epibuilder: epibuilder-1.1.xml annotate

author	bioinformatics_lab_ufsc
date	Thu, 25 Nov 2021 03:59:45 +0000
parents
children

rev	line source
2 8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	1 <tool id="epibuilder_1.1" name="EpiBuilder" version="1.1">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	2 <description>Predict B cell epitopes</description>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	3 <requirements>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	4 <requirement type="package" version=">=1.8">Java</requirement>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	5 <requirement type="package" version=">=2.11.0+">Blastp</requirement>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	6 <requirement type="package" version=">=2.11.0+">Makeblastdb</requirement>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	7 </requirements>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	8 <stdio>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	9 <regex match="command not found"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	10 source="both"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	11 level="log"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	12 description="WARNING: some methods could not be applied -> check inputs and outputs files" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	13 <regex match="makeblastdb "
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	14 source="both"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	15 level="log"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	16 description="makeblastdb and blastp must be in $PATH on your Galaxy server" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	17 <regex match="blastp "
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	18 source="both"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	19 level="log"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	20 description="makeblastdb and blastp must be in $PATH on your Galaxy server" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	21 </stdio>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	22 <command><![CDATA[
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	23 #*<!--
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	24 Methods used will be saved in $param with each threshold
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	25 Threshold is separated from method by ":"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	26 Each method is separated by ";"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	27 example: emini:0.8;parker:d;
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	28
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	29 >> d means defalt threshold
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	30 -->*#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	31
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	32 #<!-- Set variables that concatenate methods -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	33 #set param = ''
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	34 #set nomethod = ''
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	35 #set proteomes = ''
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	36
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	37 #<!-- Add Bepipred2.0 method -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	38 #if $bepi_type.bepipred_origin == 'y':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	39 #set bepipred_origin = '-o'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	40 #<!-- jobid -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	41 #elif $bepi_type.bepipred_origin == 'id':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	42 #set bepipred_origin = '-jobid ' + str($bepi_type.job_id)
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	43 #else:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	44 #set bepipred_origin = ''
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	45 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	46
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	47 #<!-- Add Emini method -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	48 #if $emini_method.emini_choice == 'eminiyes':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	49 #if $emini_method.emini_t.t_emini == 't_emini_choice'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	50 #set param += 'emini:' + str($emini_method.emini_t.thresh_em_value) + ';'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	51 #else:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	52 #set param += 'emini:d;'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	53 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	54 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	55
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	56 #<!-- Add Parker method -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	57 #if $parker_method.parker_choice == 'parkeryes':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	58 #if $parker_method.parker_t.t_parker == 't_parker_choice'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	59 #set param += 'parker:' + str($parker_method.parker_t.thresh_park_value) + ';'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	60 #else:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	61 #set param += 'parker:d;'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	62 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	63 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	64
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	65 #<!-- Add Chou method -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	66 #if $chou_method.chou_choice == 'chouyes':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	67 #if $chou_method.chou_t.t_chou == 't_chou_choice'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	68 #set param += 'chou_fosman:' + str($chou_method.chou_t.thresh_chou_value) + ';'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	69 #else:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	70 #set param += 'chou_fosman:d;'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	71 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	72 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	73
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	74 #<!-- Add Karplus method -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	75 #if $karplus_method.karplus_choice == 'karplusyes':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	76 #if $karplus_method.karplus_t.t_karplus == 't_karplus_choice'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	77 #set param += 'karplus_schulz:' + str($karplus_method.karplus_t.thresh_karplus_value) + ';'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	78 #else:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	79 #set param += 'karplus_schulz:d;'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	80 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	81 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	82
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	83 #<!-- Add Kolaskar method -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	84 #if $kolaskar_method.kolaskar_choice == 'kolaskaryes':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	85 #if $kolaskar_method.kolaskar_t.t_kolaskar == 't_kolaskar_choice'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	86 #set param += 'kolaskar:' + str($kolaskar_method.kolaskar_t.thresh_kolaskar_value) + ';'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	87 #else:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	88 #set param += 'kolaskar:d;'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	89 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	90 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	91
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	92
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	93
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	94 #<!-- Clean $proteome if there's no protome -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	95 #if proteomes == '-proteomes ':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	96 #set proteomes = ''
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	97 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	98
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	99
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	100 #<!-- Parse blast command -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	101
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	102 #if $use_search.search_use_bool == "use":
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	103 #<!-- Add proteomes, as many as given -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	104 #if $use_search.prot_input:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	105 #for $file in $use_search.prot_input:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	106 #set proteomes += str($file.prot_name) + '=' + str($file.prot_file) + ';'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	107 #end for
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	108 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	109 #if $use_search.prot_input:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	110 #if $use_search.blast.blast_search == 'blastyes':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	111 #set blast_command = 'task=' + str($use_search.blast.blast_task)
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	112 #set blast_command += ';identity=' + str($use_search.blast.blast_id) + ';cover=' + str($use_search.blast.blast_cover) + ';word-size=' + str($use_search.blast.blast_wordsize)
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	113 #set blast_command += ';makeblastdb_path=makeblastdb;blastp_path=blastp'
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	114 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	115 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	116 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	117
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	118 #<!-- Paste Command-line and run -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	119
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	120 java -jar $__tool_directory__/epibuilder-1.1.jar
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	121
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	122 #<!-- bepipred_origin give -o if online, nothing if command and -jobid if jobID -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	123 #<!-- if origin is not jobid, there is a file, and -b must be passed -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	124 #if $bepi_type.bepipred_origin != 'id':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	125 -b ${bepi_type.bepi_out}
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	126 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	127 -t ${tresh_bepi2}
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	128 ${bepipred_origin}
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	129 #if $param:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	130 -p "${param}"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	131 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	132 -f "${basename}"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	133 -min_len ${min_length}
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	134 -max_len ${max_length}
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	135 #if $proteomes:
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	136 -proteomes
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	137 "${proteomes}"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	138 #if $use_search.blast.blast_search == 'blastyes':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	139 -blast "${blast_command}"
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	140 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	141 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	142
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	143 #if $use_search.check_use_hit == 'nousehit':
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	144 -nohitacc
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	145 #end if
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	146 #<!-- DONT REMOVE THIS ; -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	147 >log.log 2>log.log;
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	148
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	149 mv $basename-epibuilder.xlsx EpiBuilder_report.xlsx;
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	150
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	151 #<!-- Rename output files -->#
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	152 mv ${basename}-epibuilder.txt EpiBuilder;
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	153
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	154
