Mercurial > repos > iuc > dexseq
changeset 18:ffa256d657b2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
| author | iuc |
|---|---|
| date | Fri, 31 Jan 2025 18:00:29 +0000 |
| parents | d104044e4257 |
| children | |
| files | dexseq.R dexseq_count.xml macros.xml plotdexseq.R plotdexseq.xml test-data/plotdexseq.pdf test-data/plotdexseq_multi.pdf test-data/plotdexseq_multi_custom_dim.pdf |
| diffstat | 8 files changed, 64 insertions(+), 28 deletions(-) [+] |
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--- a/dexseq.R Tue Apr 04 08:25:36 2023 +0000 +++ b/dexseq.R Fri Jan 31 18:00:29 2025 +0000 @@ -16,8 +16,8 @@ options(stringAsfactors = FALSE, useFancyQuotes = FALSE) args <- commandArgs(trailingOnly = TRUE) -#get options, using the spec as defined by the enclosed list. -#we read the options from the default: commandArgs(TRUE). +# get options, using the spec as defined by the enclosed list. +# we read the options from the default: commandArgs(TRUE). spec <- matrix(c( "verbose", "v", 2, "integer", "help", "h", 0, "logical", @@ -109,7 +109,7 @@ export_table <- as.data.frame(res_sorted) last_column <- ncol(export_table) for (i in seq_len(nrow(export_table))) { - export_table[i, last_column] <- paste(export_table[i, last_column][[1]], collapse = ", ") + export_table[i, last_column] <- paste(export_table[i, last_column][[1]], collapse = ", ") } export_table[, c(last_column)] <- sapply(export_table[, c(last_column)], as.character) write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
--- a/dexseq_count.xml Tue Apr 04 08:25:36 2023 +0000 +++ b/dexseq_count.xml Fri Jan 31 18:00:29 2025 +0000 @@ -16,18 +16,20 @@ <command><![CDATA[ #if $mode.mode_select == "prepare": dexseq_prepare_annotation.py - -r $mode.aggregate - '$mode.gtffile' + -r '${mode.aggregate}' + '${mode.gtffile}' '$flattened_gtf_out' #elif $mode.mode_select == "count": + ln -s -f '${mode.bamfile}' 'input.bam' && + ln -s -f '${mode.bamfile.metadata.bam_index}' 'input.bam.bai' && dexseq_count.py --format bam - --paired $mode.paired - --stranded $mode.stranded - --minaqual $mode.qual - --order $mode.order - $mode.flattened_gtf_in - '$mode.bamfile' + --paired '${mode.paired}' + --stranded '${mode.stranded}' + --minaqual '${mode.qual}' + --order '${mode.order}' + '${mode.flattened_gtf_in}' + 'input.bam' '$counts_file' && sed -i 's/\"//g' '$counts_file' @@ -73,14 +75,14 @@ </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="mode_select" value="prepare" /> <param name="gtffile" ftype="gff" value="original.gtf"/> <param name="aggregate" value="True"/> <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/> </test> <!-- Ensure count mode works --> - <test> + <test expect_num_outputs="1"> <param name="mode_select" value="count" /> <param name="bamfile" ftype="bam" value="in.bam" /> <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/>
--- a/macros.xml Tue Apr 04 08:25:36 2023 +0000 +++ b/macros.xml Fri Jan 31 18:00:29 2025 +0000 @@ -1,12 +1,11 @@ -<?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.44</token> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@PROFILE@">22.01</token> + <token name="@TOOL_VERSION@">1.48.0</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">23.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-dexseq</requirement> - <requirement type="package" version="1.20.3">r-getopt</requirement> + <requirement type="package" version="1.20.4">r-getopt</requirement> <requirement type="package" version="0.2.21">r-rjson</requirement> </requirements> </xml>
--- a/plotdexseq.R Tue Apr 04 08:25:36 2023 +0000 +++ b/plotdexseq.R Fri Jan 31 18:00:29 2025 +0000 @@ -14,8 +14,8 @@ options(stringAsfactors = FALSE, useFancyQuotes = FALSE) args <- commandArgs(trailingOnly = TRUE) -#get options, using the spec as defined by the enclosed list. -#we read the options from the default: commandArgs(TRUE). +# get options, using the spec as defined by the enclosed list. +# we read the options from the default: commandArgs(TRUE). spec <- matrix(c( "rdata", "r", 1, "character", "primaryfactor", "p", 1, "character", @@ -25,7 +25,9 @@ "transcripts", "t", 1, "logical", "names", "a", 1, "logical", "normcounts", "n", 1, "logical", - "splicing", "s", 1, "logical" + "splicing", "s", 1, "logical", + "pl_width", "w", 2, "integer", + "pl_height", "h", 2, "integer" ), byrow = TRUE, ncol = 4) opt <- getopt(spec) @@ -38,12 +40,18 @@ genes <- opt$geneid } -pdf("plot.pdf") +pl_width <- pl_height <- 7 +if (!is.null(opt$pl_width)) pl_width <- opt$pl_width +if (!is.null(opt$pl_height)) pl_height <- opt$pl_height +pdf("plot.pdf", width = pl_width, height = pl_height) for (i in genes) { - plotDEXSeq(res, i, FDR = opt$fdr, fitExpToVar = opt$primaryfactor, + par(oma = c(pl_height * 0.2, pl_width * 0.2, pl_height * 0.2, pl_width * 0.2)) + plotDEXSeq(res, i, + FDR = opt$fdr, fitExpToVar = opt$primaryfactor, norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing, displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE, - color = NULL, color.samples = NULL, transcriptDb = NULL) + color = NULL, color.samples = NULL, transcriptDb = NULL + ) } dev.off()
--- a/plotdexseq.xml Tue Apr 04 08:25:36 2023 +0000 +++ b/plotdexseq.xml Fri Jan 31 18:00:29 2025 +0000 @@ -22,9 +22,15 @@ -a $names -n $normcounts -s $splicing + #if $pl_width: + -w $pl_width + #end if + #if $pl_height: + -h $pl_height + #end if ]]></command> <inputs> - <param name="rdata" type="data" format="rdata" label="DEXSeqResults object" help="A DEXSeqResults object in RDS format. This can be output from the DEXSeq tool"/> + <param name="rdata" type="data" format="rds" label="DEXSeqResults object" help="A DEXSeqResults object in RDS format. This can be output from the DEXSeq tool"/> <param name="primaryfactor" type="text" value="FactorName" label="Specify the primary factor name in the DEXSeqResults object" help="Only letters, numbers and underscores will be retained in this field"> <sanitizer> <valid initial="string.letters,string.digits"><add value="_" /></valid> @@ -38,7 +44,7 @@ <when value="single"> <param name="geneid" type="text" label="Gene identifier" help="Gene identifier to visualize"> <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> + <valid initial="string.letters,string.digits,string.punctuation"><add value="_" /></valid> </sanitizer> </param> </when> @@ -51,6 +57,8 @@ <param name="names" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Display transcript names" help="If Yes, the names of the transcripts are shown. Default: No"/> <param name="normcounts" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot count values from the individual samples" help="If yes, provides a plot of the counts normalized by the size factors. Default: No"/> <param name="splicing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot exon usage" help="If yes, the samples gene expression effects are averaged out, leaving only exon usage coefficients. Default: No" /> + <param name="pl_width" type="integer" optional="true" value="" label="Width of the plot" help="In inches, Default: 7" /> + <param name="pl_height" type="integer" optional="true" value="" label="Height of the plot" help="In inches, Default: 7" /> </inputs> <outputs> @@ -61,7 +69,10 @@ <test expect_num_outputs="1"> <param name="rdata" ftype="rdata" value="dexseq.rds"/> <param name="primaryfactor" value="condition"/> - <param name="geneid" value="FBgn0000053"/> + <conditional name="genes"> + <param name="genes_select" value="single" /> + <param name="geneid" value="FBgn0000053"/> + </conditional> <param name="fdr_cutoff" value="1"/> <output name="dexseq_plot" ftype="pdf" file="plotdexseq.pdf" compare="sim_size"/> </test> @@ -69,10 +80,26 @@ <test expect_num_outputs="1"> <param name="rdata" ftype="rdata" value="dexseq.rds"/> <param name="primaryfactor" value="condition"/> - <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/> + <conditional name="genes"> + <param name="genes_select" value="list" /> + <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/> + </conditional> <param name="fdr_cutoff" value="1"/> <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi.pdf" compare="sim_size"/> </test> + <!-- Ensure plotting with non-default dimensions works--> + <test expect_num_outputs="1"> + <param name="rdata" ftype="rdata" value="dexseq.rds"/> + <param name="primaryfactor" value="condition"/> + <conditional name="genes"> + <param name="genes_select" value="list" /> + <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/> + </conditional> + <param name="fdr_cutoff" value="1"/> + <param name="pl_width" value="5"/> + <param name="pl_height" value="3"/> + <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi_custom_dim.pdf" compare="sim_size"/> + </test> </tests> <help><![CDATA[ .. class:: infomark