# HG changeset patch
# User bioinformatics_lab_ufsc
# Date 1615237991 0
# Node ID dd573dcdbb03d8b204c79663da20f9ebb2adacfc
# Parent  43f31f6c3b5908a9ef256d1b1c112c3a43939859
Uploaded

diff -r 43f31f6c3b59 -r dd573dcdbb03 predict_antibody_epitope.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict_antibody_epitope.xml	Mon Mar 08 21:13:11 2021 +0000
@@ -0,0 +1,173 @@
+<tool id="anti_ep_pred" name="IEDB BCELL Antibody Epitope Prediction" version="v3.0">
+  <description>BCELL IEDB Tool</description>
+    <requirements>
+        <requirement type="package" version="3.0">IEDB_BCELL</requirement>
+        <requirement type="package" version="1.0d">Netsurfp</requirement>
+        <requirement type="package">hh-suite</requirement>
+        <requirement type="package">MM-seqs2</requirement>
+        <requirement type="package">nunpy</requirement>
+        <requirement type="package" version="2.0.0">matplotlib</requirement>
+        <requirement type="package" version="0.18">scikit-learn</requirement>
+        <requirement type="package">scipy</requirement>
+	<requirement type="package" version=">2.7">Python</requirement>
+    </requirements>
+    <command interpreter="python">
+	#if $input_type.choice == "fchoice":
+		#if $win_size.cutoff != "def":
+	 	predict_antibody_epitope.py -m $method -f $input_type.file $png > prediction.txt 
+		#else:
+		predict_antibody_epitope.py -m $method -f $input_type.file -w $win_size.threshold $png > prediction.txt
+		#end if
+	#else:
+		#if $win_size.cutoff != "def":
+	 	predict_antibody_epitope.py -m $method -s $input_type.swissid $png > prediction.txt
+		#else:
+		predict_antibody_epitope.py -m $method -s $input_type.swissid -w $win_size.threshold $png > prediction.txt	 
+		#end if
+	#end if
+    </command>
+    <inputs> 
+	<conditional name="input_type">
+		<param name="choice" type="select" display="radio" label="File or Swissprot ID?" >
+		 	<option value="fchoice" selected="true">File</option>
+		 	<option value="schoice">Swissprot ID</option>
+		</param>
+		<when value="fchoice">
+			<param name="file" type="data" format="fasta" label="Fasta File" help="Fasta or multifasta with protein(s) sequênce(s)" />
+		</when>
+		<when value="schoice">
+			<param name="swissid" type="text" label="SwissprotID"/>
+		</when>
+	</conditional>
+	<param name="method" type="select" display="radio" label="Prediction method">
+		<option value="Chou-Fasman" selected="true">Chou-Fasman</option>
+		<option value="Emini">Emini</option>
+		<option value="Karplus-Schulz">Karplus-Schulz</option>
+		<option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
+		<option value="Parker">Parker</option>
+		<option value="Bepipred">Bepipred</option>
+		<option value="Bepipred-2.0">Bepipred-2.0</option>
+	</param>
+	<conditional name="win_size" >
+	<param name="cutoff" type="select" display="radio" label="Window Size" >
+		 <option value="" selected="true">Default, defined by method</option>
+		 <option value="def">Set threshold</option>
+	</param>
+		 <when value="def">
+			<param name="threshold" type="integer" value="6" label="Threshold"/>
+		 </when>
+	</conditional>
+	<param name="png" type="select" display="radio" label="Plot png graph?">
+		<option value="--plot .">Yes</option>
+		<option value=" " selected="true">No</option>
+	</param>
+    </inputs>
+    <outputs>
+	<data name="pred" format="txt" from_work_dir="prediction.txt" label="Antibody Epitope prediction with $method - ${on_string}" />
+	<data name="png_out" format="png" label="${tool.name} Plot png: ${on_string}" >
+		<discover_datasets pattern="plot_" ext="png" visible="true" assign_primary_output="true" />
+		<filter>png == "--plot ."</filter>
+    	</data>
+    </outputs>
+<tests>
+        <test>
+                <!-- Testing Chou-Fasman method -->
+                <param name="method" value="Chou-Fasman" />
+                <param name="file" value="test/single_sequence.txt" />
