# HG changeset patch # User galaxyp # Date 1489515115 14400 # Node ID 45755942ae7b1aedd3c4f97bc6484b12bf164dea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66 diff -r 000000000000 -r 45755942ae7b COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Tue Mar 14 14:11:55 2017 -0400 @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES + REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS + PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM + THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED + HEREUNDER. + +Statement of Purpose + +The laws of most jurisdictions throughout the world automatically confer +exclusive Copyright and Related Rights (defined below) upon the creator +and subsequent owner(s) (each and all, an "owner") of an original work of +authorship and/or a database (each, a "Work"). + +Certain owners wish to permanently relinquish those rights to a Work for +the purpose of contributing to a commons of creative, cultural and +scientific works ("Commons") that the public can reliably and without fear +of later claims of infringement build upon, modify, incorporate in other +works, reuse and redistribute as freely as possible in any form whatsoever +and for any purposes, including without limitation commercial purposes. +These owners may contribute to the Commons to promote the ideal of a free +culture and the further production of creative, cultural and scientific +works, or to gain reputation or greater distribution for their Work in +part through the use and efforts of others. + +For these and/or other purposes and motivations, and without any +expectation of additional consideration or compensation, the person +associating CC0 with a Work (the "Affirmer"), to the extent that he or she +is an owner of Copyright and Related Rights in the Work, voluntarily +elects to apply CC0 to the Work and publicly distribute the Work under its +terms, with knowledge of his or her Copyright and Related Rights in the +Work and the meaning and intended legal effect of CC0 on those rights. + +1. Copyright and Related Rights. A Work made available under CC0 may be +protected by copyright and related or neighboring rights ("Copyright and +Related Rights"). Copyright and Related Rights include, but are not +limited to, the following: + + i. the right to reproduce, adapt, distribute, perform, display, + communicate, and translate a Work; + ii. moral rights retained by the original author(s) and/or performer(s); +iii. publicity and privacy rights pertaining to a person's image or + likeness depicted in a Work; + iv. rights protecting against unfair competition in regards to a Work, + subject to the limitations in paragraph 4(a), below; + v. rights protecting the extraction, dissemination, use and reuse of data + in a Work; + vi. database rights (such as those arising under Directive 96/9/EC of the + European Parliament and of the Council of 11 March 1996 on the legal + protection of databases, and under any national implementation + thereof, including any amended or successor version of such + directive); and +vii. other similar, equivalent or corresponding rights throughout the + world based on applicable law or treaty, and any national + implementations thereof. + +2. Waiver. To the greatest extent permitted by, but not in contravention +of, applicable law, Affirmer hereby overtly, fully, permanently, +irrevocably and unconditionally waives, abandons, and surrenders all of +Affirmer's Copyright and Related Rights and associated claims and causes +of action, whether now known or unknown (including existing as well as +future claims and causes of action), in the Work (i) in all territories +worldwide, (ii) for the maximum duration provided by applicable law or +treaty (including future time extensions), (iii) in any current or future +medium and for any number of copies, and (iv) for any purpose whatsoever, +including without limitation commercial, advertising or promotional +purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each +member of the public at large and to the detriment of Affirmer's heirs and +successors, fully intending that such Waiver shall not be subject to +revocation, rescission, cancellation, termination, or any other legal or +equitable action to disrupt the quiet enjoyment of the Work by the public +as contemplated by Affirmer's express Statement of Purpose. + +3. Public License Fallback. Should any part of the Waiver for any reason +be judged legally invalid or ineffective under applicable law, then the +Waiver shall be preserved to the maximum extent permitted taking into +account Affirmer's express Statement of Purpose. In addition, to the +extent the Waiver is so judged Affirmer hereby grants to each affected +person a royalty-free, non transferable, non sublicensable, non exclusive, +irrevocable and unconditional license to exercise Affirmer's Copyright and +Related Rights in the Work (i) in all territories worldwide, (ii) for the +maximum duration provided by applicable law or treaty (including future +time extensions), (iii) in any current or future medium and for any number +of copies, and (iv) for any purpose whatsoever, including without +limitation commercial, advertising or promotional purposes (the +"License"). The License shall be deemed effective as of the date CC0 was +applied by Affirmer to the Work. Should any part of the License for any +reason be judged legally invalid or ineffective under applicable law, such +partial invalidity or ineffectiveness shall not invalidate the remainder +of the License, and in such case Affirmer hereby affirms that he or she +will not (i) exercise any of his or her remaining Copyright and Related +Rights in the Work or (ii) assert any associated claims and causes of +action with respect to the Work, in either case contrary to Affirmer's +express Statement of Purpose. + +4. Limitations and Disclaimers. + + a. No trademark or patent rights held by Affirmer are waived, abandoned, + surrendered, licensed or otherwise