<tool id="epifinder_0.2" name="EpiFinder" version="1.0">
  <description>Predict B cell epitopes</description>
    <requirements>
		<requirement type="package" version=">=1.8">Java</requirement>
		<requirement type="package" version=">=2.11.0+">Blastp</requirement>
		<requirement type="package" version=">=2.11.0+">Makeblastdb</requirement>
    </requirements>
	<stdio>
		<regex match="command not found"
           source="both"
           level="log"
           description="WARNING: some methods could not be applied -> check inputs and outputs files" />
		<regex match="makeblastdb "
           source="both"
           level="log"
           description="makeblastdb and blastp must be in $PATH on your Galaxy server" />  
		<regex match="blastp "
           source="both"
           level="log"
           description="makeblastdb and blastp must be in $PATH on your Galaxy server" />  
	</stdio>
    <command><![CDATA[
	#*<!-- 
		Methods used will be saved in $param with each threshold 
		Threshold is separated from method by ":"
		Each method is separated by ";"
		example: emini:0.8;parker:d;

		>> d means defalt threshold
	-->*#

	#*<!-- Set variables that concatenate methods -->*#
	#set param = ''
	#set nomethod = ''
	#set proteomes = ''

	#*<!-- Add Bepipred2.0 method -->*#
	#if $bepi_type.bepipred_origin == 'y':
		#set bepipred_origin = '-o'
	#*<!-- jobid -->*#
	#elif $bepi_type.bepipred_origin == 'id':
		#set bepipred_origin = '-jobid ' + str($bepi_type.job_id)
	#else:
		#set bepipred_origin = ''
	#end if
	
	#*<!-- Add Emini method -->*#
	#if $emini_method.emini_choice == 'eminiyes':
		#if $emini_method.emini_t.t_emini == 't_emini_choice'
			#set param += 'emini:' + str($emini_method.emini_t.thresh_em_value) + ';'
		#else:
			#set param += 'emini:d;'		
		#end if
	#end if

	#*<!-- Add Parker method -->*#
	#if $parker_method.parker_choice == 'parkeryes':
		#if $parker_method.parker_t.t_parker == 't_parker_choice'
			#set param += 'parker:' + str($parker_method.parker_t.thresh_park_value) + ';'
		#else:
			#set param += 'parker:d;'		
		#end if
    #end if

	#*<!-- Add Chou method -->*#
	#if $chou_method.chou_choice == 'chouyes':
		#if $chou_method.chou_t.t_chou == 't_chou_choice'
			#set param += 'chou_fosman:' + str($chou_method.chou_t.thresh_chou_value) + ';'
		#else:
			#set param += 'chou_fosman:d;'		
		#end if
    #end if

	#*<!-- Add Karplus method -->*#
	#if $karplus_method.karplus_choice == 'karplusyes':
		#if $karplus_method.karplus_t.t_karplus == 't_karplus_choice'
			#set param += 'karplus_schulz:' + str($karplus_method.karplus_t.thresh_karplus_value) + ';'
		#else:
			#set param += 'karplus_schulz:d;'		
		#end if
    #end if

	#*<!-- Add Kolaskar method -->*#
	#if $kolaskar_method.kolaskar_choice == 'kolaskaryes':
		#if $kolaskar_method.kolaskar_t.t_kolaskar == 't_kolaskar_choice'
			#set param += 'kolaskar:' + str($kolaskar_method.kolaskar_t.thresh_kolaskar_value) + ';'
		#else:
			#set param += 'kolaskar:d;'		
		#end if
    #end if



	#*<!-- Clean $proteome if there's no protome -->*#
	#if proteomes == '-proteomes ':
		#set proteomes = ''	
	#end if


	#*<!-- Parse blast command -->*#
	
	#if $use_blast.blast_use_bool == "use":
		#*<!-- Add proteomes, as many as given -->*#
		#if $use_blast.prot_input: 
			#for $file in $use_blast.prot_input:
				#set proteomes += str($file.prot_name) + '=' + str($file.prot_file) + ';'
			#end for
		#end if
		#if $use_blast.prot_input:
			#if $use_blast.blast.blast_search == 'blastyes':
				#set blast_command = 'task=' + str($use_blast.blast.blast_task) 		
				#set blast_command += ';identity=' + str($use_blast.blast.blast_id) + ';cover=' + str($use_blast.blast.blast_cover) + ';word-size=' + str($use_blast.blast.blast_wordsize)
				#set blast_command += ';makeblastdb_path=makeblastdb;blastp_path=blastp'
			#end if
		#end if
	#end if

