demonstrate how the `
 
     $ chewBBACA.py AlleleCall -i sagalactiae_genomes/subset2/ -g sagalactiae_snapshot/Streptococcus_agalactiae_tut/ -o subset2_results 
 
+::
+
     ...
 
     Classified a total of 75 CDSs.
@@ -512,6 +524,8 @@ To perform this last synchronization, execute:
 
     $ chewBBACA.py SyncSchema -sc sagalactiae_snapshot/Streptococcus_agalactiae_tut/ --submit
 
+::
+
     ...
 
     Received 47 new alleles for 7 loci and sent 33 for 7 loci.