| Previous changeset 11:5e08a1e22dbc (2025-01-29) Next changeset 13:11c344627e52 (2025-05-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 85f81cd54f7bd9e2e8b6f0ba1260520ad24d28cd |
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modified:
volcanoplot.xml |
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added:
macros.xml |
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| diff -r 5e08a1e22dbc -r 3af838dc0637 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu May 15 12:51:53 2025 +0000 |
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| @@ -0,0 +1,9 @@ +<macros> + <xml name="columns" tokens="header"> + <param name="fdr_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="FDR (adjusted P value) column number" /> + <param name="pval_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="P value (raw) column number" /> + <param name="lfc_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="Log Fold Change column number" /> + <param name="label_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="Labels column number" /> + <param name="shape_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="Categories that can be used to plot different shapes or facet (useful if multivariable associations are investigated)" optional="true" /> + </xml> +</macros> \ No newline at end of file |
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| diff -r 5e08a1e22dbc -r 3af838dc0637 volcanoplot.xml --- a/volcanoplot.xml Wed Jan 29 10:37:54 2025 +0000 +++ b/volcanoplot.xml Thu May 15 12:51:53 2025 +0000 |
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| @@ -1,13 +1,20 @@ -<tool id="volcanoplot" name="Volcano Plot" version="0.0.7" profile="20.09"> +<tool id="volcanoplot" name="Volcano Plot" version="@TOOL_VERSION@+galaxy0" profile="20.09"> <description>create a volcano plot</description> + <macros> + <import>macros.xml</import> + <token name="@TOOL_VERSION@">3.3.3</token> + </macros> + <edam_topics> <edam_topic>topic_0092</edam_topic> </edam_topics> + <edam_operations> <edam_operation>operation_0337</edam_operation> </edam_operations> + <requirements> - <requirement type="package" version="3.3.3">r-ggplot2</requirement> + <requirement type="package" version="@TOOL_VERSION@">r-ggplot2</requirement> <requirement type="package" version="0.9.1">r-ggrepel</requirement> <requirement type="package" version="1.0.6">r-dplyr</requirement> </requirements> @@ -203,16 +210,23 @@ </configfiles> <inputs> <param name="input" type="data" format="tabular" label="Specify an input file" /> - <param name="header" type="select" label="File has header?" help="Does the differentially expressed results file contain a header row. The tool can auto-detect by checking if the first row in the P value column is a number or not. Default: Auto-detect"> - <option value="auto" selected="True">Auto-detect</option> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="fdr_col" type="data_column" data_ref="input" label="FDR (adjusted P value) column number" /> - <param name="pval_col" type="data_column" data_ref="input" label="P value (raw) column number" /> - <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change column number" /> - <param name="label_col" type="data_column" data_ref="input" label="Labels column number" /> - <param name="shape_col" type="data_column" data_ref="input" label="Categories that can be used to plot different shapes or facet (useful if multivariable associations are investigated)" optional="true" /> + <conditional name="with_header"> + <param name="header" type="select" label="File has header?" refresh_on_change="true" help="Does the differentially expressed results file contain a header row. The tool can auto-detect by checking if the first row in the P value column is a number or not. Default: Auto-detect"> + <option value="auto" selected="True">Auto-detect</option> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="auto"> + <expand macro="columns" header="false"/> + </when> + <when value="yes"> + <expand macro="columns" header="true"/> + </when> + <when value="no"> + <expand macro="columns" header="false"/> + </when> + </conditional> + <param name="shape_or_facet" type="select" label="Display categories by:" help="Choose whether to display categories by faceting the plot or using shape." optional="true"> <option value="facet">Facet</option> <option value="shape">Shape</option> |