| Next changeset 1:9b4ee836e35b (2017-06-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66 |
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COPYING data_manager/customProDB_annotation.R data_manager/customProDB_annotation.xml data_manager_conf.xml tool-data/customProDB.loc.sample tool_data_table_conf.xml.sample |
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| 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 |
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| 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 |
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| @@ -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") +}) |
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| 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 |
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| @@ -0,0 +1,40 @@ +<tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1"> + <description>builder</description> + <requirements> + <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement> + </requirements> + <stdio> + <exit_code range=":-1" /> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + Rscript --vanilla '$__tool_directory__/customProDB_annotation.R' + --outputFile '${out_file}' + --dbkey '${dbkey}' + --dbsnp '${dbsnp}' + $cosmic + --dbkey_description '${ dbkey.get_display_text() }' + 2>1 +]]> + </command> + <inputs> + <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" /> + <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" /> + <param type="boolean" name="cosmic" truevalue="--cosmic true" falsevalue="" label="Annotate somatic SNPs from COSMIC (human only)" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <help> + +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btt543</citation> + <citation type="bibtex">@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}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> + </citations> +</tool> |
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| 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 |
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| @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<data_managers> + + <data_manager tool_file="data_manager/customProDB_annotation.xml" id="custom_pro_db_annotation_builder" version="0.0.1"> + <data_table name="customProDB"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/customProDB</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/customProDB</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> + +</data_managers> |
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| 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 |
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| @@ -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): +# +#<unique_build_id> <dbkey> <display_name> <path to annotation files> +# +#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. +# |
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| 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 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all customProDB annotations under genome directory --> + <table name="customProDB" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/customProDB.loc" /> + </table> +</tables> |