From 79e5a4ab9727d8721adeec4c9d2c3677d84c6f88 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Mon, 29 Apr 2024 17:58:07 +0100
Subject: [PATCH 1/9] Make title and others visible in volcanoplot.xml

Current version is not considering inputs in plot title and other options.
---
 tools/volcanoplot/volcanoplot.xml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tools/volcanoplot/volcanoplot.xml b/tools/volcanoplot/volcanoplot.xml
index 1487d7392a9..f1c7f5d7238 100644
--- a/tools/volcanoplot/volcanoplot.xml
+++ b/tools/volcanoplot/volcanoplot.xml
@@ -145,28 +145,28 @@ p <- p + geom_text_repel(data = filter(results, labels != ""), aes(label = label
     #end if
 #end if
 
-#if not '$plot_options.title'
+#if '$plot_options.title'
 p <- p + ggtitle('$plot_options.title')
 #end if
 
-#if not '$plot_options.xlab'
+#if '$plot_options.xlab'
 p <- p + xlab('$plot_options.xlab')
 #end if
 
-#if not '$plot_options.ylab'
+#if '$plot_options.ylab'
 p <- p + ylab('$plot_options.ylab')
 #end if
 
-#if not '$plot_options.xmin' and '$plot_options.xmax'
+#if '$plot_options.xmin' and '$plot_options.xmax'
 p <- p + xlim('$plot_options.xmin', '$plot_options.xmax')
 #end if
 
-#if not '$plot_options.ymax'
+#if '$plot_options.ymax'
 p <- p + ylim(0, '$plot_options.ymax')
 #end if
 
 # Set legend title
-#if not '$plot_options.legend'
+#if '$plot_options.legend'
 p <- p + theme(legend.title = '$plot_options.legend')
 #else
 p <- p + theme(legend.title = element_blank())
@@ -322,4 +322,4 @@ A PDF containing a Volcano plot like below. The R code can be output through *Ou
     ]]></help>
     <citations>
     </citations>
-</tool>
\ No newline at end of file
+</tool>

From b07709df900fcaa2805e810ccbfd4fefbebbabff Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Mon, 29 Apr 2024 17:59:28 +0100
Subject: [PATCH 2/9] Bumps version

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

diff --git a/tools/volcanoplot/volcanoplot.xml b/tools/volcanoplot/volcanoplot.xml
index f1c7f5d7238..8086bb41f88 100644
--- a/tools/volcanoplot/volcanoplot.xml
+++ b/tools/volcanoplot/volcanoplot.xml
@@ -1,4 +1,4 @@
-<tool id="volcanoplot" name="Volcano Plot" version="0.0.5">
+<tool id="volcanoplot" name="Volcano Plot" version="0.0.6">
     <description>create a volcano plot</description>
     <edam_topics>
         <edam_topic>topic_0092</edam_topic>

From 18a7b2c7a655046a8bcef9b00024d4110213fbd8 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Mon, 29 Apr 2024 23:42:58 +0100
Subject: [PATCH 3/9] Profile and citation

---
 tools/volcanoplot/volcanoplot.xml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/tools/volcanoplot/volcanoplot.xml b/tools/volcanoplot/volcanoplot.xml
index 8086bb41f88..5ed8220b9a7 100644
--- a/tools/volcanoplot/volcanoplot.xml
+++ b/tools/volcanoplot/volcanoplot.xml
@@ -1,4 +1,4 @@
-<tool id="volcanoplot" name="Volcano Plot" version="0.0.6">
+<tool id="volcanoplot" name="Volcano Plot" version="0.0.6" profile="20.09">
     <description>create a volcano plot</description>
     <edam_topics>
         <edam_topic>topic_0092</edam_topic>
@@ -191,10 +191,10 @@ sessionInfo()
             <option value="yes">Yes</option>
             <option value="no">No</option>
         </param>
-        <param name="fdr_col" type="data_column" data_ref="input" label="FDR (adjusted P value)" />
-        <param name="pval_col" type="data_column" data_ref="input" label="P value (raw)" />
-        <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change" />
-        <param name="label_col" type="data_column" data_ref="input" label="Labels" />
+        <param name="fdr_col" type="data_column" data_ref="input" label="FDR (adjusted P value) column number" />
+        <param name="pval_col" type="data_column" data_ref="input" label="P value (raw) column number" />
+        <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change column number" />
+        <param name="label_col" type="data_column" data_ref="input" label="Labels column number" />
         <param name="signif_thresh" type="float" max="1" value="0.05" label="Significance threshold" help="Default: 0.05"/>
         <param name="lfc_thresh" type="float" value="0" label="LogFC threshold to colour" help="Default: 0"/>
         <conditional name="labels">
@@ -321,5 +321,6 @@ A PDF containing a Volcano plot like below. The R code can be output through *Ou
 
