# HG changeset patch
# User jay
# Date 1641700331 0
# Node ID 24184ea66557ad427d9abe89bcd9a038e0a9c2be
# Parent  92bdc5cbf028af32201961109569daf82cbb6fb1
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"

diff -r 92bdc5cbf028 -r 24184ea66557 PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py
--- a/PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py	Sun Jan 31 02:09:47 2021 +0000
+++ b/PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py	Sun Jan 09 03:52:11 2022 +0000
@@ -16,12 +16,12 @@
 filterduplicates = subparsers.add_parser('filterduplicates')
 filterduplicates.add_argument("-I","--InFile", required=True, default=None, help="Input file")
 filterduplicates.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file")
-
+filterduplicates.add_argument("-A","--FilterAA", required=True, default=None, help="Filter amino acide")
 
 keepnaturalaa = subparsers.add_parser('keepnaturalaa')
 keepnaturalaa.add_argument("-I","--InFile", required=True, default=None, help="Inputt file")
 keepnaturalaa.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file")
-
+keepnaturalaa.add_argument("-A","--FilterAA", required=True, default=None, help="Filter amino acide")
 
 filteraa = subparsers.add_parser('filteraa')
 filteraa.add_argument("-I","--InFile", required=True, default=None, help="Input file")
diff -r 92bdc5cbf028 -r 24184ea66557 PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml
--- a/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml	Sun Jan 31 02:09:47 2021 +0000
+++ b/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml	Sun Jan 09 03:52:11 2022 +0000
@@ -13,13 +13,29 @@
 
         python '$__tool_directory__/PDAUG_Peptide_Data_Access.py' -d '$SelectDatasets.DataBaseType' -o '$output1'
 
+            #if $SelectDatasets.DataBaseType == "AMPvsTMP"
+                -d 'AMPvsTMP'
+            #end if
+
+            #if $SelectDatasets.DataBaseType == "AMPvsUniProt"
+                -d 'AMPvsUniProt'
+            #end if     
+
+            #if $SelectDatasets.DataBaseType == "ACPvsTMP"
+                -d 'ACPvsTMP'
+            #end if    
+
+            #if $SelectDatasets.DataBaseType == "ACPvsRandom"
+                -d 'ACPvsRandom'
+            #end if   
+
             #if $SelectDatasets.DataBaseType == "query_apd"
                 -L '$SelectDatasets.list1'
             #end if
 
             #if $SelectDatasets.DataBaseType == "query_camp"
-                -L '$SelectDatasets.list2'
-            #end if            
+                -L '$SelectDatasets.list1'
+            #end if
                   
     ]]></command>
 
@@ -37,12 +53,20 @@
           <option value="query_camp" > Query CAMP Database </option>
       </param> 
 
+       <when value="AMPvsTMP">
 
+       </when>
+
+       <when value="AMPvsUniProt">
 
-       <when value="AMPvsTMP"/>
-       <when value="AMPvsUniProt"/>
-       <when value="ACPvsTMP"/>
-       <when value="ACPvsRandom"/>
+       </when>
+
+       <when value="ACPvsTMP">
+       </when>
+
+       <when value="ACPvsRandom">
+       </when>
+
        <when value="query_apd">
           <param name="list1" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" />
        </when>