versioning to 0.3.1

Author: gtrichard

README.md

@@ -2,14 +2,14 @@
 
 ![](docs/images/deepStats_logo.png?raw=true "Title")
 
-**deepStats v0.3 is a statistical and dataviz toolbox for deeptools, genomic signals, and more (GOterms, etc).**
+**deepStats 0.3.1 is a statistical and dataviz toolbox for deeptools, genomic signals, and more (GOterms, etc).**
 
 **This is currently a Work In Progress**
 
 ## Citation
 
 If you use deepStats in your work, please cite this repository using the DOI from the following link:
-https://zenodo.org/badge/latestdoi/189997890
+https://doi.org/10.5281/zenodo.3336593
 
 ## Installation
 
@@ -23,6 +23,8 @@ conda activate deepStats
 
 - **As R Notebooks**
 
+Currently, R notebooks are not up-to-date.
+
 Install the following packages in your R environment:
 ```
 install.packages('optparse',repos = "http://cran.us.r-project.org")
@@ -41,11 +43,12 @@ git clone https://github.com/gtrichard/deepStats
 
 - **As Galaxy wrappers**
 
-You can install deepStats in a Galaxy instance through the Tool Shed:
-https://toolshed.g2.bx.psu.edu/view/gtrichard/deepstats_dscomparecurves/cbeae0f83ff8
+You can install deepStats in a Galaxy instance through the `Galaxy Tool Shed <https://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&operation=view_or_manage_repository&f-free-text-search=deepstats&id=4125c47ee1118a75>`_
 
 ## Tools
 
+The tools complete description are available on the Wiki: https://github.com/gtrichard/deepStats/wiki
+
 - **dsCompareCurves**
 
 Compares the curves derived from multiple genomic signals and region sets by using bootstrapping and Wilcoxon rank-sum tests in order to identify significantly different loci (bins). It uses `deeptools reference-point computeMatrix --outFileNameMatrix matrix.txt` (can be `reference-point` or `scaled-region`) as an input file. `dsCompareCurves --help` will give you all required information to use the tool. For further documentation about deepTools and how to generate the input file, please refer to: https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html.

bin/dsCompareCurves

@@ -104,7 +104,7 @@ option_list = list(
 );
 
 opt_parser = OptionParser( description= "
-                           This tool assesses if multiple genomics signals ( ChIP-seq, ATAC-seq... ) are significantly different or
+                           dsCompareCurves 0.3.1 assesses if multiple genomics signals ( ChIP-seq, ATAC-seq... ) are significantly different or
                            not between conditions ( control, KO1, KO2, etc ). `dsCompareCurves` uses bootstraps and corrected
                            Wilcoxon Rank-sum tests to do so. The input of this tool corresponds to the output of deepTools
                            `computeMatrix --outFileNameMatrix`. If multiple region sets have been used in deepTools, one plot and

galaxy/wrapper/deepStats_macros.xml

@@ -1,10 +1,10 @@
 <macros>
    <token name="@THREADS@">--CPU "\${GALAXY_SLOTS:-4}"</token>
-   <token name="@WRAPPER_VERSION@">1.0.0</token>
+   <token name="@WRAPPER_VERSION@">1.1.0</token>
    <token name="@REFERENCES@">https://github.com/gtrichard/deepStats</token>
    <xml name="requirements">
      <requirements>
-       <requirement type="package" version="0.3">deepstats</requirement>
+       <requirement type="package" version="0.3.1">deepstats</requirement>
      </requirements>
    </xml>
    <xml name="citations">

notebooks/compareCurves.Rmd

@@ -1,9 +1,9 @@
 ---
-title: "deepStats - compareCurves"
+title: "deepStats - compareCurves 0.2"
 output: html_notebook
 ---
 
-/!\ This Notebook is not yet updated /!\
+THIS NOTEBOOK IS NOT UP TO DATE YET
 
 This tool assesses if multiple genomics signals ( ChIP-seq, ATAC-seq... ) are significantly different or
 not between conditions ( control, KO1, KO2, etc ). DeepStats compareCurves uses bootstraps and corrected