--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml	Wed Oct 28 02:07:30 2020 +0000
@@ -0,0 +1,154 @@
+<tool id="pdaug_peptide_core_functions" name="PDAUG Peptide Core Functions" version="0.1.0">
+  <description> Peptide sequence related core functions </description>
+
+  <requirements>
+    <requirement type="package" version="0.24.2">pandas</requirement>
+    <requirement type="package" version="4.1.2">modlamp</requirement> 
+  </requirements>
+  <stdio>
+    <exit_code range="1" level="fatal" />
+  </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+
+
+        python '$__tool_directory__/PDAUG_Peptide_Core_Functions.py'  '$SelCoreFunction.CoreFunction'
+
+              --InFile '$InFile'
+
+              #if $SelCoreFunction.CoreFunction == 'mutateAA'
+                  --nr $SelCoreFunction.nr
+                  --Prob $SelCoreFunction.prob
+              #end if 
+
+              #if $SelCoreFunction.CoreFunction == 'filteraa'
+                  --FilterAA $SelCoreFunction.FilterAA
+              #end if 
+
+              --FastOut '$output1'
+
+    ]]></command>
+
+  <inputs>
+
+    <param name="InFile" type="data" format="fasta" label="Input file" argument= "--InFile" help="Input fasta file with peptides"/>
+
+    <conditional name='SelCoreFunction' >
+
+        <param name="CoreFunction" type="select" label="Analysis options" argument="">
+          <option value="mutateAA">Mutate Amino Acid</option>
+          <option value="filterduplicates">Filter Duplicates</option>
+          <option value="keepnaturalaa">Keep Naturalaa</option>
+          <option value="filteraa">Filter Amino Acid</option>
+        </param>
+
+        <when value="mutateAA">
+            <param name="nr" type="integer" label="Number of mutations" value="3" argument="--nr" help="Number of mutations"/>
+            <param name="prob" type="float" label="Probability" value="1.0" argument="--Prob"  help="Probability of mutating a sequence" />
+        </when>
+
+        <when value="filterduplicates">
+        </when>
+
+        <when value="keepnaturalaa">
+        </when>
+
+        <when value="filteraa">
+            <param name="FilterAA" type="text" value="eisenberg" label="Filter AA" argument="--FilterAA" help="Amino acids to be filtered" />
+        </when>
+
+    </conditional>
+  </inputs>
+
+  <outputs>
+        <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelCoreFunction.CoreFunction} (fasta)" />    
+  </outputs>
+  <tests>
+    <test>
+      <param name="InFile" value="test1.fasta"/>
+      <param name="CoreFunction" value="mutateAA" />
+      <param name="nr" value="3"/>
+      <param name="prob" value="1.0"/>
+      <output name="output1" file="out1.fasta" lines_diff="2"/>
+    </test>
+    <test>
+      <param name="InFile" value="test2.fasta"/>
+      <param name="CoreFunction" value="filterduplicates" />
+      <output name="output1" file="out2.fasta" />
+    </test>
+    <test>
+      <param name="InFile" value="test3.fasta"/>
+      <param name="CoreFunction" value="keepnaturalaa" />
+      <output name="output1" file="out3.fasta" />
+    </test>
+    <test>
+      <param name="InFile" value="test4.fasta"/>
+      <param name="CoreFunction" value="filteraa" />
+      <param name="FilterAA" value="eisenberg" />
+      <output name="output1" file="out4.fasta" />
+    </test>
+  </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool performs some core functions on the peptide sequences and equipped with various options
+
+  * **Mutated Amino Acid** Method to mutate with prob probability an nr of positions per sequence randomly.
+  * **Filter Duplicates** Method to filter duplicates in the sequences from the class attribute sequences.
+  * **Keep Naturalaa** Method to filter out sequences that do not contain natural amino acids. If the sequence contains a character.
+  * **Filter Amino Acid** Method to filter out corresponding names and descriptor values of sequences with given amino acids in the argument list aminoacids.
+
+-----
+
+**Inputs**
+    
+    1 **Mutate Amino Acid**
+        * **--InFile** takes Fasta file with peptide sequences.  
+        * **--nr**  Number of mutations. 
+        * **--probability** Probability of mutating a sequence.
+
+    2 **Filter Duplicates***
+        * **--InFile** takes Fasta file with peptide sequences. 
+
+    3 **Keep Naturalaa**
+        * **--InFile** takes Fasta file with peptide sequences. 
+
+    4 **Filter Amino Acid**
+        * **--InFile** takes Fasta file with peptide sequences. 
+
+-----
+
+**Outputs**
+    * Returns a fasta file.]]></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>
+
+
+