epibuilder: epibuilder-1.1.xml annotate

annotate epibuilder-1.1.xml @ 3:0fccf1695099 draft

Deleted selected files

author	bioinformatics_lab_ufsc
date	Thu, 25 Nov 2021 04:24:01 +0000
parents	8fa9e663cca5
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>
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 parents: diff changeset	540 Outputs
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	541
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	542
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	543 Summary : Prediction overview
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	544
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	545 Protein Summary : Show proteins that have epitopes predicted
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	546
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	547 Fasta : Epitopes' sequences
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	548
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	549 Topology : Show epitope match in each method, aminoacid per aminoacid
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	550
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	551 Score : Detailed score for aminoacids
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	552
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	553 Epitope Detail : Properties of each predicted epitope
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	554
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	555 Parameters : Softwares, thresholds and parameters used for prediction
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	556
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	557 Xls Report : Table with epitope detail, protein summary, topology and scores
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	558
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	559 Collection with blast files : All blast results for each proteome
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	560
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	561
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	562 -----
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	563
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	564 .. class:: infomark
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	565
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	566 For more information, checkout our GitHub page: https://github.com/bioinfo-ufsc/EpiBuilder
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	567
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	568 -----
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	569
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	570 Please cite methods used in your analysis, available bellow
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	571
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	572 \| Bioinformatics Lab - UFSC - 2021
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	573
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	574 </help>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	575 <citations>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	576 <citation type="doi">10.1093/nar/gkx346</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	577 <citation type="doi">10.1016/0014-5793(90)80535-q</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	578 <citation type="doi">10.1002/9780470122921.ch2</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	579 <citation type="doi">10.1021/bi00367a013</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	580 <citation type="doi">https://doi.org/10.1007/BF01195768</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	581 <citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	582 <citation type="doi">10.1371/journal.pcbi.1006791</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	583 <citation type="doi">https://doi.org/10.1093/nar/gky379</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	584 </citations>
8fa9e663cca5 Uploaded corrected condition for use_hit bioinformatics_lab_ufsc parents: diff changeset	585 </tool>

Mercurial > repos > bioinformatics_lab_ufsc > epibuilder

annotate epibuilder-1.1.xml @ 3:0fccf1695099 draft