Mercurial > repos > bioinformatics_lab_ufsc > epibuilder
changeset 1:57555f63bbd3 draft
Deleted xml interface
| author | bioinformatics_lab_ufsc |
|---|---|
| date | Thu, 25 Nov 2021 03:59:02 +0000 |
| parents | ef26009cd70a |
| children | 8fa9e663cca5 |
| files | ._epibuilder-1.1.jar ._epibuilder-1.1.xml ._test-data epibuilder-1.1.xml |
| diffstat | 4 files changed, 0 insertions(+), 586 deletions(-) [+] |
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--- a/epibuilder-1.1.xml Thu Nov 25 01:26:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,586 +0,0 @@ -<tool id="epibuilder_1.1" name="EpiBuilder" version="1.1"> - <description>Predict B cell epitopes</description> - <requirements> - <requirement type="package" version=">=1.8">Java</requirement> - <requirement type="package" version=">=2.11.0+">Blastp</requirement> - <requirement type="package" version=">=2.11.0+">Makeblastdb</requirement> - </requirements> - <stdio> - <regex match="command not found" - source="both" - level="log" - description="WARNING: some methods could not be applied -> check inputs and outputs files" /> - <regex match="makeblastdb " - source="both" - level="log" - description="makeblastdb and blastp must be in $PATH on your Galaxy server" /> - <regex match="blastp " - source="both" - level="log" - description="makeblastdb and blastp must be in $PATH on your Galaxy server" /> - </stdio> - <command><![CDATA[ - #*<!-- - Methods used will be saved in $param with each threshold - Threshold is separated from method by ":" - Each method is separated by ";" - example: emini:0.8;parker:d; - - >> d means defalt threshold - -->*# - - #*<!-- Set variables that concatenate methods -->*# - #set param = '' - #set nomethod = '' - #set proteomes = '' - - #*<!-- Add Bepipred2.0 method -->*# - #if $bepi_type.bepipred_origin == 'y': - #set bepipred_origin = '-o' - #*<!-- jobid -->*# - #elif $bepi_type.bepipred_origin == 'id': - #set bepipred_origin = '-jobid ' + str($bepi_type.job_id) - #else: - #set bepipred_origin = '' - #end if - - #*<!-- Add Emini method -->*# - #if $emini_method.emini_choice == 'eminiyes': - #if $emini_method.emini_t.t_emini == 't_emini_choice' - #set param += 'emini:' + str($emini_method.emini_t.thresh_em_value) + ';' - #else: - #set param += 'emini:d;' - #end if - #end if - - #*<!-- Add Parker method -->*# - #if $parker_method.parker_choice == 'parkeryes': - #if $parker_method.parker_t.t_parker == 't_parker_choice' - #set param += 'parker:' + str($parker_method.parker_t.thresh_park_value) + ';' - #else: - #set param += 'parker:d;' - #end if - #end if - - #*<!-- Add Chou method -->*# - #if $chou_method.chou_choice == 'chouyes': - #if $chou_method.chou_t.t_chou == 't_chou_choice' - #set param += 'chou_fosman:' + str($chou_method.chou_t.thresh_chou_value) + ';' - #else: - #set param += 'chou_fosman:d;' - #end if - #end if - - #*<!-- Add Karplus method -->*# - #if $karplus_method.karplus_choice == 'karplusyes': - #if $karplus_method.karplus_t.t_karplus == 't_karplus_choice' - #set param += 'karplus_schulz:' + str($karplus_method.karplus_t.thresh_karplus_value) + ';' - #else: - #set param += 'karplus_schulz:d;' - #end if - #end if - - #*<!-- Add Kolaskar method -->*# - #if $kolaskar_method.kolaskar_choice == 'kolaskaryes': - #if $kolaskar_method.kolaskar_t.t_kolaskar == 't_kolaskar_choice' - #set param += 'kolaskar:' + str($kolaskar_method.kolaskar_t.thresh_kolaskar_value) + ';' - #else: - #set param += 'kolaskar:d;' - #end if - #end if - - - - #*<!-- Clean $proteome if there's no protome -->*# - #if proteomes == '-proteomes ': - #set proteomes = '' - #end if - - - #*<!-- Parse blast command -->*# - - #if $use_search.search_use_bool == "use": - #*<!-- Add proteomes, as many as given -->*# - #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 - - #*<!-- Paste Command-line and run -->*# - - java -jar $__tool_directory__/epibuilder-1.1.jar - - #*<!-- bepipred_origin give -o if online, nothing if command and -jobid if jobID -->*# - #*<!-- if origin is not jobid, there is a file, and -b must be passed -->*# - #if $bepi_type.bepipred_origin != 'id': - -b ${bepi_type.bepi_out} - #end if - -t ${tresh_bepi2} - ${bepipred_origin} - #if $param: - -p "${param}" - #end if - -f "${basename}" - -min_len ${min_length} - -max_len ${max_length} - #if $proteomes: - -proteomes - "${proteomes}" - #if $use_search.blast.blast_search == 'blastyes': - -blast "${blast_command}" - #end if - #end if - - #if $use_search.check_use_hit == 'nousehit': - -nohitacc - #end if - #*<!