--- a/Get_ms-ms_observations.xml	Tue Dec 18 09:50:50 2018 -0500
+++ b/Get_ms-ms_observations.xml	Fri Feb 01 11:34:12 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2018.12.18">
+<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.01">
     <description>[Peptide Atlas]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -16,7 +16,7 @@
             --column_number="$input.ncol"
             --header="$input.header"
         #end if
-        --atlas=${",".join([$__tool_data_path__+"/"+str(ref) for ref in str($atlas).split(",")])}
+        --atlas=${",".join([$__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])}
         --output="$output"
     </command>
 
@@ -46,7 +46,7 @@
         </conditional>
         <!-- Peptide Atlas options -->
         <param name="atlas" type="select" display="checkboxes" multiple="true" label="Proteomics dataset (biological sample)" optional="false" >
-            <options from_data_table="peptide_atlas">
+            <options from_data_table="proteore_peptide_atlas">
                 <filter type="sort_by" column="2"/>
             </options>
         </param>
@@ -91,13 +91,13 @@
 
 **Parameters**
 
-"Proteomics dataset (biological sample)": available human biological samples analyzed by MS/MS are the following: brain, heart, kidney, liver, plasma, urine and cerebrospinal fluid (CSF). 
+"Proteomics dataset (biological sample - date of downloading)": available human biological samples (tissue/organ/body fluid) analyzed by MS/MS and processed by Peptide Atlas are the following: adrenal gland, brain, breast, CSF (cerebrospinal fluid), colon cancer, digestive system, female and male reproductive system, heart, kidney, liver, lung, pancreas, plasma (non-glycosylated), spleen, testis, urinary bladder, urine. 
 
 ----
 
 **Output**
 
-Additional columns are created for each selected proteomics sample reporting the number of times all peptides corresponding to a protein have been observed by LC-MS/MS according to Peptide Atlas. 
+Additional columns are created for each selected proteomics sample reporting the total number of observation (called "ProteinProphet-adjusted N Obs") of all peptides detected by LC-MS/MS and assigned to a protein according to Peptide Atlas. 
 
 a “NA” means that no information has been reported suggesting that this protein has not been observed in the sample of interest.
 
@@ -105,7 +105,26 @@
 
 **Data source (release date)**
 
-Data were retrieved from Peptide Atlas release (January 2018) through their query interface.
+  Data source (release date)" - replace "MS/MS Proteomics dataset (also called "build") were retrieved from Peptide Atlas website through their query interface (in January 2019) with name and release date as follow:
+
+- Human Adrenal Gland 2014-08
+- Human Brain 2015-01
+- Human Breast 2014-08
+- Human CSF 2014-09
+- Human Colon Cancer 2013-02
+- Human Digestive System 2014-08
+- Human Female Reproductive System 2014-08
+- Human Heart 2014-08
+- Human Kidney 2014-08
+- Human Liver 2014-08
+- Human Lung 2014-08
+- Human Male Reproductive System 2014-08
+- Human Pancreas 2014-08
+- Human Plasma Non-Glyco 2017-04
+- Human Spleen 2014-08
+- Human Testis 2017-01
+- Human Urinary Bladder 2014-08
+- Human Urine 2014-08
 
 ----