From 589795c240ea48accbb89cd0c3263f8eba301125 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Wed, 15 May 2024 10:52:27 +0100
Subject: [PATCH] Make title and others visible in volcanoplot (#5977)

* Make title and others visible in volcanoplot.xml

Current version is not considering inputs in plot title and other options.

* Bumps version

* Profile and citation

* Add homepage URL to .shed.yml

* Avoid element_blank for legend title

* Fix legend title handling

* Update test sizes

* Hopefully fixes last test

* Update test sizes
---
 tools/volcanoplot/.shed.yml       |  1 +
 tools/volcanoplot/volcanoplot.xml | 33 ++++++++++++++++---------------
 2 files changed, 18 insertions(+), 16 deletions(-)

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
diff --git a/tools/volcanoplot/volcanoplot.xml b/tools/volcanoplot/volcanoplot.xml
index 1487d7392a9..0ec71adc6f4 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" profile="20.09">
     <description>create a volcano plot</description>
     <edam_topics>
         <edam_topic>topic_0092</edam_topic>
@@ -145,29 +145,29 @@ 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'
-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 not '$plot_options.ymax'
-p <- p + ylim(0, '$plot_options.ymax')
+#if $plot_options.ymax:
+p <- p + ylim(0, $plot_options.ymax)
 #end if
 
 # Set legend title
-#if not '$plot_options.legend'
-p <- p + theme(legend.title = '$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())
 #end if
@@ -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">
@@ -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= "933830" delta="1000" />
                 </assert_contents>
             </output>
         </test>
@@ -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>
\ No newline at end of file
+</tool>