# HG changeset patch
# User iuc
# Date 1747314135 0
# Node ID f87634b127493a60f8020ac06502d5db893d0121
# Parent  5298e06f14f96f58df0279d81ace9275b669b386
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158

diff -r 5298e06f14f9 -r f87634b12749 ggplot_point.xml
--- a/ggplot_point.xml	Mon Sep 30 15:40:11 2024 +0000
+++ b/ggplot_point.xml	Thu May 15 13:02:15 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@TOOL_VERSION@+galaxy1" profile="20.01">
+<tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@TOOL_VERSION@+galaxy2" profile="23.0">
     <macros>
         <import>macros.xml</import>
         <token name="@SIMPLE_GGLINE@">gg_line = geom_line(size=1, alpha=1, gg_factor)</token>
@@ -24,7 +24,7 @@
 
 @LEGEND@
 
-input <- read.csv('$input1', sep='\t', header=TRUE)
+input <- read.csv('$input1', sep='\t')
 
 ## renaming columns so ggplot can use them
 names(input)[$xplot] <- "xcol"
@@ -126,7 +126,7 @@
 #end if
 
 #this is the actual ggplot command to make the final plot(s)
-plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
+plot_out <- ggplot(input, aes_string(x=names(input)[$xplot], y=names(input)[$yplot])) + gg_point + gg_line + gg_facet +
     gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('$title') + xlab('$xlab') + ylab('$ylab')+
     gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
 
@@ -135,8 +135,22 @@
     </configfiles>
     <inputs>
         <param name="input1" type="data" format="tabular" label="Input in tabular format" />
-        <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
-        <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />
+
+        <conditional name="cols">
+            <param name="header" type="select" label="Does the dataset have a header?" help="If the table has a header, columns can be selected based on the name.">
+                <option value="yes" selected="true">yes</option>
+                <option value="no">no</option>
+            </param>
+            <when value="yes">
+                <param name="xplot"  type="data_column" data_ref="input1" use_header_names="true" label="Column to plot on x-axis" />
+                <param name="yplot"  type="data_column" data_ref="input1" use_header_names="true" label="Column to plot on y-axis" />
+            </when>
+            <when value="no">
+                <param name="xplot"  type="data_column" data_ref="input1" label="Column to plot on x-axis" />
+                <param name="yplot"  type="data_column" data_ref="input1" label="Column to plot on y-axis" />
+            </when>
+        </conditional>
+
 
         <expand macro="title" />
         <expand macro="xy_lab" />
@@ -207,11 +221,18 @@
         <test expect_num_outputs="2">
             <param name="input1" value="mtcars.txt" ftype="tabular" />
             <param name="additional_output_format" value="pdf" />
+            <param name="xplot" value="8"/>
+            <param name="yplot" value="9"/>
             <output name="output2" file="ggplot_point_result1.pdf" compare="sim_size" />
         </test>
         <!-- Test text options-->
         <test expect_num_outputs="2">
             <param name="input1" value="mtcars.txt" ftype="tabular" />
+            <conditional name="cols">
+                <param name="header" value="no"/>
+            </conditional>
+            <param name="xplot" value="8"/>
+            <param name="yplot" value="9"/>   
             <section name="adv">
                 <conditional name="type_conditional">
                     <param name="type_options" value="points"/>
@@ -230,6 +251,8 @@
         <!-- Test lines option -->
         <test expect_num_outputs="2">
             <param name="input1" value="mtcars.txt" ftype="tabular" />
+            <param name="xplot" value="8"/>
+            <param name="yplot" value="9"/>   
             <section name="adv">
                 <conditional name="type_conditional">
                     <param name="type_options" value="lines"/>
@@ -241,6 +264,8 @@
          <!-- Test defined point options options-->
         <test expect_num_outputs="2">
             <param name="input1" value="mtcars.txt" ftype="tabular" />
+            <param name="xplot" value="8"/>
+            <param name="yplot" value="9"/>   
             <section name="adv">
                 <conditional name="type_conditional">
                     <param name="type_options" value="points"/>
diff -r 5298e06f14f9 -r f87634b12749 macros.xml
--- a/macros.xml	Mon Sep 30 15:40:11 2024 +0000
+++ b/macros.xml	Thu May 15 13:02:15 2025 +0000
@@ -2,7 +2,6 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.1.1">r-base</requirement>
             <requirement type="package" version="@TOOL_VERSION@">r-ggplot2</requirement>
             <yield />
         </requirements>
@@ -12,7 +11,7 @@
             <xref type="bio.tools">ggplot2</xref>
         </xrefs>
     </xml>
-    <token name="@TOOL_VERSION@">3.4.0</token>
+    <token name="@TOOL_VERSION@">3.5.1</token>
     <token name="@VERSION_SUFFIX@">1</token>
 
