Mercurial > repos > galaxyp > custom_pro_db
changeset 3:7e078d4e40f8 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author | galaxyp |
---|---|
date | Fri, 29 Jan 2016 14:26:25 -0500 |
parents | e6f488178a45 |
children | 5bf19713c281 |
files | customProDB.R customProDB.xml |
diffstat | 2 files changed, 119 insertions(+), 28 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/customProDB.R Fri Jan 29 14:26:25 2016 -0500 @@ -0,0 +1,87 @@ +#!/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$bam <- make_option('--bam', type='character') +option_list$vcf <- make_option('--vcf', type='character') +option_list$exon_anno <- make_option('--exon_anno', type='character') +option_list$proteinseq <- make_option('--proteinseq', type='character') +option_list$procodingseq <- make_option('--procodingseq', type='character') +option_list$outputFile <- make_option('--outputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + + +customProDB <- function( + bam_file = GalaxyInputFile(required=TRUE), + vcf_file = GalaxyInputFile(required=TRUE), + exon_anno_file = GalaxyInputFile(required=TRUE), + proteinseq_file = GalaxyInputFile(required=TRUE), + procodingseq_file = GalaxyInputFile(required=TRUE), + outputFile = GalaxyOutput("FASTA","fasta")) +{ + if (dirname(exon_anno_file) != dirname(proteinseq_file) || + dirname(exon_anno_file) != dirname(procodingseq_file)) + { + gstop("parent directory of annotation files must all be the same") + } + + if (file.exists(outputFile)) + { + if (file.info(outputFile)$size > 0) { gstop("output file already exists") } + else + { + tryCatch( + { + file.remove(outputFile) + }, error=function(err) + { + gstop("failed to remove empty existing file") + }) + } + } + + suppressPackageStartupMessages(library(customProDB)) + + easyRun(bamFile=bamFile, vcfFile=vcfFile, annotation_path=dirname(exon_anno_file), outfile_path=dirname(outputFile), outfile_name=basename(outputFile)) +} + + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(customProDB, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- a/customProDB.xml Thu Jan 14 18:12:22 2016 -0500 +++ b/customProDB.xml Fri Jan 29 14:26:25 2016 -0500 @@ -4,44 +4,48 @@ <exit_code range="1:" level="fatal" description="Job Failed" /> </stdio> <command interpreter="Rscript --vanilla">PSM2SAM.R - #if str($input).strip() != "": - --passedPSM="$input" - #end if - #if str($scoreColumn).strip() != "": - --XScolumn="$scoreColumn" - #end if - #if str($optionalUserInput.exonAnno).strip() != "None": - --exon_anno="$optionalUserInput.exonAnno" - #end if - #if str($optionalUserInput.proteinSeq).strip() != "None": - --proteinseq="$optionalUserInput.proteinSeq" - #end if - #if str($optionalUserInput.proCodingSeq).strip() != "None": - --procodingseq="$optionalUserInput.proCodingSeq" - #end if - #if str($optionalUserInput.header).strip() != "None": - --header="$optionalUserInput.header" - #end if - #if str($output).strip() != "": - --OutputFile="$output" + + --bam="$bamInput" + --vcf="$vcfInput" + --outputFile="$output" + + #if str($genome_annotation.source) == "history": + --exon_anno="$genome_annotation.exonAnno" + --proteinseq="$genome_annotation.proteinSeq" + --procodingseq="$genome_annotation.proCodingSeq" + #else: + #set index_path = $genome_annotation.builtin.fields.path + --exon_anno="$index_path/exon_anno.RData" + --proteinseq="$index_path/proseq.RData" + --procodingseq="$index_path/procodingseq.RData" #end if 2>&1</command> <inputs> - <param name="input" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAMs"> + <param name="bamInput" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAM"> <validator type="empty_field" message="This field is required."/> </param> <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls"> <validator type="empty_field" message="This field is required."/> </param> - <conditional name="optionalUserInput"> - <param name="optionalUserInputCondition" type="boolean" label="Override Default Exon Annotation and Coding Sequences" /> - <when value="true"> - <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" /> - <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" /> - <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" /> + + <conditional name="genome_annotation"> + <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below"> + <option value="builtin">Use a built-in genome annotation</option> + <option value="history">Use a genome from the history and build index</option> + </param> + <when value="builtin"> + <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_data_table="customProDB"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No annotations are available for the selected input dataset"/> + </options> + </param> </when> - <when value="false"> + <when value="history"> + <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" /> + <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" /> + <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" /> </when> </conditional> </inputs>