-- DONT REMOVE THIS ; -->*# - >log.log 2>log.log; - - mv $basename-epibuilder.xlsx EpiBuilder_report.xlsx; - - #*<!-- Rename output files -->*# - mv ${basename}-epibuilder.txt EpiBuilder; - - - ]]> - </command> - <inputs> - <!-- Bepipred 2.0 --> - <conditional name="bepi_type"> - <param name="bepipred_origin" type="select" display="radio" label="Input files" help="Online prediction returns a csv file, command-line based returns a tsv file" > - <option value="y" selected="true">csv file from Bepipred 2.0</option> - <option value="n" >text file from IEDB Bcell Software standalone</option> - <option value="id">JobID from Bepipred 2.0 Server</option> - </param> - <when value="y" > - <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" /> - </when> - <when value="n" > - <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" /> - </when> - <when value="id" > - <param name="job_id" type="text" value="" label="JobID" help="Prediction must be complete - check it in: http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=YOUR_JOB_ID" > - <!-- Check if its an empty value--> - <validator type="empty_field" message="ID required"/> - </param> - </when> - </conditional> - <param name="tresh_bepi2" min="0.0" value="0.6" type="float" label="Threshold for Bepipred 2.0" help="Default = 0.6" /> - <!-- Epitope Length --> - <param name="min_length" value="10" min="1" type="integer" label="Min epitope length" help="[1-X] Minimal length must be smaller than maximal length" /> - <param name="max_length" value="30" min="2" type="integer" label="Max epitope length" help="[2-X] Maximal length must be greather than minimal length" /> - <!-- EMINI --> - <conditional name="emini_method"> - <param name="emini_choice" type="boolean" checked="true" truevalue="eminiyes" falsevalue="eminino" label="Use Emini Surface Accessibility Prediction method?" /> - <when value="eminino"> - </when> - <when value="eminiyes"> - <conditional name="emini_t"> - <param name="t_emini" display="radio" type="select" label="Threshold" help="Define threshold for Emini" > - <option value="d_emini_choice" selected="true">Default (calculated by method)</option> - <option value="t_emini_choice">Set Threshold</option> - </param> - <when value="t_emini_choice"> - <param name="thresh_em_value" value="0" type="float" label="Value" /> - </when> - <when value="d_emini_choice"> - </when> - </conditional> - </when> - </conditional> - <!-- PARKER --> - <conditional name="parker_method"> - <param name="parker_choice" type="boolean" checked="true" truevalue="parkeryes" falsevalue="parkerno" label="Use Parker Hydrophilicity Prediction method?" /> - <when value="parkerno"> - </when> - <when value="parkeryes"> - <conditional name="parker_t"> - <param name="t_parker" display="radio" type="select" label="Threshold" help="Define threshold for Parker" > - <option value="d_parker_choice" selected="true">Default (calculated by method)</option> - <option value="t_parker_choice">Set Threshold</option> - </param> - <when value="t_parker_choice"> - <param name="thresh_park_value" value="0" type="float" label="Value" /> - </when> - <when value="d_parker_choice"> - </when> - </conditional> - </when> - </conditional> - <!-- Chou --> - <conditional name="chou_method"> - <param name="chou_choice" type="boolean" checked="true" truevalue="chouyes" falsevalue="chouno" label="Use Chou & Fasman Beta-Turn Prediction method?" /> - <when value="chouno"> - </when> - <when value="chouyes"> - <conditional name="chou_t"> - <param name="t_chou" display="radio" type="select" label="Threshold" help="Define threshold for Chou & Fasman" > - <option value="d_chou_choice" selected="true">Default (calculated by method)</option> - <option value="t_chou_choice">Set Threshold</option> - </param> - <when value="t_chou_choice"> - <param name="thresh_chou_value" value="0" type="float" label="Value" /> - </when> - <when value="d_chou_choice"> - </when> - </conditional> - </when> - </conditional> - <!