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Commit message:
Uploaded corrected condition for use_hit |
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added:
epibuilder-1.1.xml |
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| 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 |
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| b'@@ -0,0 +1,585 @@\n+<tool id="epibuilder_1.1" name="EpiBuilder" version="1.1">\n+ <description>Predict B cell epitopes</description>\n+ <requirements>\n+\t\t<requirement type="package" version=">=1.8">Java</requirement>\n+\t\t<requirement type="package" version=">=2.11.0+">Blastp</requirement>\n+\t\t<requirement type="package" version=">=2.11.0+">Makeblastdb</requirement>\n+ </requirements>\n+\t<stdio>\n+\t\t<regex match="command not found"\n+ source="both"\n+ level="log"\n+ description="WARNING: some methods could not be applied -> check inputs and outputs files" />\n+\t\t<regex match="makeblastdb "\n+ source="both"\n+ level="log"\n+ description="makeblastdb and blastp must be in $PATH on your Galaxy server" /> \n+\t\t<regex match="blastp "\n+ source="both"\n+ level="log"\n+ description="makeblastdb and blastp must be in $PATH on your Galaxy server" /> \n+\t</stdio>\n+ <command><![CDATA[\n+\t#*<!-- \n+\t\tMethods used will be saved in $param with each threshold \n+\t\tThreshold is separated from method by ":"\n+\t\tEach method is separated by ";"\n+\t\texample: emini:0.8;parker:d;\n+\n+\t\t>> d means defalt threshold\n+\t-->*#\n+\n+\t#*<!-- Set variables that concatenate methods -->*#\n+\t#set param = \'\'\n+\t#set nomethod = \'\'\n+\t#set proteomes = \'\'\n+\n+\t#*<!-- Add Bepipred2.0 method -->*#\n+\t#if $bepi_type.bepipred_origin == \'y\':\n+\t\t#set bepipred_origin = \'-o\'\n+\t#*<!-- jobid -->*#\n+\t#elif $bepi_type.bepipred_origin == \'id\':\n+\t\t#set bepipred_origin = \'-jobid \' + str($bepi_type.job_id)\n+\t#else:\n+\t\t#set bepipred_origin = \'\'\n+\t#end if\n+\t\n+\t#*<!-- Add Emini method -->*#\n+\t#if $emini_method.emini_choice == \'eminiyes\':\n+\t\t#if $emini_method.emini_t.t_emini == \'t_emini_choice\'\n+\t\t\t#set param += \'emini:\' + str($emini_method.emini_t.thresh_em_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'emini:d;\'\t\t\n+\t\t#end if\n+\t#end if\n+\n+\t#*<!-- Add Parker method -->*#\n+\t#if $parker_method.parker_choice == \'parkeryes\':\n+\t\t#if $parker_method.parker_t.t_parker == \'t_parker_choice\'\n+\t\t\t#set param += \'parker:\' + str($parker_method.parker_t.thresh_park_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'parker:d;\'\t\t\n+\t\t#end if\n+ #end if\n+\n+\t#*<!-- Add Chou method -->*#\n+\t#if $chou_method.chou_choice == \'chouyes\':\n+\t\t#if $chou_method.chou_t.t_chou == \'t_chou_choice\'\n+\t\t\t#set param += \'chou_fosman:\' + str($chou_method.chou_t.thresh_chou_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'chou_fosman:d;\'\t\t\n+\t\t#end if\n+ #end if\n+\n+\t#*<!-- Add Karplus method -->*#\n+\t#if $karplus_method.karplus_choice == \'karplusyes\':\n+\t\t#if $karplus_method.karplus_t.t_karplus == \'t_karplus_choice\'\n+\t\t\t#set param += \'karplus_schulz:\' + str($karplus_method.karplus_t.thresh_karplus_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'karplus_schulz:d;\'\t\t\n+\t\t#end if\n+ #end if\n+\n+\t#*<!-- Add Kolaskar method -->*#\n+\t#if $kolaskar_method.kolaskar_choice == \'kolaskaryes\':\n+\t\t#if $kolaskar_method.kolaskar_t.t_kolaskar == \'t_kolaskar_choice\'\n+\t\t\t#set param += \'kolaskar:\' + str($kolaskar_method.kolaskar_t.thresh_kolaskar_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'kolaskar:d;\'\t\t\n+\t\t#end if\n+ #end if\n+\n+\n+\n+\t#*<!-- Clean $proteome if there\'s no protome -->*#\n+\t#if proteomes == \'-proteomes \':\n+\t\t#set proteomes = \'\'\t\n+\t#end if\n+\n+\n+\t#*<!-- Parse blast command -->*#\n+\t\n+\t#if $use_search.search_use_bool == "use":\n+\t\t#*<!