Mercurial > repos > galaxyp > custom_pro_db
changeset 9:328a1e3b5261 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author | galaxyp |
---|---|
date | Wed, 08 Jun 2016 14:04:54 -0400 |
parents | fa6aa0d5a27c |
children | ed65d110c1b5 |
files | customProDB.R customProDB.xml |
diffstat | 2 files changed, 53 insertions(+), 7 deletions(-) [+] |
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--- a/customProDB.R Mon May 09 12:55:26 2016 -0400 +++ b/customProDB.R Wed Jun 08 14:04:54 2016 -0400 @@ -23,7 +23,12 @@ option_list$proteinseq <- make_option('--proteinseq', type='character') option_list$procodingseq <- make_option('--procodingseq', type='character') option_list$ids <- make_option('--ids', type='character') +option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character') +option_list$cosmic <- make_option('--cosmic', type='character') +option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE) option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character') +#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE) +#option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE) option_list$outputFile <- make_option('--outputFile', type='character') @@ -37,14 +42,39 @@ exon_anno_file = GalaxyInputFile(required=TRUE), proteinseq_file = GalaxyInputFile(required=TRUE), procodingseq_file = GalaxyInputFile(required=TRUE), + ids_file = GalaxyInputFile(required=TRUE), + dbsnpinCoding_file = GalaxyInputFile(required=FALSE), + cosmic_file = GalaxyInputFile(required=FALSE), + annotationFromHistory = GalaxyLogicalParam(required=FALSE), rpkmCutoff = GalaxyNumericParam(required=TRUE), - ids_file = GalaxyInputFile(required=TRUE), + #outputIndels = GalaxyLogicalParam(required=FALSE), + #outputNovelJunctions = GalaxyLogicalParam(required=FALSE), outputFile = GalaxyOutput("FASTA","fasta")) { - file.symlink(exon_anno_file, "exon_anno.RData") - file.symlink(proteinseq_file, "proseq.RData") - file.symlink(procodingseq_file, "procodingseq.RData") - file.symlink(ids_file, "ids.RData") + file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/")) + file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/")) + file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/")) + file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/")) + + if (length(dbsnpinCoding_file) > 0) + { + file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/")) + labelrsid = T + } + else + { + labelrsid = F + } + + if (length(cosmic_file) > 0) + { + file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/")) + cosmic = T + } + else + { + cosmic = F + } bamLink = "input.bam" file.symlink(bam_file, bamLink) @@ -52,9 +82,9 @@ suppressPackageStartupMessages(library(customProDB)) - easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file), + easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(), rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", - nov_junction=F, INDEL=T, lablersid=F, COSMIC=F) + nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic) }
--- a/customProDB.xml Mon May 09 12:55:26 2016 -0400 +++ b/customProDB.xml Wed Jun 08 14:04:54 2016 -0400 @@ -16,12 +16,24 @@ --proteinseq="$genome_annotation.proteinSeq" --procodingseq="$genome_annotation.proCodingSeq" --ids="$genome_annotation.ids" + #if str($genome_annotation.dbsnpInCoding) != "None": + --dbsnpinCoding="$genome_annotation.dbsnpInCoding" + #end if + #if str($genome_annotation.cosmic) != "None": + --cosmic="$genome_annotation.cosmic" + #end if #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" --ids="$index_path/ids.RData" + #if $genome_annotation.dbsnpInCoding: + --dbsnpinCoding="$index_path/dbsnpinCoding.RData" + #end if + #if $genome_annotation.cosmic: + --cosmic="$index_path/cosmic.RData" + #end if #end if 2>&1</command> @@ -50,6 +62,8 @@ <validator type="unspecified_build" /> <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> </param> + <param name="labelrsid" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" /> + <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" /> </when> <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" /> @@ -63,6 +77,8 @@ <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> </param> <param name="vcfInput" type="data" format="vcf" label="VCF file" /> + <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" /> + <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" /> </when> </conditional> <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." />