# HG changeset patch
# User dchristiany
# Date 1548670615 18000
# Node ID 871a7347ca24baecb4a42558796aea7edf612878
# Parent  d235909789cac8092a115e49b92156bc44124b17
planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty

diff -r d235909789ca -r 871a7347ca24 data_manager/resource_building.py
--- a/data_manager/resource_building.py	Fri Jan 25 09:38:35 2019 -0500
+++ b/data_manager/resource_building.py	Mon Jan 28 05:16:55 2019 -0500
@@ -60,17 +60,16 @@
 # 2. Peptide Atlas
 #######################################################################################################
 def peptide_atlas_sources(data_manager_dict, tissue, target_directory):
-    # Define PA Human build released number (here  early 2018)
-    atlas_build_id = "472"
     # Define organism_id (here Human) - to be upraded when other organism added to the project
     organism_id = "2"
     # Extract sample_category_id and output filename
-    sample_category_id = tissue.split("-")[0]
-    output_file = tissue.split("-")[1] +"_"+ time.strftime("%d-%m-%Y") + ".tsv"
-    query = "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=" + \
-            atlas_build_id + "&display_options=ShowMappings&organism_id= " + \
-            organism_id + "&sample_category_id=" + sample_category_id + \
-            "&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY"
+    tissue=tissue.split(".")
+    sample_category_id = tissue[0]
+    name = tissue[1]
+    output_file = name+"_"+time.strftime("%d-%m-%Y") + ".tsv"
+    query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+sample_category_id+ \
+        "&display_options=ShowAbundances&organism_id="+organism_id+"&redundancy_constraint=4&presence_level_constraint=1%2C2"+ \ 
+        "&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY"
     download = requests.get(query)
     decoded_content = download.content.decode('utf-8')
     cr = csv.reader(decoded_content.splitlines(), delimiter='\t')
diff -r d235909789ca -r 871a7347ca24 data_manager/resource_building.xml
--- a/data_manager/resource_building.xml	Fri Jan 25 09:38:35 2019 -0500
+++ b/data_manager/resource_building.xml	Mon Jan 28 05:16:55 2019 -0500
@@ -41,6 +41,27 @@
         </when>
         <when value="peptide_atlas">
             <param name="tissues" type="select" multiple="false" label="Please select the tissue">
+                <option value="432.Human_Adrenal_gland">Human Adrenal gland proteome</option>
+                <option value="441.Human_Brain">Human Brain proteome</option>
+                <option value="427.Human_Breast">Human Breast proteome</option>
+                <option value="434.Human_CSF">Human CSF (Cerebro Spinal Fluid) proteome</option>
+                <option value="374.Human_Colon_cancer">Human Colon cancer proteome</option>
+                <option value="429.Human_Digestive_system">Human Digestive system proteome</option>
+                <option value="430.Human_Female_reproductive_system">Human Female reproductive system proteome></option>
+                <option value="418.Human_Heart">Human Heart proteome</option>
+                <option value="424.Human_Kidney">Human Kidney proteome</option>
+                <option value="425.Human_Liver">Human Liver proteome</option>
+                <option value="419.Human_Lung">Human Lung proteome</option>
+                <option value="431.Human_Male_reproductive_system">Human Male reproductive system proteome</option>
+                <option value="420.Human_Pancreas">Human Pancreas proteome</option>
+                <option value="465.Human_Plasma_non_glyco">Human Plasma non glyco proteome</option>
+                <option value="421.Human_Spleen">Human Spleen proteome</option>
+                <option value="463.Human_Testis">Human Testis proteome</option>
+                <option value="422.Human_Urinary_bladder">Human Bladder proteome</option>
+                <option value="423.Human_Urine">Human Urine proteome</option>
+
+
+
                 <option value="1-Human_Liver">Human liver</option>
                 <option value="2-Human_Brain">Human brain</option>
                 <option value="4-Human_Heart">Human heart</option>