-- Karplus --> - <conditional name="karplus_method"> - <param name="karplus_choice" type="boolean" checked="true" truevalue="karplusyes" falsevalue="karplusno" label="Use Karplus & Schulz Flexibility Prediction method?" /> - <when value="karplusno"> - </when> - <when value="karplusyes"> - <conditional name="karplus_t"> - <param name="t_karplus" display="radio" type="select" label="Threshold" help="Define threshold for Karplus & Schulz" > - <option value="d_karplus_choice" selected="true">Default (calculated by method)</option> - <option value="t_karplus_choice">Set Threshold</option> - </param> - <when value="t_karplus_choice"> - <param name="thresh_karplus_value" type="float" value="0" label="Value" /> - </when> - <when value="d_karplus_choice"> - </when> - </conditional> - </when> - </conditional> - <!-- Kolaskar --> - <conditional name="kolaskar_method"> - <param name="kolaskar_choice" type="boolean" checked="true" truevalue="kolaskaryes" falsevalue="kolaskarno" label="Use Kolaskar & Tongaonkar Antigenicity method?" /> - <when value="kolaskarno"> - </when> - <when value="kolaskaryes"> - <conditional name="kolaskar_t"> - <param name="t_kolaskar" display="radio" type="select" label="Threshold" help="Define threshold for Kolaskar & Tongaonkar" > - <option value="d_kolaskar_choice" selected="true">Default (calculated by method)</option> - <option value="t_kolaskar_choice">Set Threshold</option> - </param> - <when value="t_kolaskar_choice"> - <param name="thresh_kolaskar_value" type="float" value="0" label="Value" /> - </when> - <when value="d_kolaskar_choice"> - </when> - </conditional> - </when> - </conditional> - <!-- Insert Proteome --> - <conditional name="use_search"> - <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?" /> - <when value="dont"> - </when> - <when value="use"> - <repeat name="prot_input" title="Proteome" min="1"> - <param type="data" name="prot_file" format="fasta" label="Proteome file" help="Protein sequences in fasta format" /> - <param type="text" name="prot_name" label="Proteome name" help="Give a name to this dataset" > - <!-- Change spaces for '_' --> - <sanitizer> - <valid initial="string.printable"> - <remove value=" "/> - </valid> - <mapping initial="none"> - <add source=" " target="_"/> - </mapping> - </sanitizer> - <!-- Check if its an empty value--> - <validator type="empty_field" message="Basename required"/> - </param> - </repeat> - <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" /> - <conditional name="blast"> - <param name="blast_search" type="boolean" checked="false" truevalue="blastyes" falsevalue="blastno" label="Blastp" help="Choose this option if you want to add a blast search for epitopes in proteomes" /> - <when value="blastno"> - </when> - <when value="blastyes"> - <param name="blast_id" value="90" min="1" type="integer" label="Identity" help="[0-100] Minimal identity accepted to parse blast results" /> - <param name="blast_cover" value="90" min="2" type="integer" label="Coverage" help="[0-100] Minimal coverage accepted to parse blast results" /> - <param name="blast_wordsize" value="4" min="1" type="integer" label="Word-Size" help="Blast argument word-size" /> - <param name="blast_task" type="select" label="Task" help="How blastp should run"> - <option value="blastp-short" selected="True">Blastp-short</option> - <option value="blastp-fast">Blastp-fast</option> - <option value="blastp">Blastp</option> - </param> - </when> - </conditional> - </when> - </conditional> - <param name="basename" type="text" value="" label="Basename" help="Provide a name for this run (string text without special characters)" > - <!-- Change spaces for '_' --> - <sanitizer> - <valid initial="string.printable"> - <remove value=" "/> - </valid> - <mapping initial="none"> - <add source=" " target="_"/> - </mapping> - </sanitizer> - <!-- Check if its an empty value--> - <validator type="empty_field" message="Basename required"/> - </param> - </inputs> - <outputs> - <data name="epif_out" format="txt" from_work_dir="EpiBuilder" label="EpiBuilder Output Summary - ${basename}" /> - <data name="ep_xls" format="xlsx" from_work_dir="EpiBuilder_report.xlsx" label="EpiBuilder Report - ${basename}" /> - <collection type="list" label="EpiBuilder Files - ${basename}" name="epif_collection" > - <discover_datasets format="fasta" pattern="(?P<designation>.