	#*<!-- Paste Command-line and run -->*#

	java -jar $__tool_directory__/epifinder-1.0.jar
	
	#*<!-- bepipred_origin give -o if online, nothing if command and -jobid if jobID -->*#
	#*<!-- if origin is not jobid, there is a file, and -b must be passed  -->*#
	#if $bepi_type.bepipred_origin != 'id':
		-b ${bepi_type.bepi_out}
	#end if 
	-t ${tresh_bepi2} 
	${bepipred_origin}
	#if $param:
		-p "${param}"
	#end if
	-f "${basename}"
	-min_len ${min_length} 
	-max_len ${max_length}
	#if $proteomes:
		-proteomes
		"${proteomes}"
		#if $use_blast.blast.blast_search == 'blastyes':
			-blast "${blast_command}"
		#end if
	#end if
	#*<!-- DONT REMOVE THIS ; -->*#
	>log.log 2>log.log; 

	mv $basename-epifinder.xlsx epifinder_report.xlsx;

	#*<!-- Rename output files -->*#
	mv ${basename}-epifinder.txt epifinder;


	]]>
	</command>
    <inputs> 
		<!-- Bepipred 2.0 -->
		<conditional name="bepi_type">
			<param name="bepipred_origin" type="select" display="radio" label="Input files" help="Online prediction returns a csv file, command-line based returns a tsv file" >
				<option value="y" selected="true">csv file from Bepipred 2.0</option>
				<option value="n" >text file from IEDB Bcell Software standalone</option>
				<option value="id">JobID from Bepipred 2.0 Server</option>
			</param>
			<when value="y" >
				<param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
			</when>
			<when value="n" >
				<param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
			</when>
			<when value="id" >
				<param name="job_id" type="text" value="" label="JobID" help="Prediction must be complete - check it in: http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=YOUR_JOB_ID" >
					<!-- Check if its an empty value-->
					<validator type="empty_field" message="ID required"/>
				</param>
			</when>
		</conditional>
		<param name="tresh_bepi2" min="0.0" value="0.6" type="float" label="Threshold for Bepipred 2.0" help="Default = 0.6" />
		<!-- Epitope Length -->					
		<param name="min_length" value="10" min="1" type="integer" label="Min epitope length" help="[1-X] Minimal length must be smaller than maximal length" />
		<param name="max_length" value="30" min="2" type="integer" label="Max epitope length" help="[2-X] Maximal length must be greather than minimal length" />	
		<!-- EMINI -->
		<conditional name="emini_method">
			<param name="emini_choice" type="boolean" checked="true" truevalue="eminiyes" falsevalue="eminino" label="Use Emini Surface Accessibility Prediction method?" />
			<when value="eminino">
			</when>
			<when value="eminiyes">
			<conditional name="emini_t">
					<param name="t_emini" display="radio" type="select" label="Threshold" help="Define threshold for Emini" >
						<option value="d_emini_choice" selected="true">Default (calculated by method)</option>
						<option value="t_emini_choice">Set Threshold</option>
					</param>
					<when value="t_emini_choice">
						<param name="thresh_em_value" value="0" type="float" label="Value" />
					</when>
					<when value="d_emini_choice">
					</when>
				</conditional>
			</when>
		</conditional>
		<!-- PARKER -->
		<conditional name="parker_method">
			<param name="parker_choice" type="boolean" checked="true" truevalue="parkeryes" falsevalue="parkerno" label="Use Parker Hydrophilicity Prediction method?" />
			<when value="parkerno">
			</when>
			<when value="parkeryes">
			<conditional name="parker_t">
					<param name="t_parker" display="radio" type="select" label="Threshold" help="Define threshold for Parker" >
						<option value="d_parker_choice" selected="true">Default (calculated by method)</option>
						<option value="t_parker_choice">Set Threshold</option>
					</param>
					<when value="t_parker_choice">
						<param name="thresh_park_value" value="0" type="float" label="Value" />
					</when>
					<when value="d_parker_choice">
					</when>
				</conditional>
			</when>
		</conditional>
		<!-- Chou -->
		<conditional name="chou_method">
			<param name="chou_choice" type="boolean" checked="true" truevalue="chouyes" falsevalue="chouno" label="Use Chou &amp; Fasman Beta-Turn Prediction method?" />
			<when value="chouno">
			</when>
			<when value="chouyes">
			<conditional name="chou_t">
					<param name="t_chou" display="radio" type="select" label="Threshold" help="Define threshold for Chou &amp; Fasman" >
						<option value="d_chou_choice" selected="true">Default (calculated by method)</option>
						<option value="t_chou_choice">Set Threshold</option>
					</param>
					<when value="t_chou_choice">
						<param name="thresh_chou_value" value="0" type="float" label="Value" />
					</when>
					<when value="d_chou_choice">
					</when>
				</conditional>
			</when>
		</conditional>
		<!-- Karplus -->
		<conditional name="karplus_method">
			<param name="karplus_choice" type="boolean" checked="true" truevalue="karplusyes" falsevalue="karplusno" label="Use Karplus &amp; Schulz Flexibility Prediction method?" />
			<when value="karplusno">
			</when>
			<when value="karplusyes">
			<conditional name="karplus_t">
