# HG changeset patch
# User proteore
# Date 1561623250 14400
# Node ID 6a9db2cc54deab134f5c59a04aadc62086e442da
# Parent  1c3a5ceab3cd8a85c2c112de6d5a11111c9deeb9
planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty

diff -r 1c3a5ceab3cd -r 6a9db2cc54de get_expression_profiles.xml
--- a/get_expression_profiles.xml	Fri May 17 04:56:57 2019 -0400
+++ b/get_expression_profiles.xml	Thu Jun 27 04:14:10 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="sel_ann_hpa" name="Get expression profiles" version="2019.05.17">
+<tool id="sel_ann_hpa" name="Get expression profiles" version="2019.06.27">
     <description>by (normal or tumor) tissue/cell type [Human Protein Atlas]
     </description>
     <requirements>
@@ -38,7 +38,7 @@
     </command>
        <inputs>
            <conditional name="input" >
-            <param name="ids" type="select" label="Enter your IDs (ENSG IDs only)" help="Copy/paste or from a file (e.g. table)" >
+            <param name="ids" type="select" label="Enter your IDs (Ensembl gene ID only; e.g. ENSG00000163631)" help="Copy/paste or from a file (e.g. table)" >
                 <option value="list">Copy/paste your IDs</option>
                 <option value="file" selected="true">Input file containing your IDs</option>
             </param>
@@ -68,7 +68,7 @@
                 <option value="tumor">Human Tumor Tissue</option>
             </param>
             <when value="normal">
-                <param name="proteinatlas" type="select" label="Normal tissue HPA version" >
+                <param name="proteinatlas" type="select" label="Normal tissue HPA version 18.1" >
                     <options from_data_table="proteore_protein_atlas_normal_tissue">
                         <filter type="sort_by" column="0"/>
                     </options>
@@ -125,7 +125,7 @@
                 </param>
                 <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False">
                     <option value="High" selected="true">High</option>
-                    <option value="Medium">Medium</option>
+                    <option value="Medium" selected="true">Medium</option>
                     <option value="Low">Low</option>
                     <option value="Not detected">Not detected</option>
                 </param>
@@ -137,7 +137,7 @@
                 </param>
             </when>
             <when value="tumor">
-                <param name="proteinatlas" type="select" label="Tumor tissue HPA version" >
+                <param name="proteinatlas" type="select" label="Tumor tissue HPA version 18.1" >
                     <options from_data_table="proteore_protein_atlas_tumor_tissue">
                         <filter type="sort_by" column="0"/>
                     </options>
@@ -198,10 +198,14 @@
  
 **Input**
 
-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_Converter tool of ProteoRE.
+A list of Ensembl gene IDs (e.g. ENSG00000163631) must be entered (either via a copy/paste or by choosing a file); if it's not the case, please use the ID_Converter tool of ProteoRE.
 
 A line can contains multiple ids if separated by ";". 
 
+.. class:: warningmark
+	
+In copy/paste mode, the number of IDs considered in input is limited to 5000.
+
 -----
 
 **Parameters**
@@ -238,7 +242,7 @@
 
 **Data sources (release date)**
 
-Both normal and tumor tissues data are based on the Human Protein Atlas version 18 and Ensembl version 88.38.
+Both normal and tumor tissues data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38. More information: https://www.proteinatlas.org/about/download
 
 -----
 
@@ -252,7 +256,7 @@
 
 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
 
-Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+Help: contact@proteore.org for any questions or concerns about this tool.
         
     ]]></help>
     <citations>