*)\.fasta" visible="false" /> - <discover_datasets format="txt" pattern="(?P<designation>.*)\.tsv" visible="false" /> - <discover_datasets format="txt" pattern="(?P<designation>.*)\.txt" visible="false" /> - </collection> - <collection type="list" label="EpiBuilder Blast Run - ${basename}" name="blast_collection" > - <filter>use_search['search_use_bool'] is True and use_search['blast']['blast_search'] is True</filter> - <discover_datasets pattern="(?P<designation>.*)blast\.csv" visible="false" /> - </collection> - </outputs> - <tests> - <test> - <!-- Test all methods threshold selected, command line version of input with proteome--> - <conditional name="bepi_type"> - <param name="bepipred_origin" value="y"/> - <param name="bepi_out" value="input_bepi_online.csv"/> - </conditional> - <param name="tresh_bepi2" value="0.6"/> - - <param name="min_length" value="10" /> - <param name="max_length" value="30" /> - - <conditional name="emini_method"> - <param name="emini_choice" value="eminiyes"/> - <conditional name="emini_t"> - <param name="t_emini" value="t_emini_choice"/> - <param name="thresh_em_value" value="0.8" /> - </conditional> - </conditional> - - <conditional name="parker_method"> - <param name="parker_choice" value="parkeryes"/> - <conditional name="parker_t"> - <param name="t_parker" value="t_parker_choice"/> - <param name="thresh_park_value" value="0.8" /> - </conditional> - </conditional> - - <conditional name="chou_method"> - <param name="chou_choice" value="chouyes"/> - <conditional name="chou_t"> - <param name="t_chou" value="t_chou_choice"/> - <param name="thresh_chou_value" value="0.8" /> - </conditional> - </conditional> - - <conditional name="karplus_method"> - <param name="karplus_choice" value="karplusyes"/> - <conditional name="karplus_t"> - <param name="t_karplus" value="t_karplus_choice"/> - <param name="thresh_karplus_value" value="0.8" /> - </conditional> - </conditional> - - - <conditional name="kolaskar_method"> - <param name="kolaskar_choice" value="kolaskaryes"/> - <conditional name="kolaskar_t"> - <param name="t_kolaskar" value="t_kolaskar_choice"/> - <param name="thresh_kolaskar_value" value="0.8" /> - </conditional> - </conditional> - <!-- This first part test all methods--> - - <conditional name="use_search"> - <param name="search_use_bool" value="use" /> - <repeat name="prot_input"> - <param name="prot_name" value="test_proteom" /> - <param name="prot_file" value="proteom.fasta" /> - </repeat> - <conditional name="check_use_hit" value="usehit"/> - <conditional name="blast"> - <param name="blast_search" value="blastyes" /> - <param name="blast_id" value="90" /> - <param name="blast_cover" value="90" /> - <param name="blast_wordsize" value="4" /> - <param name="blast_task" value="blastp-short" /> - </conditional> - </conditional> - - <param name="basename" value="online" /> - - <output name="epif_out" file="online-EpiBuilder.txt" /> - <output name="ep_xls" file="online-EpiBuilder.xlsx" /> - <output_collection name= "epif_collection"> - <element name="ep_prot_sum" file="online-EpiBuilder-protein-summary.tsv" /> - <element name="ep_top" file="online-EpiBuilder-topology.tsv" /> - <element name="ep_score" file="online-EpiBuilder-socre.tsv" /> - <element name="ep_detail" file="online-EpiBuilder-epitope-detail.tsv" /> - <element name="ep_parameters" file="online-EpiBuilder-parameters.tsv" /> - <element name="ep_fasta" file="online-EpiBuilder-fasta.fasta" /> - </output_collection> - <output_collection name="blast_collection" > - <element name="test_proteom" file="online-test_proteom_blast.csv" ftype="csv" /> - </output_collection > - </test> - - <test> - <!-- Test all methods threshold selected, online version of input with proteome--> - <conditional name="bepi_type"> - <param name="bepipred_origin" value="y"/> - <param name="bepi_out" value="input_bcell_command_line.txt"/> - </conditional> - - <param name="bepipred_origin" value="n"/> - <param name="tresh_bepi2" value="0.6"/> - - <param name="min_length" value="10" /> - <param name="max_length" value="30" /> - - <conditional name="emini_method"> - <param name="emini_choice" value="eminiyes"/> - <conditional name="emini_t"> - <param name="t_emini" value="t_emini_choice"/> - <param name="thresh_em_value" value="0.8" /> - </conditional> - </conditional> - - <conditional