# HG changeset patch
# User proteore
# Date 1521044571 14400
# Node ID f294fd77b143afb83456eef62768a983abbdfe17
# Parent  d7f909ae24d91c05e90a78ea6dd4d4116ac28bd7
planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty

diff -r d7f909ae24d9 -r f294fd77b143 README.rst
--- a/README.rst	Wed Mar 07 09:56:25 2018 -0500
+++ b/README.rst	Wed Mar 14 12:22:51 2018 -0400
@@ -13,9 +13,11 @@
 
 -------------------------------------------------
 
-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. 
+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.
+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: 
 
@@ -29,4 +31,25 @@
 
   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
+  The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
+
+-----
+
+**Reliability score**
+
+Reliability score is divided into Enhanced, Supported, Approved, or Uncertain with respect 
+to the definitions from HPA:
+
+Enhanced - One or several antibodies with non-overlapping epitopes targeting the same gene 
+have obtained enhanced validation based on orthogonal or independent antibody validation method.
+
+Supported - Consistency with RNA-seq and/or protein/gene characterization data, 
+in combination with similar staining pattern if independent antibodies are available.
+
+Approved - Consistency with RNA-seq data in combination with inconsistency with, or lack of, 
+protein/gene characterization data. Alternatively, consistency with protein/gene characterization data 
+in combination with inconsistency with RNA-seq data. If independent antibodies are available, 
+the staining pattern is partly similar or dissimilar.
+
+Uncertain - Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data, 
+in combination with dissimilar staining pattern if independent antibodies are available.
diff -r d7f909ae24d9 -r f294fd77b143 sel_ann_hpa.xml
--- a/sel_ann_hpa.xml	Wed Mar 07 09:56:25 2018 -0500
+++ b/sel_ann_hpa.xml	Wed Mar 14 12:22:51 2018 -0400
@@ -51,7 +51,7 @@
             <when value="file" >
                 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of ENSG IDs" help="" />
                 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
-                <param name="ncol" type="text" label="The column number of ENSG IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+                <param name="ncol" type="text" value="c1" label="The column number of ENSG IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
             </when>
         </conditional>
         <conditional name="options">
@@ -68,7 +68,7 @@
                         <filter type="remove_value" meta_ref="proteinatlas" key="name" value="HPA Tumor Tissue" />
 	                </options>
 	            </param>
-                <param name="normal_tissue" type="select" label="Keep and annotate genes present in the following tissue(s)" multiple="True" display="checkboxes" optional="False">
+                <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False">
                     <option value="adrenal gland" >Adrenal gland</option>
                     <option value="appendix" >Appendix</option>
                     <option value="bone marrow" >Bone marrow</option>
@@ -118,16 +118,17 @@
                     <option value="urinary bladder" >Urinary bladder</option>
                     <option value="vagina" >Vagina</option>
                 </param>
-                <param name="level" type="select" label="Expression value" display="checkboxes" multiple="True" optional="False">
+                <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False">
                     <option value="High" selected="true">High</option>
-                    <option value="Medium" selected="true">Medium</option>
-                    <option value="Low" selected="true">Low</option>
-                    <option value="Not detected" selected="true">Not detected</option>
+                    <option value="Medium">Medium</option>
+                    <option value="Low">Low</option>
+                    <option value="Not detected">Not detected</option>
                 </param>
-                <param name="reliability" type="select" label="The gene reliability of the expression value" display="checkboxes" multiple="True" optional="False">
-                    <option value="Approved" selected="true">Approved</option>
+                <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False">
+                    <option value="Enhanced" selected="true">Enhanced</option>
                     <option value="Supported" selected="true">Supported</option>
-                    <option value="Uncertain" selected="true">Uncertain</option>
+                    <option value="Approved">Approved</option>
+                    <option value="Uncertain">Uncertain</option>
                 </param>
             </when>
             <when value="tumor">
@@ -188,9 +189,11 @@
         </test>
     </tests>
     <help><![CDATA[
-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. 
+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.
+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: 
 
@@ -208,6 +211,27 @@
 
 -----
 
+**Reliability score**
+
+Reliability score is divided into Enhanced, Supported, Approved, or Uncertain with respect 
+to the definitions from HPA:
+
+Enhanced - One or several antibodies with non-overlapping epitopes targeting the same gene 
+have obtained enhanced validation based on orthogonal or independent antibody validation method.
+
+Supported - Consistency with RNA-seq and/or protein/gene characterization data, 
+in combination with similar staining pattern if independent antibodies are available.
+
+Approved - Consistency with RNA-seq data in combination with inconsistency with, or lack of, 
+protein/gene characterization data. Alternatively, consistency with protein/gene characterization data 
+in combination with inconsistency with RNA-seq data. If independent antibodies are available, 
+the staining pattern is partly similar or dissimilar.
+
+Uncertain - Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data, 
+in combination with dissimilar staining pattern if independent antibodies are available.
+
+-----
+
 .. class:: infomark
 
 **Authors**