+                <output name="pred" value="test/result_chou.txt" />
+                <output name="png_out" value="test/png_chou.png" />
+        </test>
+        <test>
+                <!-- Testing Emini method -->
+                <param name="method" value="Emini" />
+                <param name="file" value="test/single_sequence.txt" />
+                <output name="pred" value="test/result_emiini.txt" />
+                <output name="png_out" value="test/png_emini.png" />
+        </test>
+        <test>
+                <!-- Testing Karplus-Schulz method -->
+                <param name="method" value="Karplus-Schulz" />
+                <param name="file" value="test/multiple_sequence.txt" />
+                <output name="pred" value="test/result_karplus.txt" />
+                <output name="png_out" value="test/png_karplus.png" />
+        </test>
+        <test>
+                <!-- Testing Kolaskar-Tongaonkar method -->
+                <param name="method" value="Kolaskar-Tongaonkar" />
+                <param name="file" value="test/single_sequence.txt" />
+                <output name="pred" value="test/result_kolaskar.txt" />
+                <output name="png_out" value="test/png_kolaskar.png" />
+        </test>
+        <test>
+                <!-- Testing Parker method -->
+                <param name="method" value="Parker" />
+                <param name="file" value="test/single_sequence.txt" />
+                <output name="pred" value="test/result_parker.txt" />
+                <output name="png_out" value="test/png_parker.png" />
+        </test>
+        <test>
+                <!-- Testing Bepipred method -->
+                <param name="method" value="Bepipred" />
+                <param name="file" value="test/single_sequence.txt" />
+                <output name="pred" value="test/result_bepipred1.0.txt" />
+                <output name="png_out" value="test/png_bepipred1.0.png" />
+        </test>
+        <test>
+                <!-- Testing Bepipred 2.0 method -->
+                <param name="method" value="Bepipred-2.0" />
+                <param name="file" value="test/single_sequence.txt" />
+                <output name="pred" value="test/result_bepipred2.0.txt" />
+                <output name="png_out" value="test/png_bepipred2.0.png" />
+        </test>
+
+</tests>
+
+    <help>
+**How it works**
+
+-----
+
+**This is only bcell interface, need bcell installed on your Galaxy server**
+
+-----
+
+This package contains a collection of methods to predict linear B cell epitopes based on
+
+sequence characteristics of the antigen using amino acid scales and HMMs. The collection
+
+is a mixture of pythons scripts and linux environment specific binaries for Bepipred method.
+
+-----
+
+**WARNING: It's allowed only aminoacid sequences without (*) X and U, please remove it from your sequence before run.**
+
+
+-----
+
+**Outputs**
+	
+	- **Antibody Epitope prediction** - Prediction with method and parameters informed;
+	- **Plot png** - Graphical representation of results;
+
+-----
+
+| We can go on forever with the darkness so far away
+| Laboratory of Bioinformatics- UFSC - 2021
+   </help>
+<citations>
+	<citation type="doi">10.1093/nar/gkx346</citation>
+	<citation type="doi">10.1110/ps.062405906</citation>
+	<citation type="doi">10.1186/1472-6807-7-64</citation>
+	<citation type="doi">10.1186/1745-7580-2-2</citation>
+	<citation type="doi">10.1021/bi00367a013</citation>
+	<citation type="doi">10.1016/0014-5793(90)80535-q</citation>
+	<citation type="doi">10.1002/9780470122921.ch2</citation>
+	<citation type="bibtex">@ARTICLE{Kim07aninterior-point,
+	   author = {Emini EA, Hughes JV, Perlow DS, Boger J.},
+	   title = {Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide.},
+	   journal = {Journal of virology vol.},
+	   year = {1985	},
+	   volume = {8},
+	   }</citation>
+</citations>
+</tool>