diff README.rst @ 0:5501e74891e4 draft

planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Fri Feb 16 04:22:54 2018 -0500
@@ -0,0 +1,32 @@
+Wrapper for Expression levels by tissue tool
+=========================
+
+**Authors**
+
+T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
+
+This work has been partially funded through the French National Agency for Research (ANR) IFB project.
+
+Contact [e-mail] for any questions or concerns about the Galaxy implementation of this tool.
+
+=========================
+
+This tool retrieve information from Human Protein Atlas (https://www.proteinatlas.org/) regarding the expression profiles of human genes both on the mRNA and protein level. 
+
+A list of ENSG (Ensembl gene) IDs must be entered (either via a copy/paste or by choosing a file), if it's not the case, please use the ID_Convert tool from ProteoRE.
+
+The resources from Human Protein Atlas that can be queried are the following: 
+
+* **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays.
+
+  The tab-separated file includes Ensembl gene identifier ("Gene"), tissue name ("Tissue"), annotated cell type ("Cell type"), expression value ("Level"), and the gene reliability of the expression value ("Reliability"). 
+
+  The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
+
+* **Human tumor tissue data**: staining profiles for proteins in human tumor tissue based on immunohistochemisty using tissue micro arrays and log-rank P value for Kaplan-Meier analysis of correlation between mRNA expression level and patient survival. 
+
+  The tab-separated file includes Ensembl gene identifier ("Gene"), gene name ("Gene name"), tumor name ("Cancer"), the number of patients annotated for different staining levels ("High", "Medium", "Low" & "Not detected") and log-rank p values for patient survival and mRNA correlation ("prognostic - favourable", "unprognostic - favourable", "prognostic - unfavourable", "unprognostic - unfavourable").
+
+  The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
\ No newline at end of file