Updated the docs to reflect the new argument style.

StuntsPT · Feb 10, 2016 · 432c9bf · 432c9bf
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diff --git a/docs/future.md b/docs/future.md
@@ -2,6 +2,6 @@
 * For now the *FASTA* format is hard-coded in the program, but this may change should there be demand for it;
     * This effectively limits *NCBI Mass Sequence Downloader* to **sequence** databases.
 * As more NCBI sequence databases become available, they will be added to *NCBI Mass Sequence Downloader*.
-* Add argument parsing and value checking as referenced in [#8](https://github.com/StuntsPT/NCBI_Mass_Downloader/issues/8) and [#9](https://github.com/StuntsPT/NCBI_Mass_Downloader/issues/9).
+* ~~Add argument parsing and value checking as referenced in [#8](https://github.com/StuntsPT/NCBI_Mass_Downloader/issues/8) and [#9](https://github.com/StuntsPT/NCBI_Mass_Downloader/issues/9).~~ Done!
 
 [Return to Introduction](index.md)
diff --git a/docs/limits.md b/docs/limits.md
@@ -1,5 +1,5 @@
 # Known limitations
-* There is **NO** argument checking of any kind. If there is a problem with your arguments, you will see no *hand holding* of any kind, just plain python error messages. (To be fixed in version 3.1)
+* ~~There is **NO** argument checking of any kind. If there is a problem with your arguments, you will see no *hand holding* of any kind, just plain python error messages.~~ (Fixed in version >= 3.1)
 * All sequences are downloaded in the *FASTA* format.
 
 [Return to Introduction](index.md)
diff --git a/docs/testing.md b/docs/testing.md
@@ -1,7 +1,7 @@
 # Testing
 In order to test the program run the following:
 
-     python NCBI_downloader.py "Lacerta monticola[organism]" "nucleotide" testdata.fasta
+     python NCBI_downloader.py -q "Lacerta monticola[organism]" -d "nucleotide" -o testdata.fasta
 
 If everything is working as it should, you should receive a fasta file with 182 sequences. However, please note that due to the changing nature of the database, this value is likely to change over time.
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -5,7 +5,7 @@ To use the GUI version:
 
 To use the command line version:
 
-    python NCBI_downloader.py "Query term" "database" outfile.fasta
+    python NCBI_downloader.py -q "Query term" -d "database" -o outfile.fasta
 
 ## Notes
 * The program will not overwrite anything in the output file, but rather append sequences to it;s