Mercurial > repos > iuc > isoformswitchanalyzer
changeset 2:2b0a6af4b85e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
| author | iuc |
|---|---|
| date | Wed, 24 May 2023 06:06:54 +0000 |
| parents | 2c4e879a81cf |
| children | 02a77166b29a |
| files | IsoformSwitchAnalyzeR.R isoformswitchanalyzer.xml macros.xml |
| diffstat | 3 files changed, 81 insertions(+), 22 deletions(-) [+] |
line wrap: on
line diff
--- a/IsoformSwitchAnalyzeR.R Fri May 19 21:26:00 2023 +0000 +++ b/IsoformSwitchAnalyzeR.R Wed May 24 06:06:54 2023 +0000 @@ -34,6 +34,7 @@ type = "integer", help = "Read length (required for stringtie)") parser$add_argument("--annotation", required = FALSE, help = "Annotation") +parser$add_argument("--stringtieAnnotation", required = FALSE, help = "Stringtie annotation") parser$add_argument("--transcriptome", required = FALSE, help = "Transcriptome") parser$add_argument( "--fixStringTieAnnotationProblem", @@ -105,6 +106,12 @@ help = "Overwrite IF values" ) parser$add_argument( + "--removeNonConvensionalChr", + required = FALSE, + action = "store_true", + help = "Remove non-conventional chromosomes" +) +parser$add_argument( "--reduceToSwitchingGenes", required = FALSE, action = "store_true", @@ -348,27 +355,50 @@ ) if (args$toolSource == "stringtie") { - SwitchList <- importRdata( - isoformCountMatrix = quantificationData$counts, - isoformRepExpression = quantificationData$abundance, - designMatrix = myDesign, - isoformExonAnnoation = args$annotation, - isoformNtFasta = args$transcriptome, - showProgress = TRUE, - fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem - ) + if (!is.null(args$stringtieAnnotation)) { + SwitchList <- importRdata( + isoformCountMatrix = quantificationData$counts, + isoformRepExpression = quantificationData$abundance, + designMatrix = myDesign, + removeNonConvensionalChr = args$removeNonConvensionalChr, + isoformExonAnnoation = args$stringtieAnnotation, + isoformNtFasta = args$transcriptome, + addAnnotatedORFs = FALSE, + showProgress = TRUE, + fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem + ) + + SwitchList <- addORFfromGTF( + SwitchList, + removeNonConvensionalChr = args$removeNonConvensionalChr, + pathToGTF = args$annotation + ) + + } else { + SwitchList <- importRdata( + isoformCountMatrix = quantificationData$counts, + isoformRepExpression = quantificationData$abundance, + designMatrix = myDesign, + removeNonConvensionalChr = args$removeNonConvensionalChr, + isoformNtFasta = args$transcriptome, + isoformExonAnnoation = args$annotation, + showProgress = TRUE, + fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem + ) + } + } else { SwitchList <- importRdata( isoformCountMatrix = quantificationData$counts, isoformRepExpression = quantificationData$abundance, designMatrix = myDesign, + removeNonConvensionalChr = args$removeNonConvensionalChr, isoformExonAnnoation = args$annotation, isoformNtFasta = args$transcriptome, showProgress = TRUE ) } - geneCountMatrix <- extractGeneExpression( SwitchList, extractCounts = TRUE, @@ -484,16 +514,18 @@ showProgress = TRUE, ) - SwitchList <- analyzeNovelIsoformORF( - SwitchList, - analysisAllIsoformsWithoutORF = TRUE, - minORFlength = args$minORFlength, - orfMethod = args$orfMethod, - PTCDistance = args$PTCDistance, - startCodons = "ATG", - stopCodons = c("TAA", "TAG", "TGA"), - showProgress = TRUE, - ) + if (!is.null(args$stringtieAnnotation)) { + SwitchList <- analyzeNovelIsoformORF( + SwitchList, + analysisAllIsoformsWithoutORF = TRUE, + minORFlength = args$minORFlength, + orfMethod = args$orfMethod, + PTCDistance = args$PTCDistance, + startCodons = "ATG", + stopCodons = c("TAA", "TAG", "TGA"), + showProgress = TRUE, + ) + } ### Extract Sequences SwitchList <- extractSequence(
