Mercurial > repos > iuc > ggplot2_pca
changeset 5:fcb6a19960c6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
| author | iuc |
|---|---|
| date | Tue, 23 Nov 2021 07:57:08 +0000 |
| parents | 7e616a1bdb07 |
| children | 2bf238af068d |
| files | ggplot2_pca.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 test-data/ggplot_point_result2.pdf |
| diffstat | 7 files changed, 55 insertions(+), 19 deletions(-) [+] |
line wrap: on
line diff
--- a/ggplot2_pca.xml Tue Oct 26 15:13:06 2021 +0000 +++ b/ggplot2_pca.xml Tue Nov 23 07:57:08 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">
--- a/macros.xml Tue Oct 26 15:13:06 2021 +0000 +++ b/macros.xml Tue Nov 23 07:57:08 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>