From dcd6bb56703d2179f0f8a8efa5ad4bbb7aca9fc2 Mon Sep 17 00:00:00 2001
From: Pavankumar Videm <pavanvidem@gmail.com>
Date: Thu, 30 Jan 2025 11:05:38 +0100
Subject: [PATCH 1/7] Change input format of plotdexseq tool from rdata to rds

---
 tools/dexseq/plotdexseq.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/dexseq/plotdexseq.xml b/tools/dexseq/plotdexseq.xml
index f79ac94b4bf..f1c54a7732d 100644
--- a/tools/dexseq/plotdexseq.xml
+++ b/tools/dexseq/plotdexseq.xml
@@ -24,7 +24,7 @@ Rscript '$__tool_directory__/plotdexseq.R'
     -s $splicing
     ]]></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>

From ad93b0ff49440cd7875d5b6fc89356fe6082024d Mon Sep 17 00:00:00 2001
From: Pavankumar Videm <pavanvidem@gmail.com>
Date: Thu, 30 Jan 2025 11:07:12 +0100
Subject: [PATCH 2/7] bump the galaxy version

---
 tools/dexseq/plotdexseq.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/dexseq/plotdexseq.xml b/tools/dexseq/plotdexseq.xml
index f1c54a7732d..f12733fcd00 100644
--- a/tools/dexseq/plotdexseq.xml
+++ b/tools/dexseq/plotdexseq.xml
@@ -1,4 +1,4 @@
-<tool id="plotdexseq" name="plotDEXSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="plotdexseq" name="plotDEXSeq" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Visualization of the per gene DEXSeq results</description>
     <macros>
         <import>macros.xml</import>

From 88064178231990f1f99b02844c17f1c3c9629c44 Mon Sep 17 00:00:00 2001
From: Pavankumar Videm <pavanvidem@gmail.com>
Date: Thu, 30 Jan 2025 16:29:52 +0100
Subject: [PATCH 3/7] added new params for plot dimensions and fixed the tests

---
 tools/dexseq/macros.xml                     |   2 +-
 tools/dexseq/plotdexseq.R                   |   9 ++++--
 tools/dexseq/plotdexseq.xml                 |  33 ++++++++++++++++++--
 tools/dexseq/test-data/plotdexseq.pdf       | Bin 5882 -> 5880 bytes
 tools/dexseq/test-data/plotdexseq_multi.pdf | Bin 0 -> 10174 bytes
 5 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/tools/dexseq/macros.xml b/tools/dexseq/macros.xml
index c5d58dd360a..4488dc78d61 100644
--- a/tools/dexseq/macros.xml
+++ b/tools/dexseq/macros.xml
@@ -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="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-dexseq</requirement>
diff --git a/tools/dexseq/plotdexseq.R b/tools/dexseq/plotdexseq.R
index 5613ae87ba3..82af8c2b0d2 100644
--- a/tools/dexseq/plotdexseq.R
+++ b/tools/dexseq/plotdexseq.R
@@ -25,7 +25,9 @@ spec <- matrix(c(
     "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)
 
@@ -38,7 +40,10 @@ if (!is.null(opt$genefile)) {
     genes <- opt$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,
diff --git a/tools/dexseq/plotdexseq.xml b/tools/dexseq/plotdexseq.xml
index f12733fcd00..1b768bd603a 100644
--- a/tools/dexseq/plotdexseq.xml
+++ b/tools/dexseq/plotdexseq.xml
@@ -22,6 +22,12 @@ Rscript '$__tool_directory__/plotdexseq.R'
     -a $names
     -n $normcounts
     -s $splicing
+    #if $pl_width:
+    -w $pl_width
+    #end if
+    #if $pl_height:
+    -h $pl_height
+    #end if
     ]]></command>
     <inputs>
         <param name="rdata" type="data" format="rds" label="DEXSeqResults object" help="A DEXSeqResults object in RDS format. This can be output from the DEXSeq tool"/>
@@ -38,7 +44,7 @@ Rscript '$__tool_directory__/plotdexseq.R'
             <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 @@ Rscript '$__tool_directory__/plotdexseq.R'
         <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 @@ Rscript '$__tool_directory__/plotdexseq.R'
         <test expect_num_outputs="1">
             <param name="rdata" ftype="rdata" value="dexseq.rds"/>
             <param name="primaryfactor" value="condition"/>
-            <param name="geneid" value="FBgn0000053"/>
+            <conditional name="genes">
+                <param name="genes_select" value="single" />
+                <param name="geneid" value="FBgn0000053"/>
+            </conditional>
             <param name="fdr_cutoff" value="1"/>
             <output name="dexseq_plot" ftype="pdf" file="plotdexseq.pdf" compare="sim_size"/>
         </test>
@@ -69,10 +80,26 @@ Rscript '$__tool_directory__/plotdexseq.R'
         <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
diff --git a/tools/dexseq/test-data/plotdexseq.pdf b/tools/dexseq/test-data/plotdexseq.pdf
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diff --git a/tools/dexseq/test-data/plotdexseq_multi.pdf b/tools/dexseq/test-data/plotdexseq_multi.pdf
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HcmV?d00001