--- a/isoformswitchanalyzer.xml Fri May 19 21:26:00 2023 +0000 +++ b/isoformswitchanalyzer.xml Wed May 24 06:06:54 2023 +0000 @@ -42,6 +42,15 @@ #end if #if $functionMode.tool_source.selector == 'stringtie' #set $filename = 't_data.ctab' + #if $functionMode.tool_source.novoisoforms.selector == 'novel' + #if $functionMode.tool_source.novoisoforms.stringtieAnnotation.is_of_type("gtf.gz"): + ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf.gz' && + #set $stringtie_annotation = './stringtie_annotation.gtf.gz' + #else + ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf' && + #set $stringtie_annotation = './stringtie_annotation.gtf' + #end if + #end if #else #set $filename = 'quant.sf' #end if @@ -61,8 +70,12 @@ --parentDir './input_files' --annotation $annotation --transcriptome $transcriptome + $functionMode.removeNonConvensionalChr --toolSource $functionMode.tool_source.selector #if $functionMode.tool_source.selector == 'stringtie' + #if $functionMode.tool_source.novoisoforms.selector == 'novel' + --stringtieAnnotation $stringtie_annotation + #end if --readLength $functionMode.tool_source.averageSize $functionMode.tool_source.fixStringTieAnnotationProblem #end if @@ -224,18 +237,32 @@ <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true" label="Fix StringTie annotation problem" help="This option will automatically try and correct some of the annoation problems created when doing transcript assembly (unassigned transcripts and merged genes)" /> + <conditional name="novoisoforms"> + <param name="selector" type="select" label="Analsys mode"> + <option value="novel">Include novel isoforms in analysis</option> + <option value="reference">Reference-only analysis</option> + </param> + <when value="novel"> + <param name="stringtieAnnotation" type="data" format="gtf,gtf.gz" label="Annotation generated by StringTie merge" + help="The merged GTF is used to recalculate expression estimates using the merged, novel transcripts." /> + </when> + <when value="reference"/> + </conditional> </when> </conditional> - <param name="genomeAnnotation" type="data" format="gtf,gtf.gz" label="Genome annotation (GTF)" + <param name="genomeAnnotation" type="data" format="gtf,gtf.gz" label="Genome annotation" help="It is used to integrate the coding sequence (CDS) regions from in the GTF file as the ORF regions used by IsoformSwitchAnalyzeR." /> <param name="transcriptome" type="data" format="fasta,fasta.gz" label="Transcriptome" help="Please note this different from a fasta file with the sequences of the entire genome." /> + <param argument="removeNonConvensionalChr" type="boolean" truevalue="--removeNonConvensionalChr" falsevalue="" checked="false" + label="Remove non-conventional chromosomes" help="These regions are typically used to annotate regions that cannot be associated to a specific region." /> <param name="countFiles" type="select" label="Generate count matrix files" help="If IsoformSwitchAnalyzeR is used for fixing Stringtie annotation problem, it can generate count files for analyzing differential expression with DESeq2 (when selecting collection) or CEMiTool (when secting the expression matrix format)."> <option value="disabled">Disabled</option> <option value="collection">Collection of count files</option> <option value="matrix">Expression matrix</option> </param> + </when> <!--WRAPPER FIRST STEP SECTION-->
--- a/macros.xml Fri May 19 21:26:00 2023 +0000 +++ b/macros.xml Wed May 24 06:06:54 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.20.0</token> - <token name="@SUFFIX_VERSION@">1</token> + <token name="@SUFFIX_VERSION@">2</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement>