| Previous changeset 8:e3a675da7fd0 (2021-10-26) Next changeset 10:299307abd804 (2022-11-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af" |
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modified:
ggplot_point.xml macros.xml test-data/ggplot_heatmap_result1.pdf test-data/ggplot_histogram_result1.pdf test-data/ggplot_pca_result1.pdf test-data/ggplot_point_result1.pdf |
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added:
test-data/ggplot_point_result2.pdf |
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| diff -r e3a675da7fd0 -r 1acf88921176 ggplot_point.xml --- a/ggplot_point.xml Tue Oct 26 15:12:15 2021 +0000 +++ b/ggplot_point.xml Tue Nov 23 07:58:14 2021 +0000 |
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| b'@@ -1,10 +1,10 @@\n-<tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@VERSION@+galaxy2" profile="18.01">\n+<tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n <expand macro="bio_tools"/>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements">\n- <requirement type="package" version="1.2.1">r-svglite</requirement>\n+ <requirement type="package" version="2.0.0">r-svglite</requirement>\n </expand>\n <command detect_errors="exit_code"><![CDATA[\n cat \'$script\' &&\n@@ -34,12 +34,12 @@\n gg_facet = facet_wrap( ~ factor)\n gg_factor = NULL\n color_scale = NULL\n- #if $adv.points.pointoptions == "default"\n+ #if $adv.type_conditional.points.pointoptions == "default"\n gg_point = geom_point(size=1, alpha=1, gg_factor)\n gg_line = geom_line(size=1, alpha=1, gg_factor)\n #else\n- gg_point = geom_point(size=$adv.points.size, alpha=$adv.points.alpha, colour=\'$adv.points.pointcolor\')\n- gg_line = geom_line(size=$adv.points.size, alpha=$adv.points.alpha, colour=\'$adv.points.pointcolor\')\n+ gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour=\'$adv.type_conditional.points.pointcolor\')\n+ gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour=\'$adv.type_conditional.points.pointcolor\')\n #end if\n \n names(input)[$adv.factor.factorcol] <- "factor"\n@@ -48,12 +48,12 @@\n gg_facet = NULL\n gg_factor = aes(colour=factor(factor))\n \n- #if $adv.points.pointoptions == "default"\n+ #if $adv.type_conditional.points.pointoptions == "default"\n gg_point = geom_point(size=1, alpha=1, gg_factor)\n gg_line = geom_line(size=1, alpha=1, gg_factor)\n #else\n- gg_point = geom_point(size=$adv.points.size, alpha=$adv.points.alpha, gg_factor)\n- gg_line = geom_line(size=$adv.points.size, alpha=$adv.points.alpha, gg_factor)\n+ gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor)\n+ gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor)\n #end if\n \n #if $adv.factor.colororder == 1\n@@ -68,12 +68,12 @@\n gg_factor = NULL\n color_scale = NULL\n \n- #if $adv.points.pointoptions == "default"\n+ #if $adv.type_conditional.points.pointoptions == "default"\n gg_point = geom_point(size=1, alpha=1, gg_factor)\n gg_line = geom_line(size=1, alpha=1, gg_factor)\n #else\n- gg_point = geom_point(size=$adv.points.size, alpha=$adv.points.alpha, colour=\'$adv.points.pointcolor\')\n- gg_line = geom_line(size=$adv.points.size, alpha=$adv.points.alpha, colour=\'$adv.points.pointcolor\')\n+ gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour=\'$adv.type_conditional.points.pointcolor\')\n+ gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour=\'$adv.type_conditional.points.pointcolor\')\n #end if\n #end if\n \n@@ -83,21 +83,21 @@\n #if $adv.axis_title_customization.axis_customization == "default"\n gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))\n #else\n- gg_axistitle = theme(axis.title = element_text(color = \'$adv.color\', size = $adv.size, face = \'$adv.face\'))\n+ gg_axistitle = theme(axis.title = element_text(color = \'$adv.axis_text_customization.color\', size = $adv.axis_text_customization.size, face = \'$adv.axis_text_customization.face\'))\n #end if\n \n ##axis text(tick) custization\n #if $adv.axis_text_customization.axis_customization == "default"\n gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))\n #else\n- gg_axistext = theme(axis.text = element_text(col'..b'>\n- <option value="red">Red</option>\n- <option value="white">White</option>\n- <option value="blue">Blue</option>\n- <option value="orange">Orange</option>\n- <option value="yellow">Yellow</option>\n- <option value="green">Green</option>\n- <option value="purple">Purple</option>\n- <option value="magenta">Magenta</option>\n- <option value="cyan">Cyan</option>\n- <option value="grey">Grey</option>\n- <option value="gold">Gold</option>\n- </param>\n+ <when value="pointslines">\n+ <expand macro="points_options"/>\n </when>\n+ <when value="lines"/>\n </conditional>\n <conditional name="factor">\n <param name="factoring" type="select" label="Plotting multiple groups" >\n@@ -197,10 +179,10 @@\n <expand macro="axis_customization" label="Plot title options" />\n </conditional>\n <param name="gridlinecust" type="select" label="Grid lines">\n- <option value="default">Default grid lines</option>\n- <option value="hidemajor">Hide major grid lines</option>\n- <option value="hideminor">Hide minor grid lines</option>\n- <option value="hideboth">Hide major and minor grid lines</option>\n+ <option value="default">Default grid lines</option>\n+ <option value="hidemajor">Hide major grid lines</option>\n+ <option value="hideminor">Hide minor grid lines</option>\n+ <option value="hideboth">Hide major and minor grid lines</option>\n </param>\n <expand macro="transform" />\n <expand macro="xy_scaling" />\n@@ -220,17 +202,35 @@\n <param name="additional_output_format" value="pdf" />\n <output name="output2" file="ggplot_point_result1.pdf" compare="sim_size" />\n </test>\n+ <!-- Test text options-->\n+ <test>\n+ <param name="input1" value="mtcars.txt" ftype="tabular" />\n+ <section name="adv">\n+ <conditional name="type_conditional">\n+ <param name="type_options" value="points"/>\n+ <conditional name="points">\n+ <param name="pointoptions" value="default"/>\n+ </conditional>\n+ </conditional>\n+ <conditional name="axis_text_customization">\n+ <param name="axis_customization" value="defined"/>\n+ <param name="color" value="red"/>\n+ </conditional>\n+ </section>\n+ <param name="additional_output_format" value="pdf" />\n+ <output name="output2" file="ggplot_point_result2.pdf" compare="sim_size" />\n+ </test>\n </tests>\n <help><![CDATA[\n This tool will generate a scatterplot representing data from two groups/conditions.\n \n The input data should be in tabular format and the user can determine which groups (columns) to plot.\n \n-Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "Advanced - plotting multiple groups".\n+Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "advanced - plotting multiple groups".\n \n Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user!\n \n-The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "Advanced - output dimensions"\n+The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "advanced - output dimensions"\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
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| diff -r e3a675da7fd0 -r 1acf88921176 macros.xml --- a/macros.xml Tue Oct 26 15:12:15 2021 +0000 +++ b/macros.xml Tue Nov 23 07:58:14 2021 +0000 |
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| @@ -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> |
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