Mercurial > repos > proteore > proteore_tissue_specific_expression_data

changeset 11:ad853c9b3232 draft

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"planemo upload commit 20b2ab253fe8386e248493316760a3fb5ccc309d-dirty"
author proteore
date Mon, 03 Feb 2020 16:28:54 +0000
parents c13a9112a345
children 0a170577648b
files Build_tissue-specific_expression_dataset.xml
diffstat 1 files changed, 10 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/Build_tissue-specific_expression_dataset.xml	Mon Feb 03 10:02:52 2020 +0000
+++ b/Build_tissue-specific_expression_dataset.xml	Mon Feb 03 16:28:54 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2020.02.03.3">
+<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2020.02.03.4">
 <description>[Human Protein Atlas]</description>
 <requirements>
   <requirement type="package" version="3.4.1">R</requirement>
@@ -110,6 +110,10 @@
         </options>
     </param>
     <param name="sample" type="select" label="Select tissue (by clicking in the box)" multiple="True" optional="False">
+        <options from_data_table="Tissue.loc">
+            <filter type="remove_value" column="3"   value="2018-10-23"/>
+            <filter type="sort_by" column="1"/>
+        </options>
       <option value="adipose tissue">Adipose tissue</option>
       <option value="adrenal gland">Adrenal gland</option>
       <option value="appendix">Appendix</option>
@@ -212,11 +216,12 @@
 
 **Data source (release date)**
 
-Release date 23/10/2018: data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38
+Release date 23/10/2018: data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38; file names: normal_tissue.tsv (for IHHC) and rna_tissue.tsv (for RNASeq); 
 
-Release date 22/01/2020: a subset of the data in the Human Protein Atlas version 19.1
+Release date 22/01/2020: a subset of the data in the Human Protein Atlas version 19.1; file names: normal_tissue.tsv (for IHHC) and rna_tissue_consensus.tsv (for RNASeq, HPA-GTEx-FANTOM5); 
 
-downloaded from:  http://www.proteinatlas.org/download/proteinatlas.tab.gz
+
+downloaded from:  https://www.proteinatlas.org/about/download
 
 -----
 
@@ -224,7 +229,7 @@
 
 **Authors**
 
-T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
 David Christiany, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR