--- a/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml	Wed Oct 28 01:59:25 2020 +0000
+++ b/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml	Tue Dec 29 04:11:02 2020 +0000
@@ -14,11 +14,11 @@
         python '$__tool_directory__/PDAUG_Peptide_Data_Access.py' -d '$SelectDatasets.DataBaseType' -o '$output1'
 
             #if $SelectDatasets.DataBaseType == "query_apd"
-                -L $SelectDatasets.list1 
+                -L '$SelectDatasets.list1'
             #end if
 
             #if $SelectDatasets.DataBaseType == "query_camp"
-                -L $SelectDatasets.list2 
+                -L '$SelectDatasets.list2'
             #end if            
                   
     ]]></command>
@@ -29,9 +29,9 @@
     <conditional name="SelectDatasets">
 
       <param name="DataBaseType" type="select" label="Datasets"   argument="--DataBaseType" help="Name of the data set.">   
-          <option value="AMPvsTM" selected="true" > AMPvsTM </option>
+          <option value="AMPvsTMP" selected="true" > AMPvsTMP </option>
           <option value="AMPvsUniProt" > AMPvsUniProt </option>
-          <option value="ACPvsTM"> ACPvsTM </option>
+          <option value="ACPvsTMP"> ACPvsTMP </option>
           <option value="ACPvsRandom"> ACPvsRandom </option>
           <option value="query_apd"> Query APD Database</option>
           <option value="query_camp" > Query CAMP Database </option>
@@ -58,8 +58,8 @@
 
   <tests>
     <test>
-      <param name="DataBaseType" value="AMPvsTM"/>
-      <output name="output1" file="out.tsv"/>
+      <param name="DataBaseType" value="AMPvsTMP"/>
+      <output name="output1" file="Out.tsv"/>
     </test>
 
     <test>
@@ -84,10 +84,12 @@
 
 This tool returns inbuild peptide data sets. 
 
-  * **AMPvsTM**  This option returns Antimicrobial peptides and transmembrane sequences. 
-  * **AMPvsUniProt** This option returns AMPs from the APD3 and  other peptides from the UniProt database.
-  * **ACPvsTM**  This option returns anticancer peptides (CancerPPD) and helical transmembrane sequences.
-  * **ACPvsRandom**  This option returns anticancer peptides (CancerPPD) and random scrambled AMP sequences.
+  * **AMPvsTMP**  Antimicrobial peptides (AMP) consist of an intersection of all activity annotations of the APD2 and CAMP databases, where gram-positive, gram-negative, and antifungal exact matches were observed versus transmenbrane peptides (TMP) extracted from alpha-helical transmembrane regions of proteins for classification.
+  * **AMPvsUniProt** AMP consisting of the whole APD3 versus UniProt peptides randomly extracted from the UniProt database, to be used for classification.
+  * **ACPvsTMP**  Anticancer Peptide (ACP) sequences from the CancerPPD database  versus TM extracted from alpha-helical transmembrane regions of proteins for classification.
+  * **ACPvsRandom** ACP sequences from the CancerPPD database versus Random peptides generated randomly with the amino acid composition of AMPs.
+  * **query_apd** Retrive sequences from the antimicrobial peptide database APD.
+  * **query_camp** Retrive sequences from the antimicrobial peptide database CAMP.
 
 -----