Remove redondant and hard to maintain documentation from README

README.md

@@ -197,152 +197,13 @@ The gui package exposes the command `cadbiom` to the current context.
 
 # Use
 
-## Command line
+## Command line & API
 
-### General:
+For up-to-date help on how to use the various commands, please visit this page:
+[link](http://cadbiom.genouest.org/doc/cadbiom/command_line_usage.html)
 
-    $ cadbiom_cmd -h
-
-    usage: cadbiom_cmd [-h] [-vv [VERBOSE]]
-                        {compute_macs,sort_solutions,parse_trajectories,merge_cams}
-                        ...
-
-    optional arguments:
-    -h, --help            show this help message and exit
-    -vv [VERBOSE], --verbose [VERBOSE]
-
-    subcommands:
-    {compute_macs,sort_solutions,parse_trajectories,merge_cams}
-        compute_macs        Parse arguments and launch Cadbiom search of MACs
-                            (Minimal Activation Conditions). - If there is no
-                            input file, there will be only one process. - If an
-                            input file is given, there will be 1 process per line
-                            (per logical formula on each line). - all_macs: Solver
-                            will try to search all macs with 0 to the maximum of
-                            steps allowed. - continue: If there is a mac file from
-                            a previous work, last frontier places will be
-                            reloaded.
-        sort_solutions      Parse a solution file and sort all frontier places in
-                            alphabetical order.
-        parse_trajectories  Parse a complete solution file and make a
-                            representation of trajectories.
-                            The output is in graphml file format and is exported
-                            in 'graphs' directory. .. note:: Requires the
-                            model file.
-        merge_cams          Merge solutions to a csv file. .. note:: CSV file:
-                            <Final property formula>;<cam>
-        model_comp          Model consistency checking. Check if the 2 given
-                            models have the same topology, nodes & edges
-                            attributes/roles. .. note:: You can export a graphml
-                            file for the 2 models.
-        model_infos         Model informations. Get number of nodes, edges,
-                            centralities (degree, closeness, betweenness). ..
-                            note:: You can export a graphml file for model.
-
-
-### compute_macs:
-
-    usage: cadbiom_cmd compute_macs [-h] [--input_file [INPUT_FILE]]
-                                    [--combinations] [--steps [STEPS]]
-                                    [--all_macs] [--continue]
-                                    [--start_prop [START_PROP]]
-                                    [--inv_prop [INV_PROP]] [--output [OUTPUT]]
-                                    chart_file [final_prop]
-
-    positional arguments:
-    chart_file
-    final_prop
-
-    optional arguments:
-    -h, --help            show this help message and exit
-    --input_file [INPUT_FILE]
-    --combinations
-    --steps [STEPS]
-    --all_macs
-    --continue
-    --start_prop [START_PROP]
-    --inv_prop [INV_PROP]
-    --output [OUTPUT]
-
-
-### parse_trajectories:
-
-    usage: cadbiom_cmd parse_trajectories [-h] chart_file sol_file
-
-    positional arguments:
-    chart_file
-    sol_file
-
-<br>
-* Result:
-
-[image](examples/graph_example_with_legend.png)
-
-* Cytoscape styles:
-
-[file](examples/cytoscape_styles.xml)
-
-
-### sort_solutions:
-
-    usage: cadbiom_cmd sort_solutions [-h] sol_file
-
-    positional arguments:
-    sol_file
-
-
-### merge_cams:
-
-    usage: cadbiom_cmd merge_cams [-h] [--output [OUTPUT]] [solutions_directory]
-
-    positional arguments:
-    solutions_directory
-
-
-### model_comp:
-
-    usage: cadbiom_cmd model_comp [-h] [--make_graphs] model_file_1 model_file_2
-
-    positional arguments:
-    model_file_1
-    model_file_2
-
-    optional arguments:
-    -h, --help     show this help message and exit
-    --graphs
-    --json
-    --output [OUTPUT]
-
-<br>
-
-Usage in scripts:
-
-    >>> from cadbiom_cmd.solution_repr import graph_isomorph_test
-    >>> print(graph_isomorph_test('test.bcx', 'test2.bcx', output_dir='graphs/',
-        make_graphs=False, make_json=False))
-    INFO: 3 transitions loaded
-    INFO: 3 transitions loaded
-    INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0
-    INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0
-    INFO: Topology checking: True
-    INFO: Nodes checking: True
-    INFO: Edges checking: True
-    {u'nodes': True, u'edges': True, u'topology': True}
-
-
-### model_infos
-
-    usage: cadbiom_cmd model_infos [-h] [--graph] [--json] [--output [OUTPUT]]
-                                model_file
-
-    positional arguments:
-    model_file
-
-    optional arguments:
-    -h, --help         show this help message and exit
-    --graph
-    --json
-    --output [OUTPUT]
+For up-to-date help on how to use the various APIs, please visit this page:
+[link](http://cadbiom.genouest.org/doc/cadbiom/command_line_doc.html)
 
 
 ## Graphical User Interface