     <token name="@R_INIT@"><![CDATA[
@@ -343,4 +342,17 @@
             </when>
         </conditional>
     </xml>
+    <xml name="data_input">
+        <param name="input_data" type="data" format="csv,tsv,txt,tabular,parquet" label="Input table" help= "Input file in a tabular/tsv/csv/parquet format"/>
+    </xml>
+
+    <xml name="axes_labels">
+        <param name="xlab" type="text" label="Label for the x axis" optional="true"/>
+        <param name="ylab" type="text" label="Label for the y axis"  optional="true"/>
+    </xml>
+    
+    <xml name="export_data">
+        <param name="export_R_script" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export the R script to reproduce the analysis"
+        help="Check this box to export the script executed in the Galaxy tool as an R file to be able to reproduce the same processing offline. Not that in this case, the file paths need to be altered and all the dependencies have to be managed manually."/>
+    </xml>
 </macros>
diff -r 5298e06f14f9 -r f87634b12749 test-data/barplot_test_data.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/barplot_test_data.txt	Thu May 15 13:02:15 2025 +0000
@@ -0,0 +1,10 @@
+Condition	Replicate	Value	ID
+ctrl	1	12	1
+ctrl	2	4	2
+ctrl	3	10	3
+trtA	1	50	4
+trtA	2	52	5
+trtA	3	49	6
+trtB	1	15	7
+trtB	2	10	8
+trtB	3	9	9
\ No newline at end of file
diff -r 5298e06f14f9 -r f87634b12749 test-data/boxplot_test_data.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/boxplot_test_data.txt	Thu May 15 13:02:15 2025 +0000
@@ -0,0 +1,15 @@
+RowID	File_1	File_2	File_3	File_4	File_5	File_6	File_7	File_8	File_9
+12	95.97218086	42.13959786	6.11506479	30.15646347	94.23814082	57.36969732	60.86347654	19.91409937	68.71355704
+14	59.66064371	64.93522126	32.32890474	40.14978233	2.891311477	32.96107785	66.75097997	0.920440008	24.22636581
+5	38.66154396	36.42452677	84.36958354	10.69964404	39.46448065	77.47277323	32.52771639	97.57285906	93.70459001
+36	32.97909046	43.52631758	59.83839323	69.87436805	98.12738555	4.751636512	47.47689026	41.3876903	67.78716531
+89	83.25413765	7.549367861	20.50592254	0.349459671	73.89946997	31.40388713	4.366449277	38.84340215	95.44116332
+965	71.74909204	40.82129731	21.73719426	32.67826786	93.7897543	92.54811762	57.16246361	98.97950241	38.61134734
+11	40.10030753	0.619259961	89.65946872	82.98278412	5.022064589	35.6513286	91.42743566	1.293400215	95.96990548
+2	82.35962922	25.48196256	47.51041934	71.45794006	90.23170047	34.52642435	88.0453423	63.2896977	28.82679247
+456	69.23813955	53.77332434	84.61367461	51.17705197	69.40525804	79.68268428	4.526957668	46.81700494	80.93458495
+68	88.78897848	85.84282896	51.53708603	71.26727107	94.03802875	77.02830433	50.12587615	30.93374275	15.06805862
+90	15.55940741	75.14719125	78.0377742	51.71345723	59.47299196	79.63191036	86.12417779	66.88062611	11.96856299
+23	51.55755631	26.99985192	85.64996749	74.54372275	97.09925394	47.50634659	43.94265016	60.73243208	89.94399967
+44	38.5549221	96.81614325	99.76966908	75.41077107	75.34246484	83.57435092	73.67006881	81.33326567	37.3100164
+567	72.74969753	17.0015972	64.01806032	37.71428705	41.30061893	84.5375675	44.21028268	9.076252458	50.67516692
diff -r 5298e06f14f9 -r f87634b12749 test-data/boxplot_test_expDesign.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/boxplot_test_expDesign.txt	Thu May 15 13:02:15 2025 +0000
@@ -0,0 +1,10 @@
+SampleID	Condition	Replicate	Batch
+File_1	control	1	1
+File_2	control	2	1
+File_3	control	3	1
+File_4	treatment_A	1	1
+File_5	treatment_A	2	1
+File_6	treatment_A	3	2
+File_7	treatment_B	1	2
+File_8	treatment_B	2	2
+File_9	treatment_B	3	2
diff -r 5298e06f14f9 -r f87634b12749 test-data/ggplot_heatmap_result1.pdf
Binary file test-data/ggplot_heatmap_result1.pdf has changed
diff -r 5298e06f14f9 -r f87634b12749 test-data/ggplot_histogram_result1.pdf
Binary file test-data/ggplot_histogram_result1.pdf has changed
diff -r 5298e06f14f9 -r f87634b12749 test-data/ggplot_line_result1.pdf
Binary file test-data/ggplot_line_result1.pdf has changed
diff -r 5298e06f14f9 -r f87634b12749 test-data/ggplot_pca_result1.pdf
Binary file test-data/ggplot_pca_result1.pdf has changed
diff -r 5298e06f14f9 -r f87634b12749 test-data/ggplot_point_result1.pdf
Binary file test-data/ggplot_point_result1.pdf has changed
diff -r 5298e06f14f9 -r f87634b12749 test-data/ggplot_point_result2.pdf
Binary file test-data/ggplot_point_result2.pdf has changed
diff -r 5298e06f14f9 -r f87634b12749 test-data/ggplot_point_result3.pdf
Binary file test-data/ggplot_point_result3.pdf has changed
diff -r 5298e06f14f9 -r f87634b12749 test-data/ggplot_violin_result1.pdf
Binary file test-data/ggplot_violin_result1.pdf has changed
diff -r 5298e06f14f9 -r f87634b12749 utils.r
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.r	Thu May 15 13:02:15 2025 +0000
@@ -0,0 +1,13 @@
+# Function for the data input
+load_data <- function(file_name, file_extension) {
+    if (file_extension == "csv") {
+        data_input <- read.csv(file_name, check.names = "false")
+    } else if (file_extension %in% c("tsv", "txt", "tabular")) {
+        data_input <- read.delim(file_name, sep = "\t", check.names = "false")
+    } else if (file_extension == "parquet") {
+        data_input <- arrow::read_parquet(file_name)
+    } else {
+        stop("Unsupported file format.")
+    }
+    return(data_input)
+}