Mercurial > repos > iuc > ggplot2_point
changeset 15:f87634b12749 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
| author | iuc |
|---|---|
| date | Thu, 15 May 2025 13:02:15 +0000 |
| parents | 5298e06f14f9 |
| children | |
| files | ggplot_point.xml macros.xml test-data/barplot_test_data.txt test-data/boxplot_test_data.txt test-data/boxplot_test_expDesign.txt test-data/ggplot_heatmap_result1.pdf test-data/ggplot_histogram_result1.pdf test-data/ggplot_line_result1.pdf test-data/ggplot_pca_result1.pdf test-data/ggplot_point_result1.pdf test-data/ggplot_point_result2.pdf test-data/ggplot_point_result3.pdf test-data/ggplot_violin_result1.pdf utils.r |
| diffstat | 14 files changed, 92 insertions(+), 7 deletions(-) [+] |
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--- 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"/>
--- 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>
--- /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
--- /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
--- /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
--- /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) +}