pdf version update

docs/index.md

@@ -1,3 +1,40 @@
 **Welcome to the UROPA documentation!**
 
-Please visit the [UROPA-manual](http://uropa-manual.readthedocs.io/en/latest/)
+UROPA is a command line based tool, intended for genomic region annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries.
+These can be sensitive for feature type, distance, strand specificity, feature attributes (eg. protein_coding) or the anchor position relative to the feature.
+UROPA can incorporate reference annotation files (GTF) from different sources, like Gencode, Ensembl, or RefSeq, as well as custom reference files produced by the user.
+
+**Advantages of UROPA**
+
+* Simple usage: No programming
+* Utilization of all available GTF files as annotation database
+* Detect the most appropriate annotation with flexible keys that allow robustness and simple customization, such as
+	* feature type
+	* feature anchor
+	* feature direction relative to peak location
+	* filter for attribute values, e.g. "protein_coding"
+	* strand specificity
+* Preparation of custom annotation files
+* One run with multiple sets of parameters by multiple queries
+* Graduated annotation due to priorization
+* Different easily-readable output tables (AllHits, FinalHits, BestperQuery_Hits).
+* Visual summary for annotation evaluation
+* Annotation with default values 
+
+**How to cite**
+
+Please cite the paper describing UROPA when using it in your research:
+tba
+
+**Contribute**
+
+Source Code [here](https://github.molgen.mpg.de/loosolab/UROPA)    
+Further details see [here](http://uropa.readthedocs.io/en/latest/install/)
+
+**Support**
+
+If you have any issue feel free to send an email to Maria Kondili (maria.kondili@mpi-bn.mpg.de)
+
+**Licence**
+
+The project is licensed under the MIT license

docs_rst/index.rst

@@ -59,9 +59,9 @@ The project is licensed under the MIT license (see :doc:`/license`)
    install
    parameter
    config
-   output
-   uropa-example
-   custom
+   output-pdf
+   uropa-example-pdf
+   custom-pdf
    license
    help
 

docs_rst/output-pdf.rst

@@ -17,12 +17,8 @@ File overview
 - **Uropa_Summary**: Statistical summary of the UROPA annotation by using the ``-s`` parameter.
 
 .. note::
-	The output files will be named additionally by the output directory name.
-	For example if uropa is used like this:
-
-	.. code:: bash
-		
-		uropa -i config.json -o ChIPanno
+	The output files will be named additionally by the output directory name. 
+	For example if uropa is used like this:	``uropa.py -i config.json -o ChIPanno``
 
 	The result would contain: ChIPannot/Uropa_AllHits_ChIPannot.txt
 

docs_rst/output.rst

@@ -17,12 +17,8 @@ File overview
 - **Uropa_Summary**: Statistical summary of the UROPA annotation by using the ``-s`` parameter.
 
 .. note::
-	The output files will be named additionally by the output directory name.
-	For example if uropa is used like this:
-
-	.. code:: bash
-	
-		uropa.py -i config.json -o ChIPanno
+	The output files will be named additionally by the output directory name. 
+	For example if uropa is used like this:	``uropa.py -i config.json -o ChIPanno``
 
 	The result would contain: ChIPannot/Uropa_AllHits_ChIPannot.txt
 

mkdocs.yml

@@ -5,12 +5,3 @@ repo_url: 'https://github.molgen.mpg.de/loosolab/UROPA'
 repo_name: 'GitHub'
 pages:
 - Home: 'index.md'
-- About UROPA: 'introduction.md'
-- Installation: 'install.md'
-- Available parameters: 'parameters.md'
-- Configuration file: 'config.md'
-- Output: 'output.md'
-- Application examples: 'uropa-example.md'
-- Side tool - 'UROPA to GTF': custom.md
-- MIT License: license.md
-- Help: help.md