     ]]></help>
     <citations>
+        <citation type="doi">doi.org/10.1007/978-3-319-24277-4</citation>
     </citations>
 </tool>

From 74a8641c0152d5f446511c63e8d5c9cf5e2c2e8c Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Mon, 29 Apr 2024 23:49:02 +0100
Subject: [PATCH 4/9] Add homepage URL to .shed.yml

---
 tools/volcanoplot/.shed.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/volcanoplot/.shed.yml b/tools/volcanoplot/.shed.yml
index 41d637c9fad..60bc17b70ae 100644
--- a/tools/volcanoplot/.shed.yml
+++ b/tools/volcanoplot/.shed.yml
@@ -8,4 +8,5 @@ long_description: |
 name: volcanoplot
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot
+homepage_url: https://ggplot2.tidyverse.org/
 type: unrestricted

From 09cd664711526c5fb4c619e88b89938873be5bc5 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Mon, 29 Apr 2024 23:58:21 +0100
Subject: [PATCH 5/9] Avoid element_blank for legend title

---
 tools/volcanoplot/volcanoplot.xml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tools/volcanoplot/volcanoplot.xml b/tools/volcanoplot/volcanoplot.xml
index 5ed8220b9a7..7b35b8ca01a 100644
--- a/tools/volcanoplot/volcanoplot.xml
+++ b/tools/volcanoplot/volcanoplot.xml
@@ -168,8 +168,6 @@ p <- p + ylim(0, '$plot_options.ymax')
 # Set legend title
 #if '$plot_options.legend'
 p <- p + theme(legend.title = '$plot_options.legend')
-#else
-p <- p + theme(legend.title = element_blank())
 #end if
 
 # Print plot

From bff1831533dd9cc8175f0a50c781973a8b17cde0 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Tue, 30 Apr 2024 20:14:43 +0100
Subject: [PATCH 6/9] Fix legend title handling

---
 tools/volcanoplot/volcanoplot.xml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tools/volcanoplot/volcanoplot.xml b/tools/volcanoplot/volcanoplot.xml
index 7b35b8ca01a..603a078d9f9 100644
--- a/tools/volcanoplot/volcanoplot.xml
+++ b/tools/volcanoplot/volcanoplot.xml
@@ -167,7 +167,9 @@ p <- p + ylim(0, '$plot_options.ymax')
 
 # Set legend title
 #if '$plot_options.legend'
-p <- p + theme(legend.title = '$plot_options.legend')
+p <- p + guides(color = guide_legend(title = '$plot_options.legend'))
+#else
+p <- p + theme(legend.title = element_blank())
 #end if
 
 # Print plot

From 893f319f3e903e2701a30e3b54bcf1c71ccf6be8 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Tue, 30 Apr 2024 20:27:03 +0100
Subject: [PATCH 7/9] Update test sizes

