# HG changeset patch # User bioinformatics_lab_ufsc # Date 1617061227 0 # Node ID 57972c12796caf6779cb9601e9e275460d824ed1 # Parent a8b913eaad2cbb5f078a439db7f1405ed4fe7dd7 Deleted selected files diff -r a8b913eaad2c -r 57972c12796c epifinder-1.0.jar Binary file epifinder-1.0.jar has changed diff -r a8b913eaad2c -r 57972c12796c epifinder-1.0.xml --- a/epifinder-1.0.xml Wed Mar 24 19:21:37 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,581 +0,0 @@ - - Predict B cell epitopes - - Java - Blastp - Makeblastdb - - - - - - - > d means defalt threshold - -->*# - - #**# - #set param = '' - #set nomethod = '' - #set proteomes = '' - - #**# - #if $bepi_type.bepipred_origin == 'y': - #set bepipred_origin = '-o' - #**# - #elif $bepi_type.bepipred_origin == 'id': - #set bepipred_origin = '-jobid ' + str($bepi_type.job_id) - #else: - #set bepipred_origin = '' - #end if - - #**# - #if $emini_method.emini_choice == 'eminiyes': - #if $emini_method.emini_t.t_emini == 't_emini_choice' - #set param += 'emini:' + str($emini_method.emini_t.thresh_em_value) + ';' - #else: - #set param += 'emini:d;' - #end if - #end if - - #**# - #if $parker_method.parker_choice == 'parkeryes': - #if $parker_method.parker_t.t_parker == 't_parker_choice' - #set param += 'parker:' + str($parker_method.parker_t.thresh_park_value) + ';' - #else: - #set param += 'parker:d;' - #end if - #end if - - #**# - #if $chou_method.chou_choice == 'chouyes': - #if $chou_method.chou_t.t_chou == 't_chou_choice' - #set param += 'chou_fosman:' + str($chou_method.chou_t.thresh_chou_value) + ';' - #else: - #set param += 'chou_fosman:d;' - #end if - #end if - - #**# - #if $karplus_method.karplus_choice == 'karplusyes': - #if $karplus_method.karplus_t.t_karplus == 't_karplus_choice' - #set param += 'karplus_schulz:' + str($karplus_method.karplus_t.thresh_karplus_value) + ';' - #else: - #set param += 'karplus_schulz:d;' - #end if - #end if - - #**# - #if $kolaskar_method.kolaskar_choice == 'kolaskaryes': - #if $kolaskar_method.kolaskar_t.t_kolaskar == 't_kolaskar_choice' - #set param += 'kolaskar:' + str($kolaskar_method.kolaskar_t.thresh_kolaskar_value) + ';' - #else: - #set param += 'kolaskar:d;' - #end if - #end if - - - - #**# - #if proteomes == '-proteomes ': - #set proteomes = '' - #end if - - - #**# - - #if $use_blast.blast_use_bool == "use": - #**# - #if $use_blast.prot_input: - #for $file in $use_blast.prot_input: - #set proteomes += str($file.prot_name) + '=' + str($file.prot_file) + ';' - #end for - #end if - #if $use_blast.prot_input: - #if $use_blast.blast.blast_search == 'blastyes': - #set blast_command = 'task=' + str($use_blast.blast.blast_task) - #set blast_command += ';identity=' + str($use_blast.blast.blast_id) + ';cover=' + str($use_blast.blast.blast_cover) + ';word-size=' + str($use_blast.blast.blast_wordsize) - #set blast_command += ';makeblastdb_path=makeblastdb;blastp_path=blastp' - #end if - #end if - #end if - - #**# - - java -cp $__tool_directory__/epifinder-1.0.jar br.ufsc.epifinder.Main - - #**# - #**# - #if $bepi_type.bepipred_origin != 'id': - -b ${bepi_type.bepi_out} - #end if - -t ${tresh_bepi2} - ${bepipred_origin} - #if $param: - -p "${param}" - #end if - -f "${basename}" - -min_len ${min_length} - -max_len ${max_length} - #if $proteomes: - -proteomes - "${proteomes}" - #if $use_blast.blast.blast_search == 'blastyes': - -blast "${blast_command}" - #end if - #end if - #**# - ; - - #**# - mv $basename-epifinder-epitope-detail.tsv epifinder-epitope-detail.tsv; - mv $basename-epifinder-epitopes-fasta.fasta epifinder-epitopes-fasta.fasta; - mv $basename-epifinder-topology.tsv epifinder-topology.tsv; - mv $basename-epifinder-scores.tsv epifinder-scores.tsv; - mv $basename-epifinder-protein-summary.tsv epifinder-protein-summary.tsv; - mv $basename-epifinder-parameters.txt epifinder-parameters.txt; - mv $basename-epifinder.xls epifinder_report.xls; - - #**# - mv ${basename}-epifinder.txt epifinder.txt; - - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - use_blast['blast_use_bool'] is True and use_blast['blast']['blast_search'] is True - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**How to Run** - -First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred's server. - -.. class:: warningmark - -Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite. - -Select methods that you want to check your epitopes for validation. - -Give a threshold for each method (or use default threshold). - -Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish. - -.. class:: warningmark - -If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server's $PATH. - ------ - -**Outputs** - - -**Summary** : Prediction overview - -**Protein Summary** : Show proteins that have epitopes predicted - -**Fasta** : Epitopes' sequences - -**Topology** : Show epitope match in each method, aminoacid per aminoacid - -**Score** : Detailed score for aminoacids - -**Epitope Detail** : Properties of each predicted epitope - -**Parameters** : Softwares, thresholds and parameters used for prediction - -**Xls Report** : Table with epitope detail, protein summary, topology and scores - -**Collection with blast files** : All blast results for each proteome - - ------ - -.. class:: infomark - -**For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/epifinder - ------ - -Please cite methods used in your analysis, available bellow - -| Bioinformatics Lab - UFSC - 2021 - - - - 10.1093/nar/gkx346 - 10.1016/0014-5793(90)80535-q - 10.1002/9780470122921.ch2 - 10.1021/bi00367a013 - https://doi.org/10.1007/BF01195768 - doi:10.1128/jvi.55.3.836-839.1985 - 10.1371/journal.pcbi.1006791 - https://doi.org/10.1093/nar/gky379 - -