					<param name="t_karplus" display="radio" type="select" label="Threshold" help="Define threshold for Karplus &amp; Schulz" >
						<option value="d_karplus_choice" selected="true">Default (calculated by method)</option>
						<option value="t_karplus_choice">Set Threshold</option>
					</param>
					<when value="t_karplus_choice">
						<param name="thresh_karplus_value" type="float" value="0" label="Value" />
					</when>
					<when value="d_karplus_choice">
					</when>
				</conditional>
			</when>
		</conditional>
		<!-- Kolaskar -->
		<conditional name="kolaskar_method">
			<param name="kolaskar_choice" type="boolean" checked="true" truevalue="kolaskaryes" falsevalue="kolaskarno" label="Use Kolaskar &amp; Tongaonkar Antigenicity method?" />
			<when value="kolaskarno">
			</when>
			<when value="kolaskaryes">
			<conditional name="kolaskar_t">
					<param name="t_kolaskar" display="radio" type="select" label="Threshold" help="Define threshold for Kolaskar &amp; Tongaonkar" >
						<option value="d_kolaskar_choice" selected="true">Default (calculated by method)</option>
						<option value="t_kolaskar_choice">Set Threshold</option>
					</param>
					<when value="t_kolaskar_choice">
						<param name="thresh_kolaskar_value" type="float" value="0" label="Value" />
					</when>
					<when value="d_kolaskar_choice">
					</when>
				</conditional>
			</when>
		</conditional>
		<!-- Insert Proteome -->
		<conditional name="use_blast">
			<param name="blast_use_bool" type="boolean" checked="false" truevalue="use" falsevalue="dont" label="Do you want to search the predicted epitopes in a proteome file?" />
			<when value="dont">
			</when>
			<when value="use">
				<repeat name="prot_input" title="Proteome" min="1">
					<param type="data" name="prot_file" format="fasta" label="Proteome file" help="Protein sequences in fasta format" />
					<param type="text" name="prot_name" label="Proteome name" help="Give a name to this dataset" >
						<!-- Change spaces for '_' -->
						<sanitizer>
							<valid initial="string.printable">
								<remove value=" "/>
							</valid>
							<mapping initial="none">
								<add source=" " target="_"/>
							</mapping>
						</sanitizer>
						<!-- Check if its an empty value-->
						<validator type="empty_field" message="Basename required"/>
					</param>
				</repeat>
				<conditional name="blast">
					<param name="blast_search" type="boolean" checked="false" truevalue="blastyes" falsevalue="blastno" label="Blastp" help="Choose this option if you want to add a blast search for epitopes in proteomes" />
					<when value="blastno">
					</when>
					<when value="blastyes">
						<param name="blast_id" value="90" min="1" type="integer" label="Identity" help="[0-100] Minimal identity accepted to parse blast results" />
						<param name="blast_cover" value="90" min="2" type="integer" label="Coverage" help="[0-100] Minimal coverage accepted to parse blast results" />			
						<param name="blast_wordsize" value="4" min="1" type="integer" label="Word-Size" help="Blast argument word-size" />
						<param name="blast_task" type="select" label="Task" help="How blastp should run">
							<option value="blastp-short" selected="True">Blastp-short</option>
							<option value="blastp-fast">Blastp-fast</option>
							<option value="blastp">Blastp</option>
						</param>	
					</when>
				</conditional>
			</when>
		</conditional>
		<param name="basename" type="text" value="" label="Basename" help="Provide a name for this run (string text without special characters)" >
		<!-- Change spaces for '_' -->
			<sanitizer>
				<valid initial="string.printable">
					<remove value=" "/>
				</valid>
				<mapping initial="none">
          			<add source=" " target="_"/>
        		</mapping>
			</sanitizer>
		<!-- Check if its an empty value-->
			<validator type="empty_field" message="Basename required"/>
		</param>
	</inputs>
    <outputs>
	<data name="epif_out" format="txt" from_work_dir="epifinder" label="EpiFinder Output Summary - ${basename}" />
	<data name="ep_xls" format="xlsx" from_work_dir="epifinder_report.xlsx" label="EpiFinder Report - ${basename}" />
	<collection type="list" label="EpiFinder Files - ${basename}" name="epif_collection" >
		<discover_datasets format="fasta" pattern="(?P&lt;designation&gt;.*)\.fasta" visible="false" />
		<discover_datasets format="txt" pattern="(?P&lt;designation&gt;.*)\.tsv" visible="false"  />
		<discover_datasets format="txt" pattern="(?P&lt;designation&gt;.*)\.txt" visible="false" />
	</collection>
	<collection type="list" label="EpiFinder Blast Run - ${basename}" name="blast_collection" >
		<filter>use_blast['blast_use_bool'] is True and use_blast['blast']['blast_search'] is True</filter>
        <discover_datasets pattern="(?P&lt;designation&gt;.*)blast\.csv" visible="false" />
    </collection>
	</outputs>
		<tests>
		<test>
			<!-- Test all methods threshold selected, command line version of input with proteome-->
			<conditional name="bepi_type">
				<param name="bepipred_origin" value="y"/>
				<param name="bepi_out" value="input_bepi_online.csv"/>
			</conditional>
			<param name="tresh_bepi2" value="0.6"/>	