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	155 ]]>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	156 </command>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	157 <inputs>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	158 <!-- Bepipred 2.0 -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	159 <conditional name="bepi_type">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	160 <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" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	161 <option value="y" selected="true">csv file from Bepipred 2.0</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	162 <option value="n" >text file from IEDB Bcell Software standalone</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	163 <option value="id">JobID from Bepipred 2.0 Server</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	164 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	165 <when value="y" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	166 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	167 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	168 <when value="n" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	169 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	170 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	171 <when value="id" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	172 <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" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	173 <!-- Check if its an empty value-->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	174 <validator type="empty_field" message="ID required"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	175 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	176 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	177 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	178 <param name="tresh_bepi2" min="0.0" value="0.6" type="float" label="Threshold for Bepipred 2.0" help="Default = 0.6" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	179 <!-- Epitope Length -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	180 <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" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	181 <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" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	182 <!-- EMINI -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	183 <conditional name="emini_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	184 <param name="emini_choice" type="boolean" checked="true" truevalue="eminiyes" falsevalue="eminino" label="Use Emini Surface Accessibility Prediction method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	185 <when value="eminino">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	186 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	187 <when value="eminiyes">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	188 <conditional name="emini_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	189 <param name="t_emini" display="radio" type="select" label="Threshold" help="Define threshold for Emini" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	190 <option value="d_emini_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	191 <option value="t_emini_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	192 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	193 <when value="t_emini_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	194 <param name="thresh_em_value" value="0" type="float" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	195 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	196 <when value="d_emini_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	197 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	198 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	199 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	200 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	201 <!-- PARKER -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	202 <conditional name="parker_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	203 <param name="parker_choice" type="boolean" checked="true" truevalue="parkeryes" falsevalue="parkerno" label="Use Parker Hydrophilicity Prediction method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	204 <when value="parkerno">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	205 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	206 <when value="parkeryes">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	207 <conditional name="parker_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	208 <param name="t_parker" display="radio" type="select" label="Threshold" help="Define threshold for Parker" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	209 <option value="d_parker_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	210 <option value="t_parker_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	211 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	212 <when value="t_parker_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	213 <param name="thresh_park_value" value="0" type="float" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	214 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	215 <when value="d_parker_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	216 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	217 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	218 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	219 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	220 <!-- Chou -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	221 <conditional name="chou_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	222 <param name="chou_choice" type="boolean" checked="true" truevalue="chouyes" falsevalue="chouno" label="Use Chou & Fasman Beta-Turn Prediction method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	223 <when value="chouno">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	224 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	225 <when value="chouyes">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	226 <conditional name="chou_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	227 <param name="t_chou" display="radio" type="select" label="Threshold" help="Define threshold for Chou & Fasman" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	228 <option value="d_chou_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	229 <option value="t_chou_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	230 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	231 <when value="t_chou_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	232 <param name="thresh_chou_value" value="0" type="float" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	233 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	234 <when value="d_chou_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	235 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	236 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	237 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	238 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	239 <!-- Karplus -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	240 <conditional name="karplus_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	241 <param name="karplus_choice" type="boolean" checked="true" truevalue="karplusyes" falsevalue="karplusno" label="Use Karplus & Schulz Flexibility Prediction method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	242 <when value="karplusno">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	243 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	244 <when value="karplusyes">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	245 <conditional name="karplus_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	246 <param name="t_karplus" display="radio" type="select" label="Threshold" help="Define threshold for Karplus & Schulz" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	247 <option value="d_karplus_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	248 <option value="t_karplus_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	249 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	250 <when value="t_karplus_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	251 <param name="thresh_karplus_value" type="float" value="0" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	252 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	253 <when value="d_karplus_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	254 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	255 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	256 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	257 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	258 <!-- Kolaskar -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	259 <conditional name="kolaskar_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	260 <param name="kolaskar_choice" type="boolean" checked="true" truevalue="kolaskaryes" falsevalue="kolaskarno" label="Use Kolaskar & Tongaonkar Antigenicity method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	261 <when value="kolaskarno">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	262 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	263 <when value="kolaskaryes">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	264 <conditional name="kolaskar_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	265 <param name="t_kolaskar" display="radio" type="select" label="Threshold" help="Define threshold for Kolaskar & Tongaonkar" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	266 <option value="d_kolaskar_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	267 <option value="t_kolaskar_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	268 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	269 <when value="t_kolaskar_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	270 <param name="thresh_kolaskar_value" type="float" value="0" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	271 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	272 <when value="d_kolaskar_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	273 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	274 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	275 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	276 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	277 <!-- Insert Proteome -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	278 <conditional name="use_search">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	279 <param name="search_use_bool" type="boolean" checked="false" truevalue="use" falsevalue="dont" label="Do you want to search the predicted epitopes in a proteome file?" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	280 <when value="dont">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	281 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	282 <when value="use">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	283 <repeat name="prot_input" title="Proteome" min="1">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	284 <param type="data" name="prot_file" format="fasta" label="Proteome file" help="Protein sequences in fasta format" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	285 <param type="text" name="prot_name" label="Proteome name" help="Give a name to this dataset" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	286 <!-- Change spaces for '_' -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	287 <sanitizer>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	288 <valid initial="string.printable">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	289 <remove value=" "/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	290 </valid>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	291 <mapping initial="none">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	292 <add source=" " target="_"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	293 </mapping>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	294 </sanitizer>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	295 <!-- Check if its an empty value-->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	296 <validator type="empty_field" message="Basename required"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	297 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	298 </repeat>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	299 <param name="check_use_hit" type="boolean" checked="true" truevalue="usehit" falsevalue="nousehit" label="Show accession ID on result files?" help="Choose this option if you want to add accession ID numbers" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	300 <conditional name="blast">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	301 <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" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	302 <when value="blastno">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	303 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	304 <when value="blastyes">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	305 <param name="blast_id" value="90" min="1" type="integer" label="Identity" help="[0-100] Minimal identity accepted to parse blast results" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	306 <param name="blast_cover" value="90" min="2" type="integer" label="Coverage" help="[0-100] Minimal coverage accepted to parse blast results" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	307 <param name="blast_wordsize" value="4" min="1" type="integer" label="Word-Size" help="Blast argument word-size" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	308 <param name="blast_task" type="select" label="Task" help="How blastp should run">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	309 <option value="blastp-short" selected="True">Blastp-short</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	310 <option value="blastp-fast">Blastp-fast</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	311 <option value="blastp">Blastp</option>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	312 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	313 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	314 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	315 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	316 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	317 <param name="basename" type="text" value="" label="Basename" help="Provide a name for this run (string text without special characters)" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	318 <!-- Change spaces for '_' -->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	319 <sanitizer>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	320 <valid initial="string.printable">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	321 <remove value=" "/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	322 </valid>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	323 <mapping initial="none">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	324 <add source=" " target="_"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	325 </mapping>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	326 </sanitizer>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	327 <!-- Check if its an empty value-->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	328 <validator type="empty_field" message="Basename required"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	329 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	330 </inputs>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	331 <outputs>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	332 <data name="epif_out" format="txt" from_work_dir="EpiBuilder" label="EpiBuilder Output Summary - ${basename}" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	333 <data name="ep_xls" format="xlsx" from_work_dir="EpiBuilder_report.xlsx" label="EpiBuilder Report - ${basename}" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	334 <collection type="list" label="EpiBuilder Files - ${basename}" name="epif_collection" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	335 <discover_datasets format="fasta" pattern="(?P<designation>.*)\.fasta" visible="false" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	336 <discover_datasets format="txt" pattern="(?P<designation>.*)\.tsv" visible="false" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	337 <discover_datasets format="txt" pattern="(?P<designation>.*)\.txt" visible="false" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	338 </collection>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	339 <collection type="list" label="EpiBuilder Blast Run - ${basename}" name="blast_collection" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	340 <filter>use_search['search_use_bool'] is True and use_search['blast']['blast_search'] is True</filter>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	341 <discover_datasets pattern="(?P<designation>.*)blast\.csv" visible="false" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	342 </collection>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	343 </outputs>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	344 <tests>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	345 <test>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	346 <!-- Test all methods threshold selected, command line version of input with proteome-->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	347 <conditional name="bepi_type">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	348 <param name="bepipred_origin" value="y"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	349 <param name="bepi_out" value="input_bepi_online.csv"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	350 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	351 <param name="tresh_bepi2" value="0.6"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	352
