diff README.rst @ 1:8dd24f13f923 draft

planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Fri Feb 16 04:09:32 2018 -0500
@@ -0,0 +1,50 @@
+Wrapper for Get annotation from RNAseq/Ab-based experiments (Human species) tool
+=========================
+
+**Authors**
+
+Lisa Peru, 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 adds expression information (RNAseq- or antibody-based experiments) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your protein list.
+
+**Input**
+
+Input can be either a list of Ensembl gene ids (copy/paste) or a file containing multiple fields but with **at least one column of Ensembl gene IDs**. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs.  
+
+**Databases**
+
+HPA source file:  http://www.proteinatlas.org/download/proteinatlas.tab.gz
+
+**Annotation**
+
+- Gene name: according to the HGNC (Hugo Gene Nomenclature Committee) 
+
+- Gene description: entry description (full text)  
+
+- Evidence: at protein level, at transcript level or no evidence
+
+- Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF
+
+- RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna .
+
+- IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if .
+
+- IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih .
+
+- Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa
+
+- RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts.
+
+- RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna.
+
+**Outputs**
+
+The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose. 
\ No newline at end of file