Mercurial > repos > iuc > dexseq
changeset 12:74ec758e63a4 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 18:00:45 +0000 |
| parents | 9a7c5b6d8f1e |
| children | |
| files | macros.xml plotdexseq.R plotdexseq.xml test-data/plotdexseq.pdf test-data/plotdexseq_multi.pdf test-data/plotdexseq_multi_custom_dim.pdf |
| diffstat | 6 files changed, 41 insertions(+), 8 deletions(-) [+] |
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--- a/macros.xml Tue Apr 02 12:59:54 2024 +0000 +++ b/macros.xml Fri Jan 31 18:00:45 2025 +0000 @@ -1,7 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1.48.0</token> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@PROFILE@">22.01</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>
--- a/plotdexseq.R Tue Apr 02 12:59:54 2024 +0000 +++ b/plotdexseq.R Fri Jan 31 18:00:45 2025 +0000 @@ -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) @@ -38,8 +40,12 @@ 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$pl_height +pdf("plot.pdf", width = pl_width, height = pl_height) for (i in genes) { + par(oma = c(pl_height * 0.2, pl_width * 0.2, pl_height * 0.2, pl_width * 0.2)) plotDEXSeq(res, i, FDR = opt$fdr, fitExpToVar = opt$primaryfactor, norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing,
--- a/plotdexseq.xml Tue Apr 02 12:59:54 2024 +0000 +++ b/plotdexseq.xml Fri Jan 31 18:00:45 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