---
 tools/volcanoplot/volcanoplot.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/volcanoplot/volcanoplot.xml b/tools/volcanoplot/volcanoplot.xml
index 603a078d9f9..d3dc0f89744 100644
--- a/tools/volcanoplot/volcanoplot.xml
+++ b/tools/volcanoplot/volcanoplot.xml
@@ -244,7 +244,7 @@ sessionInfo()
             <param name="lfc_thresh" value="0" />
             <output name="plot">
                 <assert_contents>
-                    <has_size value= "933451" delta="1000" />
+                    <has_size value= "935143" delta="1000" />
                 </assert_contents>
             </output>
         </test>
@@ -260,7 +260,7 @@ sessionInfo()
             <param name="label_file" ftype="tabular" value="labels.tab" />
             <output name="plot">
                 <assert_contents>
-                    <has_size value= "933832" delta="1000" />
+                    <has_size value= "935547" delta="1000" />
                 </assert_contents>
             </output>
         </test>
@@ -278,7 +278,7 @@ sessionInfo()
             <param name="rscript_out" value="True"/>
             <output name="plot">
                 <assert_contents>
-                    <has_size value= "933832" delta="1000" />
+                    <has_size value= "935545" delta="1000" />
                 </assert_contents>
             </output>
             <output name="rscript" value= "out.rscript" lines_diff="4"/>

From d558ad035a7a7e52323c782cdcd054e499bf8712 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Tue, 30 Apr 2024 20:48:47 +0100
Subject: [PATCH 8/9] Hopefully fixes last test

---
 tools/volcanoplot/volcanoplot.xml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tools/volcanoplot/volcanoplot.xml b/tools/volcanoplot/volcanoplot.xml
index d3dc0f89744..8c76936ad22 100644
--- a/tools/volcanoplot/volcanoplot.xml
+++ b/tools/volcanoplot/volcanoplot.xml
@@ -145,28 +145,28 @@ p <- p + geom_text_repel(data = filter(results, labels != ""), aes(label = label
     #end if
 #end if
 
-#if '$plot_options.title'
+#if $plot_options.title:
 p <- p + ggtitle('$plot_options.title')
 #end if
 
-#if '$plot_options.xlab'
+#if $plot_options.xlab:
 p <- p + xlab('$plot_options.xlab')
 #end if
 
-#if '$plot_options.ylab'
+#if $plot_options.ylab:
 p <- p + ylab('$plot_options.ylab')
 #end if
 
-#if '$plot_options.xmin' and '$plot_options.xmax'
-p <- p + xlim('$plot_options.xmin', '$plot_options.xmax')
+#if $plot_options.xmin and $plot_options.xmax:
+p <- p + xlim($plot_options.xmin, $plot_options.xmax)
 #end if
 
-#if '$plot_options.ymax'
-p <- p + ylim(0, '$plot_options.ymax')
+#if $plot_options.ymax:
+p <- p + ylim(0, $plot_options.ymax)
 #end if
 
 # Set legend title
-#if '$plot_options.legend'
+#if $plot_options.legend:
 p <- p + guides(color = guide_legend(title = '$plot_options.legend'))
 #else
 p <- p + theme(legend.title = element_blank())

From 8fd412ab9cc09f4c5e2031dc6f0eabfbf976c6f8 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Tue, 30 Apr 2024 20:57:04 +0100
Subject: [PATCH 9/9] Update test sizes

---
 tools/volcanoplot/volcanoplot.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/volcanoplot/volcanoplot.xml b/tools/volcanoplot/volcanoplot.xml
index 8c76936ad22..0ec71adc6f4 100644
--- a/tools/volcanoplot/volcanoplot.xml
+++ b/tools/volcanoplot/volcanoplot.xml
@@ -244,7 +244,7 @@ sessionInfo()
             <param name="lfc_thresh" value="0" />
             <output name="plot">
                 <assert_contents>
-                    <has_size value= "935143" delta="1000" />
+                    <has_size value= "933451" delta="1000" />
                 </assert_contents>
             </output>
         </test>
@@ -260,7 +260,7 @@ sessionInfo()
             <param name="label_file" ftype="tabular" value="labels.tab" />
             <output name="plot">
                 <assert_contents>
-                    <has_size value= "935547" delta="1000" />
+                    <has_size value= "933830" delta="1000" />
                 </assert_contents>
             </output>
         </test>
@@ -278,7 +278,7 @@ sessionInfo()
             <param name="rscript_out" value="True"/>
             <output name="plot">
                 <assert_contents>
-                    <has_size value= "935545" delta="1000" />
+                    <has_size value= "933832" delta="1000" />
                 </assert_contents>
             </output>
             <output name="rscript" value= "out.rscript" lines_diff="4"/>