		    <param name="min_length" value="10" />
			<param name="max_length" value="30" />	
			
			<conditional name="emini_method">
				<param name="emini_choice"  value="eminiyes"/>
				<conditional name="emini_t">
					<param name="t_emini" value="t_emini_choice"/>
					<param name="thresh_em_value" value="0.8" />
				</conditional>
			</conditional>

			<conditional name="parker_method">
				<param name="parker_choice"  value="parkeryes"/>
				<conditional name="parker_t">
					<param name="t_parker" value="t_parker_choice"/>
					<param name="thresh_park_value" value="0.8" />
				</conditional>
			</conditional>

			<conditional name="chou_method">
				<param name="chou_choice"  value="chouyes"/>
				<conditional name="chou_t">
					<param name="t_chou" value="t_chou_choice"/>
					<param name="thresh_chou_value" value="0.8" />
				</conditional>
			</conditional>

			<conditional name="karplus_method">
				<param name="karplus_choice"  value="karplusyes"/>
				<conditional name="karplus_t">
					<param name="t_karplus" value="t_karplus_choice"/>
					<param name="thresh_karplus_value" value="0.8" />
				</conditional>
			</conditional>


			<conditional name="kolaskar_method">
				<param name="kolaskar_choice"  value="kolaskaryes"/>
				<conditional name="kolaskar_t">
					<param name="t_kolaskar" value="t_kolaskar_choice"/>
					<param name="thresh_kolaskar_value" value="0.8" />
				</conditional>
			</conditional>
			<!-- This first part test all methods-->

			<conditional name="use_blast" >
			<param name="blast_use_bool" value="use" />
				<repeat name="prot_input">
					<param name="prot_name" value="test_proteom" />
					<param name="prot_file" value="proteom.fasta" />
				</repeat>
				<conditional name="blast">
					<param name="blast_search" value="blastyes" />
					<param name="blast_id" value="90" />
					<param name="blast_cover" value="90" />
					<param name="blast_wordsize" value="4" />
					<param name="blast_task" value="blastp-short" />
				</conditional>
			</conditional>

			<param name="basename" value="online" />

			<output name="epif_out" file="online-epifinder.txt" />
			<output name="ep_xls" file="online-epifinder.xlsx" />
			<output_collection name= "epif_collection">
				<element name="ep_prot_sum" file="online-epifinder-protein-summary.tsv" />
				<element name="ep_top" file="online-epifinder-topology.tsv" />
				<element name="ep_score" file="online-epifinder-socre.tsv" />
				<element name="ep_detail" file="online-epifinder-epitope-detail.tsv" />
				<element name="ep_parameters" file="online-epifinder-parameters.tsv" />
				<element name="ep_fasta" file="online-epifinder-fasta.fasta" />
			</output_collection>
			<output_collection  name="blast_collection" >
				<element name="test_proteom" file="online-test_proteom_blast.csv" ftype="csv" />
			</output_collection >
		</test>
		
		<test>
			<!-- Test all methods threshold selected, online version of input with proteome-->
			<conditional name="bepi_type">
				<param name="bepipred_origin" value="y"/>
				<param name="bepi_out" value="input_bcell_command_line.txt"/>
			</conditional>
			
