# HG changeset patch
# User iuc
# Date 1637654063 0
# Node ID 23cadaaf734bacf265bdfcd2a0e3d6eb4a19de0b
# Parent  67cc04848f24a89d0bcf2b54896d222c3e9824dd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"

diff -r 67cc04848f24 -r 23cadaaf734b ggplot2_pca.xml
--- a/ggplot2_pca.xml	Tue Aug 31 08:30:16 2021 +0000
+++ b/ggplot2_pca.xml	Tue Nov 23 07:54:23 2021 +0000
@@ -1,11 +1,11 @@
-<tool id="ggplot2_pca" name="PCA plot w ggplot2" version="@VERSION@">
+<tool id="ggplot2_pca" name="PCA plot w ggplot2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.3">r-ggfortify</requirement>
-        <requirement type="package" version="1.2.1">r-svglite</requirement>
+        <requirement type="package" version="0.4.13">r-ggfortify</requirement>
+        <requirement type="package" version="2.0.0">r-svglite</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 cat '$script' &&
@@ -249,11 +249,19 @@
                 <repeat name="group_names" min="2" title="Group" help="Select the samples for this group">
                     <param name="groupName" type="text" optional="false" label="Group name"
                         help="Use short names, avoid special characters and numbers at the beginning of the name (The names might be changed by the program to make them conform to processing in R)">
-                        <validator type="no_options" message="Please choose a name for this group!"/>
+                        <sanitizer invalid_char="">
+                            <valid initial="string.letters,string.digits">
+                                <add value=":" />
+                                <add value="-" />
+                                <add value=" " />
+                                <add value="_" />
+                            </valid>
+                        </sanitizer>
+                        <validator type="regex" message="Value may include alphanumeric characters, colons, dashes, underscores and spaces.">[0-9a-zA-Z:-_ ]+</validator>
                     </param>
                     <param name="groupCols" type="data_column" data_ref="input1" multiple="true" min="1" label="Columns for group"
                         help="WARNING: please use columns indices after removing the row name column if selected in second section!">
-                        <validator type="no_options" message="Select at least one column for each group!"/>
+                        <validator type="regex" message="Select at least one column for each group!">[0-9a-zA-Z:-_ ]+</validator>
                         <!--<filter type="remove_value" meta_ref="groupCols" />-->
                     </param>
                     <conditional name="color_cond">
diff -r 67cc04848f24 -r 23cadaaf734b macros.xml
--- a/macros.xml	Tue Aug 31 08:30:16 2021 +0000
+++ b/macros.xml	Tue Nov 23 07:54:23 2021 +0000
@@ -2,16 +2,19 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">r-ggplot2</requirement>
+            <requirement type="package" version="4.1.1">r-base</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">r-ggplot2</requirement>
             <yield />
         </requirements>
     </xml>
     <xml name="bio_tools">
         <xrefs>
-            <xref type="bio.tools">gemini</xref>
+            <xref type="bio.tools">ggplot2</xref>
         </xrefs>
     </xml>
-    <token name="@VERSION@">2.2.1</token>
+    <token name="@TOOL_VERSION@">3.3.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
 
     <token name="@R_INIT@"><![CDATA[
         ## Setup R error handling to go to stderr
@@ -137,9 +140,7 @@
                 <option value="Automatic" selected="true">Automatic axis scaling</option>
                 <option value="Defined">User-defined axis scales</option>
             </param>
-            <when value="Automatic">
-                <!--Do nothing here -->
-            </when>
+            <when value="Automatic"/>
             <when value="Defined">
                 <param name="xaxismin" type="float" value="0" label="minimal range of x-axis" />
                 <param name="xaxismax" type="float" value="3" label="maximal range of x-axis" />
@@ -154,10 +155,10 @@
         </param>
     </xml>
     <xml name="xy_lab">
-        <param name="xlab" type="text" value="title of x-axis" label="Label for x axis">
+        <param name="xlab" type="text" value="Title of x-axis" label="Label for x axis">
             <sanitizer sanitize="false"/>
         </param>
-        <param name="ylab" type="text" value="title of y-axis" label="Label for y axis">
+        <param name="ylab" type="text" value="Title of y-axis" label="Label for y axis">
             <sanitizer sanitize="false"/>
         </param>
     </xml>
@@ -174,7 +175,7 @@
         </param>
     </xml>
     <xml name="dimensions">
-        <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="default inches">
+        <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="Default: inches.">
             <option value="in" selected="true">Inches (in)</option>
             <option value="cm">Centimeters (cm)</option>
             <option value="mm">Millimeters (mm)</option>
@@ -182,8 +183,8 @@
         <param name="width_output_dim" type="float" value="7" label="width of output"/>
         <param name="height_output_dim" type="float" value="7" label="height of output"/>
         <param name="dpi_output_dim" type="float" value="300" label="dpi of output" help="Plot resolution. Applies only to raster output types."/>
-        <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format">
-            <option value="none" selected="true">only PNG</option>
+        <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format.">
+            <option value="none" selected="true">Only PNG</option>
             <option value="pdf">PDF</option>
             <option value="svg">SVG</option>
             <option value="eps">EPS</option>
@@ -213,9 +214,7 @@
             <option value="default" selected="true">Default</option>
             <option value="defined">User defined label options</option>
         </param>
-        <when value="default">
-            <!--Do nothing here -->
-        </when>
+        <when value="default"/>
         <when value="defined">
             <param name="size" type="float" value="12" label="Axis label size (default = 12)"/>
             <param name="color" type="select" label="Color of axis label">
@@ -293,4 +292,33 @@
             <filter>out['additional_output_format'] != "none"</filter>
         </data>
     </xml>
+    <xml name="points_options">
+        <conditional name="points">
+            <param name="pointoptions" type="select" label="Data point options">
+                <option value="default" selected="true">Default</option>
+                <option value="defined">User defined point options</option>
+            </param>
+            <when value="default">
+                <!--Do nothing here -->
+            </when>
+            <when value="defined">
+                <param name="size" type="float" value="1" label="relative size of points" />
+                <param name="alpha" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
+                <param name="pointcolor" type="select" label="Color of data points" >
+                    <option value="black">Black (default)</option>
+                    <option value="red">Red</option>
+                    <option value="white">White</option>
+                    <option value="blue">Blue</option>
+                    <option value="orange">Orange</option>
+                    <option value="yellow">Yellow</option>
+                    <option value="green">Green</option>
+                    <option value="purple">Purple</option>
+                    <option value="magenta">Magenta</option>
+                    <option value="cyan">Cyan</option>
+                    <option value="grey">Grey</option>
+                    <option value="gold">Gold</option>
+                </param>
+            </when>
+        </conditional>
+    </xml>
 </macros>
diff -r 67cc04848f24 -r 23cadaaf734b test-data/ggplot_heatmap_result1.pdf
Binary file test-data/ggplot_heatmap_result1.pdf has changed
diff -r 67cc04848f24 -r 23cadaaf734b test-data/ggplot_histogram_result1.pdf
Binary file test-data/ggplot_histogram_result1.pdf has changed
diff -r 67cc04848f24 -r 23cadaaf734b test-data/ggplot_pca_result1.pdf
Binary file test-data/ggplot_pca_result1.pdf has changed
diff -r 67cc04848f24 -r 23cadaaf734b test-data/ggplot_point_result1.pdf
Binary file test-data/ggplot_point_result1.pdf has changed
diff -r 67cc04848f24 -r 23cadaaf734b test-data/ggplot_point_result2.pdf
Binary file test-data/ggplot_point_result2.pdf has changed