-- Add proteomes, as many as given -->*#\n+\t\t#if $use_search.prot_input: \n+\t\t\t#for $file in $use_search.prot_input:\n+\t\t\t\t#set proteomes += str($file.prot_name) + \'=\' + str($file.prot_file) + \';\'\n+\t\t\t#end for\n+\t\t#end if\n+\t\t#if $use_search.prot_input:\n+\t\t\t#if $use_search.blast.blast_search == \'blastyes\':\n+\t\t\t\t#set blast_command = \'task=\' + str($use_search.blast.blast_task) \t\t\n+\t\t\t\t#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)\n+\t\t\t\t#set blast_command += \';makeblastdb_path=makeblastdb;blastp_path=blastp\'\n+\t\t\t#end if\n+\t\t#end if\n+\t#end if\n+\n+\t#*<'..b'e="t_karplus_choice"/>\n+\t\t\t\t\t<param name="thresh_karplus_value" value="0.8" />\n+\t\t\t\t</conditional>\n+\t\t\t</conditional>\n+\n+\n+\t\t\t<conditional name="kolaskar_method">\n+\t\t\t\t<param name="kolaskar_choice" value="kolaskaryes"/>\n+\t\t\t\t<conditional name="kolaskar_t">\n+\t\t\t\t\t<param name="t_kolaskar" value="t_kolaskar_choice"/>\n+\t\t\t\t\t<param name="thresh_kolaskar_value" value="0.8" />\n+\t\t\t\t</conditional>\n+\t\t\t</conditional>\n+\t\t\t<!-- This first part test all methods-->\n+\n+\t\t\t<conditional name="use_search">\n+\t\t\t\t<param name="search_use_bool" value="use"/>\n+\t\t\t\t\t<repeat name="prot_input">\n+\t\t\t\t\t\t<param name="prot_name" value="test_proteom" />\n+\t\t\t\t\t\t<param name="prot_file" value="proteom.fasta" />\n+\t\t\t\t\t</repeat>\n+\t\t\t\t\t<param name="check_use_hit" value="usehit"/>\n+\t\t\t\t\t<conditional name="blast">\n+\t\t\t\t\t\t<param name="blast_search" value="blastyes" />\n+\t\t\t\t\t\t<param name="blast_id" value="90" />\n+\t\t\t\t\t\t<param name="blast_cover" value="90"/>\n+\t\t\t\t\t\t<param name="blast_wordsize" value="4" />\n+\t\t\t\t\t\t<param name="blast_task" value="blastp-short" />\n+\t\t\t\t\t</conditional>\n+\t\t\t</conditional>\n+\t\n+\t\t\t<param name="basename" value="command" />\n+\n+\t\t\t<output name="epif_out" file="command-EpiBuilder.txt" />\n+\t\t\t<output name="ep_xls" file="command-EpiBuilder.xlsx" />\n+\t\t\t<output_collection name= "epif_collection">\n+\t\t\t\t<element name="ep_prot_sum" file="command-EpiBuilder-protein-summary.tsv" />\n+\t\t\t\t<element name="ep_top" file="command-EpiBuilder-topology.tsv" />\n+\t\t\t\t<element name="ep_score" file="command-EpiBuilder-socre.tsv" />\n+\t\t\t\t<element name="ep_detail" file="command-EpiBuilder-epitope-detail.tsv" />\n+\t\t\t\t<element name="ep_parameters" file="command-EpiBuilder-parameters.tsv" />\n+\t\t\t\t<element name="ep_fasta" file="command-EpiBuilder-fasta.fasta" />\n+\t\t\t</output_collection>\n+\t\t\t<output_collection name="blast_collection" >\n+\t\t\t\t<element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" />\n+\t\t\t</output_collection >\n+\t\t</test>\n+\t</tests>\n+ <help>\n+**How to Run**\n+\n+First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred\'s server.\n+\n+.. class:: warningmark \n+\n+Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite.\n+\n+Select methods that you want to check your epitopes for validation.\n+\n+Give a threshold for each method (or use default threshold).\n+\n+Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish.\n+\n+.. class:: warningmark \n+\n+If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server\'s $PATH.\n+\n+-----\n+\n+**Outputs**\n+\n+\n+**Summary** : Prediction overview \n+\n+**Protein Summary** : Show proteins that have epitopes predicted\n+\n+**Fasta** : Epitopes\' sequences\n+\n+**Topology** : Show epitope match in each method, aminoacid per aminoacid\n+\n+**Score** : Detailed score for aminoacids\n+\n+**Epitope Detail** : Properties of each predicted epitope\n+\n+**Parameters** : Softwares, thresholds and parameters used for prediction\n+\n+**Xls Report** : Table with epitope detail, protein summary, topology and scores\n+\n+**Collection with blast files** : All blast results for each proteome \n+\n+\n+-----\n+\n+.. class:: infomark\n+\n+**For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/EpiBuilder\n+\n+-----\n+\n+Please cite methods used in your analysis, available bellow\n+\n+| Bioinformatics Lab - UFSC - 2021\n+\n+</help>\n+<citations>\n+\t<citation type="doi">10.1093/nar/gkx346</citation>\n+\t<citation type="doi">10.1016/0014-5793(90)80535-q</citation>\n+\t<citation type="doi">10.1002/9780470122921.ch2</citation>\n+\t<citation type="doi">10.1021/bi00367a013</citation>\n+\t<citation type="doi">https://doi.org/10.1007/BF01195768</citation>\n+\t<citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation>\n+\t<citation type="doi">10.1371/journal.pcbi.1006791</citation>\n+\t<citation type="doi">https://doi.org/10.1093/nar/gky379</citation>\n+</citations>\n+</tool>\n' |