			<param name="bepipred_origin" value="n"/>
			<param name="tresh_bepi2" value="0.6"/>	

		    <param name="min_length" value="10" />
			<param name="max_length" value="30" />	
			
			<conditional name="emini_method">
				<param name="emini_choice"  value="eminiyes"/>
				<conditional name="emini_t">
					<param name="t_emini" value="t_emini_choice"/>
					<param name="thresh_em_value" value="0.8" />
				</conditional>
			</conditional>

			<conditional name="parker_method">
				<param name="parker_choice"  value="parkeryes"/>
				<conditional name="parker_t">
					<param name="t_parker" value="t_parker_choice"/>
					<param name="thresh_park_value" value="0.8" />
				</conditional>
			</conditional>

			<conditional name="chou_method">
				<param name="chou_choice"  value="chouyes"/>
				<conditional name="chou_t">
					<param name="t_chou" value="t_chou_choice"/>
					<param name="thresh_chou_value" value="0.8" />
				</conditional>
			</conditional>

			<conditional name="karplus_method">
				<param name="karplus_choice"  value="karplusyes"/>
				<conditional name="karplus_t">
					<param name="t_karplus" value="t_karplus_choice"/>
					<param name="thresh_karplus_value" value="0.8" />
				</conditional>
			</conditional>


			<conditional name="kolaskar_method">
				<param name="kolaskar_choice"  value="kolaskaryes"/>
				<conditional name="kolaskar_t">
					<param name="t_kolaskar" value="t_kolaskar_choice"/>
					<param name="thresh_kolaskar_value" value="0.8" />
				</conditional>
			</conditional>
			<!-- This first part test all methods-->

			<conditional name="use_blast">
				<param name="blast_use_bool" value="use"/>
					<repeat name="prot_input">
						<param name="prot_name" value="test_proteom" />
						<param name="prot_file" value="proteom.fasta" />
					</repeat>
					<conditional name="blast">
						<param name="blast_search" value="blastyes" />
						<param name="blast_id" value="90" />
						<param name="blast_cover" value="90"/>
						<param name="blast_wordsize" value="4" />
						<param name="blast_task" value="blastp-short" />
					</conditional>
			</conditional>
	
			<param name="basename" value="command" />

			<output name="epif_out" file="command-epifinder.txt" />
			<output name="ep_xls" file="command-epifinder.xlsx" />
			<output_collection name= "epif_collection">
				<element name="ep_prot_sum" file="command-epifinder-protein-summary.tsv" />
				<element name="ep_top" file="command-epifinder-topology.tsv" />
				<element name="ep_score" file="command-epifinder-socre.tsv" />
				<element name="ep_detail" file="command-epifinder-epitope-detail.tsv" />
				<element name="ep_parameters" file="command-epifinder-parameters.tsv" />
				<element name="ep_fasta" file="command-epifinder-fasta.fasta" />
			</output_collection>
			<output_collection  name="blast_collection" >
				<element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" />
			</output_collection >
		</test>
	</tests>
    <help>
**How to Run**

First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred's server.

.. class:: warningmark 

Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite.

Select methods that you want to check your epitopes for validation.

Give a threshold for each method (or use default threshold).

Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish.

.. class:: warningmark 

If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server's $PATH.

-----

**Outputs**


**Summary** : Prediction overview 

**Protein Summary** : Show proteins that have epitopes predicted

**Fasta** : Epitopes' sequences

**Topology** : Show epitope match in each method, aminoacid per aminoacid

**Score** : Detailed score for aminoacids

**Epitope Detail** : Properties of each predicted epitope

**Parameters** : Softwares, thresholds and parameters used for prediction

**Xls Report** : Table with epitope detail, protein summary, topology and scores

**Collection with blast files** : All blast results for each proteome 


-----

.. class:: infomark

**For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/epifinder

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Please cite methods used in your analysis, available bellow

| Bioinformatics Lab - UFSC - 2021

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	<citation type="doi">10.1093/nar/gkx346</citation>
	<citation type="doi">10.1016/0014-5793(90)80535-q</citation>
	<citation type="doi">10.1002/9780470122921.ch2</citation>
	<citation type="doi">10.1021/bi00367a013</citation>
	<citation type="doi">https://doi.org/10.1007/BF01195768</citation>
	<citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation>
	<citation type="doi">10.1371/journal.pcbi.1006791</citation>
	<citation type="doi">https://doi.org/10.1093/nar/gky379</citation>
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