From d5c33b2de56c848194ee6282e9fb10dabe092de6 Mon Sep 17 00:00:00 2001
From: Pavankumar Videm <pavanvidem@gmail.com>
Date: Thu, 30 Jan 2025 16:55:28 +0100
Subject: [PATCH 4/7] fix r linting

---
 tools/dexseq/plotdexseq.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/dexseq/plotdexseq.R b/tools/dexseq/plotdexseq.R
index 82af8c2b0d2..2679af4fb44 100644
--- a/tools/dexseq/plotdexseq.R
+++ b/tools/dexseq/plotdexseq.R
@@ -43,7 +43,7 @@ if (!is.null(opt$genefile)) {
 pl_width <- pl_height <- 7
 if (!is.null(opt$pl_width)) pl_width <- opt$pl_width
 if (!is.null(opt$pl_height)) pl_height <- opt$pl_height
-pdf("plot.pdf", width=pl_width, height=pl_height)
+pdf("plot.pdf", width = pl_width, height = pl_height)
 for (i in genes) {
     plotDEXSeq(res, i,
         FDR = opt$fdr, fitExpToVar = opt$primaryfactor,

From 6a8362d412748388549ef03374d1dbde8bca343d Mon Sep 17 00:00:00 2001
From: Pavankumar Videm <pavanvidem@gmail.com>
Date: Fri, 31 Jan 2025 10:49:28 +0100
Subject: [PATCH 5/7] add outer margins and test data

---
 tools/dexseq/plotdexseq.R                       |   1 +
 .../test-data/plotdexseq_multi_custom_dim.pdf   | Bin 0 -> 10106 bytes
 2 files changed, 1 insertion(+)
 create mode 100644 tools/dexseq/test-data/plotdexseq_multi_custom_dim.pdf

diff --git a/tools/dexseq/plotdexseq.R b/tools/dexseq/plotdexseq.R
index 2679af4fb44..9600941eb4a 100644
--- a/tools/dexseq/plotdexseq.R
+++ b/tools/dexseq/plotdexseq.R
@@ -45,6 +45,7 @@ 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,
diff --git a/tools/dexseq/test-data/plotdexseq_multi_custom_dim.pdf b/tools/dexseq/test-data/plotdexseq_multi_custom_dim.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..c5640711c5b417971721dcbb8f232f6da4aa4d91
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From 5d053c25268937417f7e25f009e0d7d5543a8a13 Mon Sep 17 00:00:00 2001
From: Pavankumar Videm <pavanvidem@gmail.com>
Date: Fri, 31 Jan 2025 11:18:52 +0100
Subject: [PATCH 6/7] fix lint-r

---
 tools/dexseq/plotdexseq.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/dexseq/plotdexseq.R b/tools/dexseq/plotdexseq.R
index 9600941eb4a..f8445ae29ae 100644
--- a/tools/dexseq/plotdexseq.R
+++ b/tools/dexseq/plotdexseq.R
@@ -45,7 +45,7 @@ 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))
+    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,

From b3c9a8916d34b1e88a0c0fdb425353590e274702 Mon Sep 17 00:00:00 2001
From: Pavankumar Videm <pavanvidem@gmail.com>
Date: Fri, 31 Jan 2025 16:00:20 +0100
Subject: [PATCH 7/7] bump version in macros

---
 tools/dexseq/macros.xml     | 2 +-
 tools/dexseq/plotdexseq.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/dexseq/macros.xml b/tools/dexseq/macros.xml
index 4488dc78d61..dfd7268954a 100644
--- a/tools/dexseq/macros.xml
+++ b/tools/dexseq/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.48.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirements>
diff --git a/tools/dexseq/plotdexseq.xml b/tools/dexseq/plotdexseq.xml
index 1b768bd603a..31e2d4ffc81 100644
--- a/tools/dexseq/plotdexseq.xml
+++ b/tools/dexseq/plotdexseq.xml
@@ -1,4 +1,4 @@
-<tool id="plotdexseq" name="plotDEXSeq" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="plotdexseq" name="plotDEXSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Visualization of the per gene DEXSeq results</description>
     <macros>
         <import>macros.xml</import>