name="parker_method"> - <param name="parker_choice" value="parkeryes"/> - <conditional name="parker_t"> - <param name="t_parker" value="t_parker_choice"/> - <param name="thresh_park_value" value="0.8" /> - </conditional> - </conditional> - - <conditional name="chou_method"> - <param name="chou_choice" value="chouyes"/> - <conditional name="chou_t"> - <param name="t_chou" value="t_chou_choice"/> - <param name="thresh_chou_value" value="0.8" /> - </conditional> - </conditional> - - <conditional name="karplus_method"> - <param name="karplus_choice" value="karplusyes"/> - <conditional name="karplus_t"> - <param name="t_karplus" value="t_karplus_choice"/> - <param name="thresh_karplus_value" value="0.8" /> - </conditional> - </conditional> - - - <conditional name="kolaskar_method"> - <param name="kolaskar_choice" value="kolaskaryes"/> - <conditional name="kolaskar_t"> - <param name="t_kolaskar" value="t_kolaskar_choice"/> - <param name="thresh_kolaskar_value" value="0.8" /> - </conditional> - </conditional> - <!-- This first part test all methods--> - - <conditional name="use_search"> - <param name="search_use_bool" value="use"/> - <repeat name="prot_input"> - <param name="prot_name" value="test_proteom" /> - <param name="prot_file" value="proteom.fasta" /> - </repeat> - <conditional name="check_use_hit" value="usehit"/> - <conditional name="blast"> - <param name="blast_search" value="blastyes" /> - <param name="blast_id" value="90" /> - <param name="blast_cover" value="90"/> - <param name="blast_wordsize" value="4" /> - <param name="blast_task" value="blastp-short" /> - </conditional> - </conditional> - - <param name="basename" value="command" /> - - <output name="epif_out" file="command-EpiBuilder.txt" /> - <output name="ep_xls" file="command-EpiBuilder.xlsx" /> - <output_collection name= "epif_collection"> - <element name="ep_prot_sum" file="command-EpiBuilder-protein-summary.tsv" /> - <element name="ep_top" file="command-EpiBuilder-topology.tsv" /> - <element name="ep_score" file="command-EpiBuilder-socre.tsv" /> - <element name="ep_detail" file="command-EpiBuilder-epitope-detail.tsv" /> - <element name="ep_parameters" file="command-EpiBuilder-parameters.tsv" /> - <element name="ep_fasta" file="command-EpiBuilder-fasta.fasta" /> - </output_collection> - <output_collection name="blast_collection" > - <element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" /> - </output_collection > - </test> - </tests> - <help> -**How to Run** - -First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred's server. - -.. class:: warningmark - -Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite. - -Select methods that you want to check your epitopes for validation. - -Give a threshold for each method (or use default threshold). - -Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish. - -.. class:: warningmark - -If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server's $PATH. - ------ - -**Outputs** - - -**Summary** : Prediction overview - -**Protein Summary** : Show proteins that have epitopes predicted - -**Fasta** : Epitopes' sequences - -**Topology** : Show epitope match in each method, aminoacid per aminoacid - -**Score** : Detailed score for aminoacids - -**Epitope Detail** : Properties of each predicted epitope - -**Parameters** : Softwares, thresholds and parameters used for prediction - -**Xls Report** : Table with epitope detail, protein summary, topology and scores - -**Collection with blast files** : All blast results for each proteome - - ------ - -.. class:: infomark - -**For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/EpiBuilder - ------ - -Please cite methods used in your analysis, available bellow - -| Bioinformatics Lab - UFSC - 2021 - -</help> -<citations> - <citation type="doi">10.1093/nar/gkx346</citation> - <citation type="doi">10.1016/0014-5793(90)80535-q</citation> - <citation type="doi">10.1002/9780470122921.ch2</citation> - <citation type="doi">10.1021/bi00367a013</citation> - <citation type="doi">https://doi.org/10.1007/BF01195768</citation> - <citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation> - <citation type="doi">10.1371/journal.pcbi.1006791</citation> - <citation type="doi">https://doi.org/10.1093/nar/gky379</citation> -</citations> -</tool> -