Mercurial > repos > dchristiany > data_manager_proteore

changeset 34:0c0586ac3e29 draft

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planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
author dchristiany
date Mon, 28 Jan 2019 09:21:28 -0500
parents cdeffb3670c3
children b312ea6438a2
files data_manager/resource_building.py data_manager/resource_building.xml
diffstat 2 files changed, 25 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.py	Mon Jan 28 08:44:47 2019 -0500
+++ b/data_manager/resource_building.py	Mon Jan 28 09:21:28 2019 -0500
@@ -63,10 +63,10 @@
     # 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
-    tissue=tissue.split("-")
+    tissue=tissue.split(".")
     sample_category_id = tissue[0]
-    name = tissue[1]
-    output_file = name+"_"+time.strftime("%d-%m-%Y") + ".tsv"
+    tissue_name = tissue[1]
+    output_file = tissue_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+ \
@@ -84,8 +84,8 @@
 
     #columns of data table peptide_atlas
     date = time.strftime("%d-%m-%Y")
-    tissue_id = name+"_"+date
-    tissue_name = tissue_id.replace("-","/").replace("_"," ")
+    tissue_id = tissue_name+"_"+date
+    name = tissue_id.replace("-","/").replace("_"," ")
     path = os.path.join(output_file)
 
     with open(path,"w") as out :
@@ -93,7 +93,7 @@
         w.writerow(["Uniprot_AC","nb_obs"])
         w.writerows(uni_dict.items())
         
-    data_table_entry = dict(id=tissue_id, name=tissue_name, value = path, tissue = tissue)
+    data_table_entry = dict(id=tissue_id, name=name, value = path, tissue = tissue_name)
     _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_peptide_atlas")
 
 #function to count the number of observations by uniprot id
--- a/data_manager/resource_building.xml	Mon Jan 28 08:44:47 2019 -0500
+++ b/data_manager/resource_building.xml	Mon Jan 28 09:21:28 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.25.4" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.25.5" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
@@ -41,24 +41,24 @@
         </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="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>
             </param>
         </when>
         <when value="id_mapping">