# HG changeset patch
# User galaxy-australia
# Date 1729464600 0
# Node ID 501dcf66c0cec74c1b1f36bc6e2921349d6557d5
# Parent  c1bed78b9ed5d1f24f0da24fa27fd33c03e300c9
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 950dfdfeb072cf49f35c16759bf9c69ffb138ec8

diff -r c1bed78b9ed5 -r 501dcf66c0ce plot_ragtag_paf.R
--- a/plot_ragtag_paf.R	Tue Oct 15 04:25:30 2024 +0000
+++ b/plot_ragtag_paf.R	Sun Oct 20 22:50:00 2024 +0000
@@ -253,7 +253,9 @@
             q_y + (y_axis_space / 3)
         ),
         hjust = 0.5,
-        vjust = 0.5
+        vjust = 0.5,
+        size = fontsize,
+        size.unit = "pt"
     ) +
     annotate(
         geom = "text",
@@ -264,7 +266,9 @@
             t_y - (y_axis_space / 3)
         ),
         hjust = 0.5,
-        vjust = 0.5
+        vjust = 0.5,
+        size = fontsize,
+        size.unit = "pt"
     )
 
 # Reverse the scales and the limits to plot reference on top
@@ -285,6 +289,8 @@
     )
 }
 
+
+
 # reference contig names
 if (label_ref_contigs == TRUE) {
     gp <- gp + geom_text(
@@ -295,7 +301,9 @@
             label = tname
         ),
         angle = 30,
-        hjust = ifelse(upside_down == TRUE, 0, 1)
+        hjust = ifelse(upside_down == TRUE, 0, 1),
+        size = 2 * fontsize / 3,
+        size.unit = "pt"
     )
 }
 
@@ -310,6 +318,8 @@
         ),
         angle = 30,
         hjust = ifelse(upside_down == TRUE, 1, 0),
+        size = 2 * fontsize / 3,
+        size.unit = "pt"
     )
 }
 
diff -r c1bed78b9ed5 -r 501dcf66c0ce plot_ragtag_paf.xml
--- a/plot_ragtag_paf.xml	Tue Oct 15 04:25:30 2024 +0000
+++ b/plot_ragtag_paf.xml	Sun Oct 20 22:50:00 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="plot_ragtag_paf" name="Plot RagTag output" version="0.0.3" profile="24.1" license="MIT">
+<tool id="plot_ragtag_paf" name="Plot RagTag output" version="0.0.4" profile="24.1" license="MIT">
     <description>to compare query contigs to the reference</description>
     <requirements>
         <container type="docker">ghcr.io/tomharrop/r-containers:r2u_24.04_cv1</container>
@@ -103,8 +103,11 @@
         Accepts the PAF and AGP produced by the RagTag Scaffold and draws a plot
         showing the alignment of the query contigs to the reference contigs.
         
-        .. figure:: $PATH_TO_IMAGES/ragtag.png
+        .. figure:: https://raw.githubusercontent.com/usegalaxy-au/tools-au/refs/heads/master/tools/plot_ragtag_paf/static/images/ragtag.png
            :alt: RagTag plot
+           :width: 600px
+           :height: 400px
+           :align: center
         
     </help>
     <citations>