--- a/predict_antibody_epitope.xml	Mon Mar 08 19:36:42 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,173 +0,0 @@
-<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>