Mercurial > repos > galaxyp > custom_pro_db
changeset 7:b83a4002aab1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
| author | galaxyp |
|---|---|
| date | Fri, 06 May 2016 15:56:07 -0400 |
| parents | 61e45c111ef7 |
| children | fa6aa0d5a27c |
| files | customProDB.R customProDB.xml |
| diffstat | 2 files changed, 5 insertions(+), 1 deletions(-) [+] |
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--- a/customProDB.R Wed Feb 03 12:37:47 2016 -0500 +++ b/customProDB.R Fri May 06 15:56:07 2016 -0400 @@ -23,6 +23,7 @@ option_list$proteinseq <- make_option('--proteinseq', type='character') option_list$procodingseq <- make_option('--procodingseq', type='character') option_list$ids <- make_option('--ids', type='character') +option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character') option_list$outputFile <- make_option('--outputFile', type='character') @@ -36,6 +37,7 @@ exon_anno_file = GalaxyInputFile(required=TRUE), proteinseq_file = GalaxyInputFile(required=TRUE), procodingseq_file = GalaxyInputFile(required=TRUE), + rpkmCutoff = GalaxyNumericParam(required=TRUE), ids_file = GalaxyInputFile(required=TRUE), outputFile = GalaxyOutput("FASTA","fasta")) { @@ -51,7 +53,7 @@ suppressPackageStartupMessages(library(customProDB)) easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file), - outfile_path=".", outfile_name="output", + rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", nov_junction=F, INDEL=T, lablersid=F, COSMIC=F) }
--- a/customProDB.xml Wed Feb 03 12:37:47 2016 -0500 +++ b/customProDB.xml Fri May 06 15:56:07 2016 -0400 @@ -8,6 +8,7 @@ --bam="$genome_annotation.bamInput" --bai="${genome_annotation.bamInput.metadata.bam_index}" --vcf="$genome_annotation.vcfInput" + --rpkmCutoff=$rpkmCutoff --outputFile="${output_rpkm}" #if str($genome_annotation.source) == "history": @@ -64,6 +65,7 @@ <param name="vcfInput" type="data" format="vcf" label="VCF file" /> </when> </conditional> + <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." /> </inputs> <outputs> <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>