Mercurial > repos > dchristiany > data_manager_proteore

changeset 28:d235909789ca draft

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planemo upload commit e694c4b0df30a4286ba09721696e8ec3af25fd97-dirty
author dchristiany
date Fri, 25 Jan 2019 09:38:35 -0500
parents 592c59530c32
children 871a7347ca24
files data_manager/resource_building.py data_manager/resource_building.xml
diffstat 2 files changed, 12 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.py	Thu Jan 24 12:06:21 2019 -0500
+++ b/data_manager/resource_building.py	Fri Jan 25 09:38:35 2019 -0500
@@ -123,8 +123,8 @@
 
 def id_mapping_sources (data_manager_dict, species, target_directory) :
 
-    human = species == "human"
-    species_dict = { "human" : "HUMAN_9606", "mouse" : "MOUSE_10090", "rat" : "RAT_10116" }
+    human = species == "Human"
+    species_dict = { "Human" : "HUMAN_9606", "Mouse" : "MOUSE_10090", "Rat" : "RAT_10116" }
     files=["idmapping_selected.tab.gz","idmapping.dat.gz"]
 
     #header
@@ -218,8 +218,8 @@
         w = csv.writer(out,delimiter='\t')
         w.writerows(tab)
 
-    name_dict={"human" : "Homo sapiens", "mouse" : "Mus musculus", "rat" : "Rattus norvegicus"}
-    name = name_dict[species]+" "+time.strftime("%d/%m/%Y")
+    name_dict={"Human" : "Homo sapiens", "Mouse" : "Mus musculus", "Rat" : "Rattus norvegicus"}
+    name = species +" (" + name_dict[species]+" "+time.strftime("%d/%m/%Y")+")"
     id = species+"_id_mapping_"+ time.strftime("%d-%m-%Y")
 
     data_table_entry = dict(id=id, name = name, value = species, path = path)
@@ -276,7 +276,7 @@
 
 def PPI_ref_files(data_manager_dict, species, interactome, target_directory):
 
-    species_dict={'human':'Homo sapiens',"mouse":"Mus musculus","rat":"Rattus norvegicus"}
+    species_dict={'Human':'Homo sapiens',"Mouse":"Mus musculus","Rat":"Rattus norvegicus"}
 
     ##BioGRID
     if interactome=="biogrid":
--- a/data_manager/resource_building.xml	Thu Jan 24 12:06:21 2019 -0500
+++ b/data_manager/resource_building.xml	Fri Jan 25 09:38:35 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.24.2" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.25" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
@@ -52,9 +52,9 @@
         </when>
         <when value="id_mapping">
             <param name="species" type="select" multiple="false" label="Please select the species">
-                <option value="human">Human (Homo sapiens)</option>
-                <option value="mouse">Mouse (Mus musculus)</option>
-                <option value="rat">Rat (Rattus norvegicus)</option>
+                <option value="Human">Human (Homo sapiens)</option>
+                <option value="Mouse">Mouse (Mus musculus)</option>
+                <option value="Rat">Rat (Rattus norvegicus)</option>
             </param>
         </when>
         <when value="PPI">
@@ -64,9 +64,9 @@
                 <option value="humap">Hu.map</option>
             </param>
             <param name="species" type="select" multiple="false" label="Please select the species">
-                <option value="human">Human (Homo sapiens)</option>
-                <option value="mouse">Mouse (Mus musculus)</option>
-                <option value="rat">Rat (Rattus norvegicus)</option>
+                <option value="Human">Human (Homo sapiens)</option>
+                <option value="Mouse">Mouse (Mus musculus)</option>
+                <option value="Rat">Rat (Rattus norvegicus)</option>
             </param>
         </when>
     </conditional>