| Previous changeset 0:ef26009cd70a (2021-11-25) Next changeset 2:8fa9e663cca5 (2021-11-25) |
|
Commit message:
Deleted xml interface |
|
removed:
._epibuilder-1.1.jar ._epibuilder-1.1.xml ._test-data epibuilder-1.1.xml |
| b |
| diff -r ef26009cd70a -r 57555f63bbd3 ._epibuilder-1.1.jar |
| b |
| Binary file ._epibuilder-1.1.jar has changed |
| b |
| diff -r ef26009cd70a -r 57555f63bbd3 ._epibuilder-1.1.xml |
| b |
| Binary file ._epibuilder-1.1.xml has changed |
| b |
| diff -r ef26009cd70a -r 57555f63bbd3 ._test-data |
| b |
| Binary file ._test-data has changed |
| b |
| diff -r ef26009cd70a -r 57555f63bbd3 epibuilder-1.1.xml --- a/epibuilder-1.1.xml Thu Nov 25 01:26:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,586 +0,0 @@\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'plus_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<conditional 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-\n' |