# HG changeset patch # User bioinformatics_lab_ufsc # Date 1637812785 0 # Node ID 8fa9e663cca50c863a96ba1944848e522c9878e8 # Parent 57555f63bbd3de1b616054528b40a1cbe8dd9b02 Uploaded corrected condition for use_hit diff -r 57555f63bbd3 -r 8fa9e663cca5 epibuilder-1.1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epibuilder-1.1.xml Thu Nov 25 03:59:45 2021 +0000 @@ -0,0 +1,585 @@ + + 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_search.search_use_bool == "use": + #**# + #if $use_search.prot_input: + #for $file in $use_search.prot_input: + #set proteomes += str($file.prot_name) + '=' + str($file.prot_file) + ';' + #end for + #end if + #if $use_search.prot_input: + #if $use_search.blast.blast_search == 'blastyes': + #set blast_command = 'task=' + str($use_search.blast.blast_task) + #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) + #set blast_command += ';makeblastdb_path=makeblastdb;blastp_path=blastp' + #end if + #end if + #end if + + #**# + + java -jar $__tool_directory__/epibuilder-1.1.jar + + #**# + #**# + #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 $use_search.blast.blast_search == 'blastyes': + -blast "${blast_command}" + #end if + #end if + + #if $use_search.check_use_hit == 'nousehit': + -nohitacc + #end if + #**# + >log.log 2>log.log; + + mv $basename-epibuilder.xlsx EpiBuilder_report.xlsx; + + #**# + mv ${basename}-epibuilder.txt EpiBuilder; + + + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + use_search['search_use_bool'] is True and use_search['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/EpiBuilder + +----- + +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 + +