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	353 <param name="min_length" value="10" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	354 <param name="max_length" value="30" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	355
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	356 <conditional name="emini_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	357 <param name="emini_choice" value="eminiyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	358 <conditional name="emini_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	359 <param name="t_emini" value="t_emini_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	360 <param name="thresh_em_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	361 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	362 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	363
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	364 <conditional name="parker_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	365 <param name="parker_choice" value="parkeryes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	366 <conditional name="parker_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	367 <param name="t_parker" value="t_parker_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	368 <param name="thresh_park_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	369 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	370 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	371
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	372 <conditional name="chou_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	373 <param name="chou_choice" value="chouyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	374 <conditional name="chou_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	375 <param name="t_chou" value="t_chou_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	376 <param name="thresh_chou_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	377 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	378 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	379
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	380 <conditional name="karplus_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	381 <param name="karplus_choice" value="karplusyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	382 <conditional name="karplus_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	383 <param name="t_karplus" value="t_karplus_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	384 <param name="thresh_karplus_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	385 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	386 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	387
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	388
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	389 <conditional name="kolaskar_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	390 <param name="kolaskar_choice" value="kolaskaryes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	391 <conditional name="kolaskar_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	392 <param name="t_kolaskar" value="t_kolaskar_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	393 <param name="thresh_kolaskar_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	394 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	395 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	396 <!-- This first part test all methods-->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	397
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	398 <conditional name="use_search">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	399 <param name="search_use_bool" value="use" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	400 <repeat name="prot_input">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	401 <param name="prot_name" value="test_proteom" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	402 <param name="prot_file" value="proteom.fasta" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	403 </repeat>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	404 <param name="check_use_hit" value="usehit"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	405 <conditional name="blast">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	406 <param name="blast_search" value="blastyes" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	407 <param name="blast_id" value="90" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	408 <param name="blast_cover" value="90" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	409 <param name="blast_wordsize" value="4" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	410 <param name="blast_task" value="blastp-short" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	411 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	412 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	413
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	414 <param name="basename" value="online" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	415
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	416 <output name="epif_out" file="online-EpiBuilder.txt" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	417 <output name="ep_xls" file="online-EpiBuilder.xlsx" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	418 <output_collection name= "epif_collection">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	419 <element name="ep_prot_sum" file="online-EpiBuilder-protein-summary.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	420 <element name="ep_top" file="online-EpiBuilder-topology.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	421 <element name="ep_score" file="online-EpiBuilder-socre.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	422 <element name="ep_detail" file="online-EpiBuilder-epitope-detail.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	423 <element name="ep_parameters" file="online-EpiBuilder-parameters.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	424 <element name="ep_fasta" file="online-EpiBuilder-fasta.fasta" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	425 </output_collection>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	426 <output_collection name="blast_collection" >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	427 <element name="test_proteom" file="online-test_proteom_blast.csv" ftype="csv" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	428 </output_collection >
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	429 </test>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	430
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	431 <test>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	432 <!-- Test all methods threshold selected, online version of input with proteome-->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	433 <conditional name="bepi_type">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	434 <param name="bepipred_origin" value="y"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	435 <param name="bepi_out" value="input_bcell_command_line.txt"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	436 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	437
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	438 <param name="bepipred_origin" value="n"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	439 <param name="tresh_bepi2" value="0.6"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	440
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	441 <param name="min_length" value="10" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	442 <param name="max_length" value="30" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	443
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	444 <conditional name="emini_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	445 <param name="emini_choice" value="eminiyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	446 <conditional name="emini_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	447 <param name="t_emini" value="t_emini_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	448 <param name="thresh_em_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	449 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	450 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	451
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	452 <conditional name="parker_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	453 <param name="parker_choice" value="parkeryes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	454 <conditional name="parker_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	455 <param name="t_parker" value="t_parker_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	456 <param name="thresh_park_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	457 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	458 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	459
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	460 <conditional name="chou_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	461 <param name="chou_choice" value="chouyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	462 <conditional name="chou_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	463 <param name="t_chou" value="t_chou_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	464 <param name="thresh_chou_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	465 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	466 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	467
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	468 <conditional name="karplus_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	469 <param name="karplus_choice" value="karplusyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	470 <conditional name="karplus_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	471 <param name="t_karplus" value="t_karplus_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	472 <param name="thresh_karplus_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	473 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	474 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	475
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	476
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	477 <conditional name="kolaskar_method">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	478 <param name="kolaskar_choice" value="kolaskaryes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	479 <conditional name="kolaskar_t">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	480 <param name="t_kolaskar" value="t_kolaskar_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	481 <param name="thresh_kolaskar_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	482 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	483 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	484 <!-- This first part test all methods-->
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	485
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	486 <conditional name="use_search">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	487 <param name="search_use_bool" value="use"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	488 <repeat name="prot_input">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	489 <param name="prot_name" value="test_proteom" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	490 <param name="prot_file" value="proteom.fasta" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	491 </repeat>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	492 <param name="check_use_hit" value="usehit"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	493 <conditional name="blast">
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	494 <param name="blast_search" value="blastyes" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	495 <param name="blast_id" value="90" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	496 <param name="blast_cover" value="90"/>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	497 <param name="blast_wordsize" value="4" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	498 <param name="blast_task" value="blastp-short" />
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	499 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	500 </conditional>

