Add file formats description in documentation

src/dgenies/md/formats.md

+# Description of file formats used in D-Genies
+
+##PAF (Pairwise mApping Format)
+
+Default output format of minimap2.
+
+It's a tabulated file. Description of columns below.
+
+Col | Type   | Description                               
+--- | ------ | -----------------------------------------
+1   | string | Query sequence name                       
+2   | int    | Query sequence length                     
+3   | int    | Query start coordinate (0-based)                     
+4   | int    | Query end coordinate (0-based)                       
+5   | char   | ‘+’ if query/target on the same strand; ‘-’ if opposite               
+6   | string | Target sequence name                      
+7   | int    | Target sequence length                    
+8   | int    | Target start on original strand (0-based) 
+9   | int    | Target end on original strand (0-based)   
+10  | int    | Number of matching bases in the mapping                 
+11  | int    | Number bases, including gaps, in the mapping                    
+12  | int    | Mapping quality (0-255; 255 for missing)  
+
+Column 11 gives the total number of sequence matches, mismatches and gaps in the alignment; column 10 divided by column 11 gives the BLAST-like alignment identity.
+
+PAF may optionally have additional fields in the SAM-like typed key-value format. Minimap2 may output the following tags:
+ 
+Tag | Type | Description
+--- | ---- | -----------------------------------------
+tp  | A	   | Type of aln: P/primary, S/secondary and I,i/inversion
+cm	| i    | Number of minimizers on the chain
+s1	| i	   | Chaining score
+s2	| i	   | Chaining score of the best secondary chain
+NM	| i	   | Total number of mismatches and gaps in the alignment
+AS	| i	   | DP alignment score
+ms	| i	   | DP score of the max scoring segment in the alignment
+nn	| i	   | Number of ambiguous bases in the alignment
+
+Source: [minimap2 documentation](https://lh3.github.io/minimap2/minimap2.html).
+
+
+## Maf (Multiple Alignment File)
+
+Description of the format is available [here](http://www.bx.psu.edu/~dcking/man/maf.xhtml).
+
+## Index file
+
+Index files used in D-Genies are built as follow.
+
+First line contains the name of the sample. Next lines describes contigs of the sample. They are composed of two columns, tab separated. First it the name of the contig, second it's size in bases.
+
+Example:
+
+    Homo sapiens  
+    chr1    248956422  
+    chr2    242193529  
+    chr3    198295559
+
+## Backup file
+
+Backup file is a TAR archive. It contains three files:
+
+* The alignment file, in paf format, named `map.paf`.
+* The target index, named `target.idx`.
+* The query index, named `query.idx`.
+
+Names of files must be kept. Otherwise, the backup file will not be accepted by the run form.
\ No newline at end of file

src/dgenies/templates/base.html

@@ -57,12 +57,13 @@
                         {% if mode == "webserver" %}
                             <li class="{% if(menu == 'gallery') %}active{% endif %}"><a href="/gallery">Gallery</a></li>
                         {% endif %}
-                        <li class="dropdown">
+                        <li class="dropdown documentation {% if(menu == 'documentation') %}active{% endif %}">
                             <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span
                                     class="caret"></span></a>
                             <ul class="dropdown-menu" role="menu">
                                 <li><a href="/documentation/run">Launch a job</a></li>
                                 <li><a href="/documentation/result">Results</a></li>
+                                <li><a href="/documentation/formats">File formats</a></li>
                             </ul>
                         </li>
                         <li class="{% if(menu == 'install') %}active{% endif %}"><a href="/install">Install</a></li>

src/dgenies/templates/documentation.html

@@ -33,6 +33,12 @@
             margin-left: 295px !important;
         }
     </style>
+
+    <script type="text/javascript">
+        $(document).ready(function() {
+            $("table").addClass("table table-striped");
+        });
+    </script>
 {% endblock %}
 {% block content %}
 

src/dgenies/views.py

@@ -17,6 +17,7 @@ from dgenies.lib.fasta import Fasta
 from dgenies.tools import Tools
 from markdown import Markdown
 from markdown.extensions.toc import TocExtension
+from markdown.extensions.tables import TableExtension
 import tarfile
 from jinja2 import Environment
 if MODE == "webserver":
@@ -358,6 +359,17 @@ def documentation_result():
     return render_template("documentation.html", menu="documentation", content=content, toc=toc)
 
 
+@app.route("/documentation/formats", methods=['GET'])
+def documentation_formats():
+    with open(os.path.join(app_folder, "md", "formats.md"), "r",
+              encoding='utf-8') as install_instr:
+        content = install_instr.read()
+    md = Markdown(extensions=[TocExtension(baselevel=1), TableExtension()])
+    content = Markup(md.convert(content))
+    toc = Markup(md.toc)
+    return render_template("documentation.html", menu="documentation", content=content, toc=toc)
+
+
 @app.route("/install", methods=['GET'])
 def install():
     with open(os.path.join(app_folder, "md", "INSTALL.md"), "r", encoding='utf-8') as install_instr: