--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml	Wed Oct 28 01:59:25 2020 +0000
@@ -0,0 +1,132 @@
+<tool id="pdaug_peptide_data_access" name="PDAUG Peptide Data Access" version="0.1.0">
+  <description>Fetch peptide data from inbuild datasets and public databases</description>
+
+  <requirements>
+    <requirement type="package" version="0.24.2">pandas</requirement>
+    <requirement type="package" version="4.1.2">modlamp</requirement> 
+    <requirement type="package" version="8.0.21">mysql-connector-python</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1" level="fatal" />
+  </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+
+        python '$__tool_directory__/PDAUG_Peptide_Data_Access.py' -d '$SelectDatasets.DataBaseType' -o '$output1'
+
+            #if $SelectDatasets.DataBaseType == "query_apd"
+                -L $SelectDatasets.list1 
+            #end if
+
+            #if $SelectDatasets.DataBaseType == "query_camp"
+                -L $SelectDatasets.list2 
+            #end if            
+                  
+    ]]></command>
+
+
+  <inputs>
+
+    <conditional name="SelectDatasets">
+
+      <param name="DataBaseType" type="select" label="Datasets"   argument="--DataBaseType" help="Name of the data set.">   
+          <option value="AMPvsTM" selected="true" > AMPvsTM </option>
+          <option value="AMPvsUniProt" > AMPvsUniProt </option>
+          <option value="ACPvsTM"> ACPvsTM </option>
+          <option value="ACPvsRandom"> ACPvsRandom </option>
+          <option value="query_apd"> Query APD Database</option>
+          <option value="query_camp" > Query CAMP Database </option>
+      </param> 
+
+
+
+       <when value="query_apd">
+          <param name="list1" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" />
+       </when>
+
+       <when value="query_camp">
+          <param name="list2" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" />
+        </when>
+
+      </conditional>
+
+
+  </inputs>
+
+  <outputs>
+        <data name='output1' format='tabular' label="${tool.name} $on_string - ${SelectDatasets.DataBaseType} (tabular)" />    
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="DataBaseType" value="AMPvsTM"/>
+      <output name="output1" file="out.tsv"/>
+    </test>
+
+    <test>
+      <param name="DataBaseType" value="query_apd"/>
+      <param name="list1" value="4,5,6" />
+      <output name="output1" file="apd.tsv" lines_diff="8"/>
+    </test>
+
+    <test>
+      <param name="DataBaseType" value="query_camp"/>
+       <param name="list2" value="3,4,5,9" />
+      <output name="output1" file="camp.tsv" lines_diff="10"/>
+    </test>
+
+
+  </tests>
+  
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+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.
+
+-----
+
+**Inputs**
+    * **--DataBaseType** Takes dataset name as input. 
+
+-----
+
+**Outputs**
+    * Returns a tabular file with peptide sequences and class labels.]]></help>
+
+
+<citations>
+  <citation type="bibtex">
+    @misc{PDAUGGITHUB, 
+      author = {Joshi, Jayadev  and Blankenberg, Daniel}, 
+      year = {2020}, 
+      title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, 
+      publisher = {GitHub}, 
+      journal = {GitHub repository}, 
+      url =
+      {https://github.com/jaidevjoshi83/pdaug.git}, 
+    }
+</citation>
+
+<citation type="bibtex">
+    @article{müller_gabernet_hiss_schneider_2017, 
+      title={modlAMP: Python for antimicrobial peptides}, 
+      volume={33}, 
+      DOI={10.1093/bioinformatics/btx285}, 
+      number={17}, 
+      journal={Bioinformatics}, 
+      author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, 
+      year={2017}, 
+      pages={2753–2755}
+    }
+  </citation>
+</citations>
+</tool>
+
+
+