2

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

1 <tool id="epibuilder_1.1" name="EpiBuilder" version="1.1">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

2 <description>Predict B cell epitopes</description>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

3 <requirements>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

4 <requirement type="package" version=">=1.8">Java</requirement>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

5 <requirement type="package" version=">=2.11.0+">Blastp</requirement>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

6 <requirement type="package" version=">=2.11.0+">Makeblastdb</requirement>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

7 </requirements>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

8 <stdio>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

9 <regex match="command not found"

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

10 source="both"

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

11 level="log"

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

12 description="WARNING: some methods could not be applied -> check inputs and outputs files" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

13 <regex match="makeblastdb "

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

14 source="both"

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

15 level="log"

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

16 description="makeblastdb and blastp must be in $PATH on your Galaxy server" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

17 <regex match="blastp "

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

18 source="both"

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

19 level="log"

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

20 description="makeblastdb and blastp must be in $PATH on your Galaxy server" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

21 </stdio>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

22 <command><![CDATA[

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

23 #*<!--

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

24 Methods used will be saved in $param with each threshold

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

25 Threshold is separated from method by ":"

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

26 Each method is separated by ";"

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

27 example: emini:0.8;parker:d;

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

28

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

29 >> d means defalt threshold

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

30 -->*#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

31

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

32 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

33 #set param = ''

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

34 #set nomethod = ''

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

35 #set proteomes = ''

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

36

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

37 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

38 #if $bepi_type.bepipred_origin == 'y':

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

39 #set bepipred_origin = '-o'

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

40 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

41 #elif $bepi_type.bepipred_origin == 'id':

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

42 #set bepipred_origin = '-jobid ' + str($bepi_type.job_id)

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

43 #else:

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

44 #set bepipred_origin = ''

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

45 #end if

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

46

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

47 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

48 #if $emini_method.emini_choice == 'eminiyes':

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

49 #if $emini_method.emini_t.t_emini == 't_emini_choice'

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

50 #set param += 'emini:' + str($emini_method.emini_t.thresh_em_value) + ';'

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

51 #else:

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

52 #set param += 'emini:d;'

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bioinformatics_lab_ufsc

parents:

diff changeset

53 #end if

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bioinformatics_lab_ufsc

parents:

diff changeset

54 #end if

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bioinformatics_lab_ufsc

parents:

diff changeset

55

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

56 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

57 #if $parker_method.parker_choice == 'parkeryes':

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bioinformatics_lab_ufsc

parents:

diff changeset

58 #if $parker_method.parker_t.t_parker == 't_parker_choice'

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bioinformatics_lab_ufsc

parents:

diff changeset

59 #set param += 'parker:' + str($parker_method.parker_t.thresh_park_value) + ';'

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

60 #else:

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

61 #set param += 'parker:d;'

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bioinformatics_lab_ufsc

parents:

diff changeset

62 #end if

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parents:

diff changeset

63 #end if

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bioinformatics_lab_ufsc

parents:

diff changeset

64

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

65 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

66 #if $chou_method.chou_choice == 'chouyes':

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

67 #if $chou_method.chou_t.t_chou == 't_chou_choice'

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bioinformatics_lab_ufsc

parents:

diff changeset

68 #set param += 'chou_fosman:' + str($chou_method.chou_t.thresh_chou_value) + ';'

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

69 #else:

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parents:

diff changeset

70 #set param += 'chou_fosman:d;'

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parents:

diff changeset

71 #end if

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parents:

diff changeset

72 #end if

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

73

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

74 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

75 #if $karplus_method.karplus_choice == 'karplusyes':

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

76 #if $karplus_method.karplus_t.t_karplus == 't_karplus_choice'

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

77 #set param += 'karplus_schulz:' + str($karplus_method.karplus_t.thresh_karplus_value) + ';'

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

78 #else:

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parents:

diff changeset

79 #set param += 'karplus_schulz:d;'

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parents:

diff changeset

80 #end if

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bioinformatics_lab_ufsc

parents:

diff changeset

81 #end if

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bioinformatics_lab_ufsc

parents:

diff changeset

82

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

83 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

84 #if $kolaskar_method.kolaskar_choice == 'kolaskaryes':

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bioinformatics_lab_ufsc

parents:

diff changeset

85 #if $kolaskar_method.kolaskar_t.t_kolaskar == 't_kolaskar_choice'

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parents:

diff changeset

86 #set param += 'kolaskar:' + str($kolaskar_method.kolaskar_t.thresh_kolaskar_value) + ';'

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

87 #else:

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parents:

diff changeset

88 #set param += 'kolaskar:d;'

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parents:

diff changeset

89 #end if

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parents:

diff changeset

90 #end if

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parents:

diff changeset

91

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

92

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

93

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

94 #**#

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bioinformatics_lab_ufsc

parents:

diff changeset

95 #if proteomes == '-proteomes ':

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parents:

diff changeset

96 #set proteomes = ''

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parents:

diff changeset

97 #end if

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parents:

diff changeset

98

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

99

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

100 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

101

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

102 #if $use_search.search_use_bool == "use":

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bioinformatics_lab_ufsc

parents:

diff changeset

103 #**#

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bioinformatics_lab_ufsc

parents:

diff changeset

104 #if $use_search.prot_input:

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parents:

diff changeset

105 #for $file in $use_search.prot_input:

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parents:

diff changeset

106 #set proteomes += str($file.prot_name) + '=' + str($file.prot_file) + ';'

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parents:

diff changeset

107 #end for

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parents:

diff changeset

108 #end if

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bioinformatics_lab_ufsc

parents:

diff changeset

109 #if $use_search.prot_input:

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bioinformatics_lab_ufsc

parents:

diff changeset

110 #if $use_search.blast.blast_search == 'blastyes':

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parents:

diff changeset

111 #set blast_command = 'task=' + str($use_search.blast.blast_task)

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parents:

diff changeset

112 #set blast_command += ';identity=' + str($use_search.blast.blast_id) + ';cover=' + str($use_search.blast.blast_cover) + ';word-size=' + str($use_search.blast.blast_wordsize)

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parents:

diff changeset

113 #set blast_command += ';makeblastdb_path=makeblastdb;blastp_path=blastp'

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parents:

diff changeset

114 #end if

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parents:

diff changeset

115 #end if

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parents:

diff changeset

116 #end if

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parents:

diff changeset

117

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parents:

diff changeset

118 #**#

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parents:

diff changeset

119

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

120 java -jar $__tool_directory__/epibuilder-1.1.jar

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bioinformatics_lab_ufsc

parents:

diff changeset

121

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

122 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

123 #**#

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bioinformatics_lab_ufsc

parents:

diff changeset

124 #if $bepi_type.bepipred_origin != 'id':

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parents:

diff changeset

125 -b ${bepi_type.bepi_out}

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parents:

diff changeset

126 #end if

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parents:

diff changeset

127 -t ${tresh_bepi2}

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bioinformatics_lab_ufsc

parents:

diff changeset

128 ${bepipred_origin}

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bioinformatics_lab_ufsc

parents:

diff changeset

129 #if $param:

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parents:

diff changeset

130 -p "${param}"

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bioinformatics_lab_ufsc

parents:

diff changeset

131 #end if

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bioinformatics_lab_ufsc

parents:

diff changeset

132 -f "${basename}"

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bioinformatics_lab_ufsc

parents:

diff changeset

133 -min_len ${min_length}

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bioinformatics_lab_ufsc

parents:

diff changeset

134 -max_len ${max_length}

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bioinformatics_lab_ufsc

parents:

diff changeset

135 #if $proteomes:

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bioinformatics_lab_ufsc

parents:

diff changeset

136 -proteomes

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bioinformatics_lab_ufsc

parents:

diff changeset

137 "${proteomes}"

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bioinformatics_lab_ufsc

parents:

diff changeset

138 #if $use_search.blast.blast_search == 'blastyes':

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bioinformatics_lab_ufsc

parents:

diff changeset

139 -blast "${blast_command}"

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bioinformatics_lab_ufsc

parents:

diff changeset

140 #end if

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bioinformatics_lab_ufsc

parents:

diff changeset

141 #end if

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parents:

diff changeset

142

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bioinformatics_lab_ufsc

parents:

diff changeset

143 #if $use_search.check_use_hit == 'nousehit':

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bioinformatics_lab_ufsc

parents:

diff changeset

144 -nohitacc

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bioinformatics_lab_ufsc

parents:

diff changeset

145 #end if

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bioinformatics_lab_ufsc

parents:

diff changeset

146 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

147 >log.log 2>log.log;

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bioinformatics_lab_ufsc

parents:

diff changeset

148

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bioinformatics_lab_ufsc

parents:

diff changeset

149 mv $basename-epibuilder.xlsx EpiBuilder_report.xlsx;

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bioinformatics_lab_ufsc

parents:

diff changeset

150

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

151 #**#

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

152 mv ${basename}-epibuilder.txt EpiBuilder;

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bioinformatics_lab_ufsc

parents:

diff changeset

153

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

154

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

155 ]]>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

156 </command>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

157 <inputs>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

158

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

159 <conditional name="bepi_type">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

160 <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" >

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

161 <option value="y" selected="true">csv file from Bepipred 2.0</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