affected by this document. + b. Affirmer offers the Work as-is and makes no representations or + warranties of any kind concerning the Work, express, implied, + statutory or otherwise, including without limitation warranties of + title, merchantability, fitness for a particular purpose, non + infringement, or the absence of latent or other defects, accuracy, or + the present or absence of errors, whether or not discoverable, all to + the greatest extent permissible under applicable law. + c. Affirmer disclaims responsibility for clearing rights of other persons + that may apply to the Work or any use thereof, including without + limitation any person's Copyright and Related Rights in the Work. + Further, Affirmer disclaims responsibility for obtaining any necessary + consents, permissions or other rights required for any use of the + Work. + d. Affirmer understands and acknowledges that Creative Commons is not a + party to this document and has no duty or obligation with respect to + this CC0 or use of the Work. diff -r 000000000000 -r 45755942ae7b data_manager/customProDB_annotation.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/customProDB_annotation.R Tue Mar 14 14:11:55 2017 -0400 @@ -0,0 +1,125 @@ +#!/usr/bin/env Rscript + +initial.options <- commandArgs(trailingOnly = FALSE) +script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)])) + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() +option_list$dbkey <- make_option('--dbkey', type='character') +option_list$dbsnp <- make_option('--dbsnp', type='character') +option_list$cosmic <- make_option('--cosmic', type='logical') +option_list$outputFile <- make_option('--outputFile', type='character') +option_list$dbkey_description <- make_option('--dbkey_description', type='character') + +opt <- parse_args(OptionParser(option_list=option_list)) + + +customProDB_annotation <- function( + dbkey = GalaxyCharacterParam(required=TRUE), + dbsnp_str = GalaxyCharacterParam(required=FALSE), + cosmic = GalaxyLogicalParam(required=FALSE), + dbkey_description = GalaxyCharacterParam(required=FALSE), + outputFile = GalaxyOutput("output","json")) +{ + if (!file.exists(outputFile)) + { + gstop("json params file does not exist") + } + + if (length(dbkey_description) < 1) + { + dbkey_description = dbkey + } + + if (length(dbsnp_str) > 0) + { + dbsnp = dbsnp_str + } + else + { + dbsnp = NULL + } + + use_cosmic = FALSE + if (length(cosmic) > 0) + { + if (grepl("^hg", dbkey)) + { + use_cosmic = TRUE + } + else + { + gstop("COSMIC annotation requested but dbkey does not indicate a human genome (e.g. hg19)") + } + } + + suppressPackageStartupMessages(library(rjson)) + params = fromJSON(file=outputFile) + target_directory = params$output_data[[1]]$extra_files_path + dir.create(target_directory) + + tryCatch( + { + file.remove(outputFile) + }, error=function(err) + { + gstop("failed to remove json params file after reading") + }) + + ucscTableCodingFastaURL = paste("http://genome.ucsc.edu/cgi-bin/hgTables?db=", dbkey, "&hgSeq.cdsExon=on&hgSeq.granularity=gene&hgSeq.casing=exon&hgSeq.repMasking=lower&hgta_doGenomicDna=get+sequence&hgta_group=genes&hgta_track=refGene&hgta_table=refGene&hgta_regionType=genome", sep="") + ucscTableProteinFastaURL = paste("http://genome.ucsc.edu/cgi-bin/hgTables?db=", dbkey, "&hgta_geneSeqType=protein&hgta_doGenePredSequence=submit&hgta_track=refGene&hgta_table=refGene", sep="") + codingFastaFilepath = paste(target_directory, "/", dbkey, ".cds.fa", sep="") + proteinFastaFilepath = paste(target_directory, "/", dbkey, ".protein.fa", sep="") + + suppressPackageStartupMessages(library(customProDB)) + options(timeout=3600) + + cat(paste("Downloading coding FASTA from:", ucscTableCodingFastaURL, "\n")) + download.file(ucscTableCodingFastaURL, codingFastaFilepath, quiet=T, mode='wb') + + cat(paste("Downloading protein FASTA from:", ucscTableProteinFastaURL, "\n")) + download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb') + + cat(paste("Preparing Refseq annotation files\n")) + customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory, dbsnp=dbsnp, COSMIC=use_cosmic) + + outputPath = paste(dbkey, "/customProDB", sep="") + output = list(data_tables = list()) + output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=dbkey, value=dbkey) + write(toJSON(output), file=outputFile) +} + + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(customProDB_annotation, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +}) diff -r 000000000000 -r 45755942ae7b data_manager/customProDB_annotation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/customProDB_annotation.xml Tue Mar 14 14:11:55 2017 -0400 @@ -0,0 +1,40 @@ + + builder + + bioconductor-customprodb + + + + + + 1 +]]> + + + + + + + + + + + +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + + + + 10.1093/bioinformatics/btt543 + @misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, + year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}} + + diff -r 000000000000 -r 45755942ae7b data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Mar 14 14:11:55 2017 -0400 @@ -0,0 +1,22 @@ + + + + + + + + + + + + + ${dbkey}/customProDB + + ${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/customProDB + abspath + + + + + + diff -r 000000000000 -r 45755942ae7b tool-data/customProDB.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/customProDB.loc.sample Tue Mar 14 14:11:55 2017 -0400 @@ -0,0 +1,16 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "customProDB" directory (a subdirectory of a genome build). +#This file has the format (white space characters are TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3 +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19 +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19full +# +#Your customProDB.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# diff -r 000000000000 -r 45755942ae7b tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Mar 14 14:11:55 2017 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+