162 <option value="n" >text file from IEDB Bcell Software standalone</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

163 <option value="id">JobID from Bepipred 2.0 Server</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

164 </param>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

165 <when value="y" >

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

166 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

167 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

168 <when value="n" >

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

169 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />

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bioinformatics_lab_ufsc

parents:

diff changeset

170 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

171 <when value="id" >

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

172 <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" >

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

173

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

174 <validator type="empty_field" message="ID required"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

175 </param>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

176 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

177 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

178 <param name="tresh_bepi2" min="0.0" value="0.6" type="float" label="Threshold for Bepipred 2.0" help="Default = 0.6" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

179

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

180 <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" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

181 <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" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

182

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

183 <conditional name="emini_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

184 <param name="emini_choice" type="boolean" checked="true" truevalue="eminiyes" falsevalue="eminino" label="Use Emini Surface Accessibility Prediction method?" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

185 <when value="eminino">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

186 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

187 <when value="eminiyes">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

188 <conditional name="emini_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

189 <param name="t_emini" display="radio" type="select" label="Threshold" help="Define threshold for Emini" >

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bioinformatics_lab_ufsc

parents:

diff changeset

190 <option value="d_emini_choice" selected="true">Default (calculated by method)</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

191 <option value="t_emini_choice">Set Threshold</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

192 </param>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

193 <when value="t_emini_choice">

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bioinformatics_lab_ufsc

parents:

diff changeset

194 <param name="thresh_em_value" value="0" type="float" label="Value" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

195 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

196 <when value="d_emini_choice">

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bioinformatics_lab_ufsc

parents:

diff changeset

197 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

198 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

199 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

200 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

201

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

202 <conditional name="parker_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

203 <param name="parker_choice" type="boolean" checked="true" truevalue="parkeryes" falsevalue="parkerno" label="Use Parker Hydrophilicity Prediction method?" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

204 <when value="parkerno">

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bioinformatics_lab_ufsc

parents:

diff changeset

205 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

206 <when value="parkeryes">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

207 <conditional name="parker_t">

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bioinformatics_lab_ufsc

parents:

diff changeset

208 <param name="t_parker" display="radio" type="select" label="Threshold" help="Define threshold for Parker" >

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bioinformatics_lab_ufsc

parents:

diff changeset

209 <option value="d_parker_choice" selected="true">Default (calculated by method)</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

210 <option value="t_parker_choice">Set Threshold</option>

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bioinformatics_lab_ufsc

parents:

diff changeset

211 </param>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

212 <when value="t_parker_choice">

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bioinformatics_lab_ufsc

parents:

diff changeset

213 <param name="thresh_park_value" value="0" type="float" label="Value" />

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bioinformatics_lab_ufsc

parents:

diff changeset

214 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

215 <when value="d_parker_choice">

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diff changeset

216 </when>

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parents:

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217 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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218 </when>

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219 </conditional>

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220

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

221 <conditional name="chou_method">

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parents:

diff changeset

222 <param name="chou_choice" type="boolean" checked="true" truevalue="chouyes" falsevalue="chouno" label="Use Chou & Fasman Beta-Turn Prediction method?" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

223 <when value="chouno">

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parents:

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224 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

225 <when value="chouyes">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

226 <conditional name="chou_t">

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parents:

diff changeset

227 <param name="t_chou" display="radio" type="select" label="Threshold" help="Define threshold for Chou & Fasman" >

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parents:

diff changeset

228 <option value="d_chou_choice" selected="true">Default (calculated by method)</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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229 <option value="t_chou_choice">Set Threshold</option>

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230 </param>

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parents:

diff changeset

231 <when value="t_chou_choice">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

232 <param name="thresh_chou_value" value="0" type="float" label="Value" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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233 </when>

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parents:

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234 <when value="d_chou_choice">

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235 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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236 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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237 </when>

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238 </conditional>

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239

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

240 <conditional name="karplus_method">

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parents:

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241 <param name="karplus_choice" type="boolean" checked="true" truevalue="karplusyes" falsevalue="karplusno" label="Use Karplus & Schulz Flexibility Prediction method?" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

242 <when value="karplusno">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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243 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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244 <when value="karplusyes">

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parents:

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245 <conditional name="karplus_t">

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parents:

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246 <param name="t_karplus" display="radio" type="select" label="Threshold" help="Define threshold for Karplus & Schulz" >

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247 <option value="d_karplus_choice" selected="true">Default (calculated by method)</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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248 <option value="t_karplus_choice">Set Threshold</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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249 </param>

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parents:

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250 <when value="t_karplus_choice">

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parents:

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251 <param name="thresh_karplus_value" type="float" value="0" label="Value" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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252 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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253 <when value="d_karplus_choice">

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254 </when>

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255 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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256 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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257 </conditional>

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258

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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259 <conditional name="kolaskar_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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260 <param name="kolaskar_choice" type="boolean" checked="true" truevalue="kolaskaryes" falsevalue="kolaskarno" label="Use Kolaskar & Tongaonkar Antigenicity method?" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

261 <when value="kolaskarno">

8fa9e663cca5 Uploaded corrected condition for use_hit

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262 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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263 <when value="kolaskaryes">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

264 <conditional name="kolaskar_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

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265 <param name="t_kolaskar" display="radio" type="select" label="Threshold" help="Define threshold for Kolaskar & Tongaonkar" >

8fa9e663cca5 Uploaded corrected condition for use_hit

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266 <option value="d_kolaskar_choice" selected="true">Default (calculated by method)</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

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267 <option value="t_kolaskar_choice">Set Threshold</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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268 </param>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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269 <when value="t_kolaskar_choice">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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270 <param name="thresh_kolaskar_value" type="float" value="0" label="Value" />

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271 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

272 <when value="d_kolaskar_choice">

8fa9e663cca5 Uploaded corrected condition for use_hit

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273 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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274 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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275 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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276 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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277

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

278 <conditional name="use_search">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

279 <param name="search_use_bool" type="boolean" checked="false" truevalue="use" falsevalue="dont" label="Do you want to search the predicted epitopes in a proteome file?" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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diff changeset

280 <when value="dont">

8fa9e663cca5 Uploaded corrected condition for use_hit

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281 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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282 <when value="use">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

283 <repeat name="prot_input" title="Proteome" min="1">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

284 <param type="data" name="prot_file" format="fasta" label="Proteome file" help="Protein sequences in fasta format" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

285 <param type="text" name="prot_name" label="Proteome name" help="Give a name to this dataset" >

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

286

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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287 <sanitizer>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

288 <valid initial="string.printable">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

289 <remove value=" "/>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

290 </valid>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

291 <mapping initial="none">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

292 <add source=" " target="_"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

293 </mapping>

8fa9e663cca5 Uploaded corrected condition for use_hit

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294 </sanitizer>

8fa9e663cca5 Uploaded corrected condition for use_hit

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295

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

296 <validator type="empty_field" message="Basename required"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

297 </param>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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298 </repeat>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

299 <param name="check_use_hit" type="boolean" checked="true" truevalue="usehit" falsevalue="nousehit" label="Show accession ID on result files?" help="Choose this option if you want to add accession ID numbers" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

300 <conditional name="blast">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

301 <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" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

302 <when value="blastno">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

303 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

304 <when value="blastyes">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

305 <param name="blast_id" value="90" min="1" type="integer" label="Identity" help="[0-100] Minimal identity accepted to parse blast results" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

306 <param name="blast_cover" value="90" min="2" type="integer" label="Coverage" help="[0-100] Minimal coverage accepted to parse blast results" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

307 <param name="blast_wordsize" value="4" min="1" type="integer" label="Word-Size" help="Blast argument word-size" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

308 <param name="blast_task" type="select" label="Task" help="How blastp should run">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

309 <option value="blastp-short" selected="True">Blastp-short</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

310 <option value="blastp-fast">Blastp-fast</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

311 <option value="blastp">Blastp</option>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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312 </param>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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313 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

314 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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315 </when>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

316 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

317 <param name="basename" type="text" value="" label="Basename" help="Provide a name for this run (string text without special characters)" >

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

318

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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319 <sanitizer>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

320 <valid initial="string.printable">

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

321 <remove value=" "/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

322 </valid>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

323 <mapping initial="none">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

324 <add source=" " target="_"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

325 </mapping>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

326 </sanitizer>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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327

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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328 <validator type="empty_field" message="Basename required"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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329 </param>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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330 </inputs>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

331 <outputs>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

332 <data name="epif_out" format="txt" from_work_dir="EpiBuilder" label="EpiBuilder Output Summary - ${basename}" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

333 <data name="ep_xls" format="xlsx" from_work_dir="EpiBuilder_report.xlsx" label="EpiBuilder Report - ${basename}" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

334 <collection type="list" label="EpiBuilder Files - ${basename}" name="epif_collection" >

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

335 <discover_datasets format="fasta" pattern="(?P<designation>.*)\.fasta" visible="false" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

336 <discover_datasets format="txt" pattern="(?P<designation>.*)\.tsv" visible="false" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

337 <discover_datasets format="txt" pattern="(?P<designation>.*)\.txt" visible="false" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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338 </collection>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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339 <collection type="list" label="EpiBuilder Blast Run - ${basename}" name="blast_collection" >

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

340 <filter>use_search['search_use_bool'] is True and use_search['blast']['blast_search'] is True</filter>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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341 <discover_datasets pattern="(?P<designation>.*)blast\.csv" visible="false" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

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342 </collection>

8fa9e663cca5 Uploaded corrected condition for use_hit

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343 </outputs>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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344 <tests>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

345 <test>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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346

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

347 <conditional name="bepi_type">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

348 <param name="bepipred_origin" value="y"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

349 <param name="bepi_out" value="input_bepi_online.csv"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

350 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

351 <param name="tresh_bepi2" value="0.6"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

352

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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353 <param name="min_length" value="10" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

354 <param name="max_length" value="30" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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355

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

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356 <conditional name="emini_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

357 <param name="emini_choice" value="eminiyes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

358 <conditional name="emini_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

359 <param name="t_emini" value="t_emini_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

360 <param name="thresh_em_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

361 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

362 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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363

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

364 <conditional name="parker_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

365 <param name="parker_choice" value="parkeryes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

diff changeset

366 <conditional name="parker_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

367 <param name="t_parker" value="t_parker_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

368 <param name="thresh_park_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

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369 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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370 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

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parents:

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371

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

372 <conditional name="chou_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

373 <param name="chou_choice" value="chouyes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

374 <conditional name="chou_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

375 <param name="t_chou" value="t_chou_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

376 <param name="thresh_chou_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

377 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

378 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

379

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

380 <conditional name="karplus_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

381 <param name="karplus_choice" value="karplusyes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

382 <conditional name="karplus_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

383 <param name="t_karplus" value="t_karplus_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

384 <param name="thresh_karplus_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

385 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

386 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

387

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

388

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

389 <conditional name="kolaskar_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

390 <param name="kolaskar_choice" value="kolaskaryes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

391 <conditional name="kolaskar_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

392 <param name="t_kolaskar" value="t_kolaskar_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

393 <param name="thresh_kolaskar_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

394 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

395 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

396

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

397

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

398 <conditional name="use_search">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

399 <param name="search_use_bool" value="use" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

400 <repeat name="prot_input">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

401 <param name="prot_name" value="test_proteom" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

402 <param name="prot_file" value="proteom.fasta" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

403 </repeat>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

404 <param name="check_use_hit" value="usehit"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

405 <conditional name="blast">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

406 <param name="blast_search" value="blastyes" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

407 <param name="blast_id" value="90" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

408 <param name="blast_cover" value="90" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

409 <param name="blast_wordsize" value="4" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

410 <param name="blast_task" value="blastp-short" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

411 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

412 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

413

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

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

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

415

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

416 <output name="epif_out" file="online-EpiBuilder.txt" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

417 <output name="ep_xls" file="online-EpiBuilder.xlsx" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

418 <output_collection name= "epif_collection">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

419 <element name="ep_prot_sum" file="online-EpiBuilder-protein-summary.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

420 <element name="ep_top" file="online-EpiBuilder-topology.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

421 <element name="ep_score" file="online-EpiBuilder-socre.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

422 <element name="ep_detail" file="online-EpiBuilder-epitope-detail.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

423 <element name="ep_parameters" file="online-EpiBuilder-parameters.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

424 <element name="ep_fasta" file="online-EpiBuilder-fasta.fasta" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

425 </output_collection>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

426 <output_collection name="blast_collection" >

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

427 <element name="test_proteom" file="online-test_proteom_blast.csv" ftype="csv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

428 </output_collection >

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

429 </test>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

430

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

431 <test>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

432

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

433 <conditional name="bepi_type">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

434 <param name="bepipred_origin" value="y"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

435 <param name="bepi_out" value="input_bcell_command_line.txt"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

436 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

437

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

438 <param name="bepipred_origin" value="n"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

439 <param name="tresh_bepi2" value="0.6"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

440

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

441 <param name="min_length" value="10" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

442 <param name="max_length" value="30" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

443

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

444 <conditional name="emini_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

445 <param name="emini_choice" value="eminiyes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

446 <conditional name="emini_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

447 <param name="t_emini" value="t_emini_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

448 <param name="thresh_em_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

449 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

450 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

451

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

452 <conditional name="parker_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

453 <param name="parker_choice" value="parkeryes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

454 <conditional name="parker_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

455 <param name="t_parker" value="t_parker_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

456 <param name="thresh_park_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

457 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

458 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

459

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

460 <conditional name="chou_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

461 <param name="chou_choice" value="chouyes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

462 <conditional name="chou_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

463 <param name="t_chou" value="t_chou_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

464 <param name="thresh_chou_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

465 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

466 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

467

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

468 <conditional name="karplus_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

469 <param name="karplus_choice" value="karplusyes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

470 <conditional name="karplus_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

471 <param name="t_karplus" value="t_karplus_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

472 <param name="thresh_karplus_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

473 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

474 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

475

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

476

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

477 <conditional name="kolaskar_method">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

478 <param name="kolaskar_choice" value="kolaskaryes"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

479 <conditional name="kolaskar_t">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

480 <param name="t_kolaskar" value="t_kolaskar_choice"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

481 <param name="thresh_kolaskar_value" value="0.8" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

482 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

483 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

484

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

485

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

486 <conditional name="use_search">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

487 <param name="search_use_bool" value="use"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

488 <repeat name="prot_input">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

489 <param name="prot_name" value="test_proteom" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

490 <param name="prot_file" value="proteom.fasta" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

491 </repeat>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

492 <param name="check_use_hit" value="usehit"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

493 <conditional name="blast">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

494 <param name="blast_search" value="blastyes" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

495 <param name="blast_id" value="90" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

496 <param name="blast_cover" value="90"/>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

497 <param name="blast_wordsize" value="4" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

498 <param name="blast_task" value="blastp-short" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

499 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

500 </conditional>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

501

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

502 <param name="basename" value="command" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

503

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

504 <output name="epif_out" file="command-EpiBuilder.txt" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

505 <output name="ep_xls" file="command-EpiBuilder.xlsx" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

506 <output_collection name= "epif_collection">

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

507 <element name="ep_prot_sum" file="command-EpiBuilder-protein-summary.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

508 <element name="ep_top" file="command-EpiBuilder-topology.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

509 <element name="ep_score" file="command-EpiBuilder-socre.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

510 <element name="ep_detail" file="command-EpiBuilder-epitope-detail.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

511 <element name="ep_parameters" file="command-EpiBuilder-parameters.tsv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

512 <element name="ep_fasta" file="command-EpiBuilder-fasta.fasta" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

513 </output_collection>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

514 <output_collection name="blast_collection" >

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

515 <element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" />

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

516 </output_collection >

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

517 </test>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

518 </tests>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

519 <help>

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

520 **How to Run**

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

521

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

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

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

523

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

524 .. class:: warningmark

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

525

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

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

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

527

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

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

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

529

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

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

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

531

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

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

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

533

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

534 .. class:: warningmark

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

535

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

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

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

537

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

538 -----

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

parents:

diff changeset

539

8fa9e663cca5 Uploaded corrected condition for use_hit

bioinformatics_lab_ufsc

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540 **Outputs**

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541

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542

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543 **Summary** : Prediction overview

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544

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

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546

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547 **Fasta** : Epitopes' sequences

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548

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

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550

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551 **Score** : Detailed score for aminoacids

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552

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

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554

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

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556

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

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558

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

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560

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561

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562 -----

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563

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564 .. class:: infomark

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565

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

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567

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568 -----

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569

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570 Please cite methods used in your analysis, available bellow

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571

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572 | Bioinformatics Lab - UFSC - 2021

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573

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574 </help>

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575 <citations>

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576 <citation type="doi">10.1093/nar/gkx346</citation>

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577 <citation type="doi">10.1016/0014-5793(90)80535-q</citation>

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578 <citation type="doi">10.1002/9780470122921.ch2</citation>

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579 <citation type="doi">10.1021/bi00367a013</citation>

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580 <citation type="doi">https://doi.org/10.1007/BF01195768</citation>

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581 <citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation>

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582 <citation type="doi">10.1371/journal.pcbi.1006791</citation>

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583 <citation type="doi">https://doi.org/10.1093/nar/gky379</citation>

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584 </citations>

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585 </tool>

Mercurial > repos > bioinformatics_lab_ufsc > epibuilder

annotate epibuilder-1.1.xml @ 2:8fa9e663cca5 draft