Mercurial > repos > iuc > volcanoplot
changeset 7:a363ba287b88 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
| author | iuc |
|---|---|
| date | Wed, 15 May 2024 10:06:58 +0000 |
| parents | 83c573f2e73c |
| children | |
| files | volcanoplot.xml |
| diffstat | 1 files changed, 17 insertions(+), 16 deletions(-) [+] |
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--- a/volcanoplot.xml Thu Jun 10 08:38:12 2021 +0000 +++ b/volcanoplot.xml Wed May 15 10:06:58 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="volcanoplot" name="Volcano Plot" version="0.0.5"> +<tool id="volcanoplot" name="Volcano Plot" version="0.0.6" profile="20.09"> <description>create a volcano plot</description> <edam_topics> <edam_topic>topic_0092</edam_topic> @@ -145,29 +145,29 @@ #end if #end if -#if not '$plot_options.title' +#if $plot_options.title: p <- p + ggtitle('$plot_options.title') #end if -#if not '$plot_options.xlab' +#if $plot_options.xlab: p <- p + xlab('$plot_options.xlab') #end if -#if not '$plot_options.ylab' +#if $plot_options.ylab: p <- p + ylab('$plot_options.ylab') #end if -#if not '$plot_options.xmin' and '$plot_options.xmax' -p <- p + xlim('$plot_options.xmin', '$plot_options.xmax') +#if $plot_options.xmin and $plot_options.xmax: +p <- p + xlim($plot_options.xmin, $plot_options.xmax) #end if -#if not '$plot_options.ymax' -p <- p + ylim(0, '$plot_options.ymax') +#if $plot_options.ymax: +p <- p + ylim(0, $plot_options.ymax) #end if # Set legend title -#if not '$plot_options.legend' -p <- p + theme(legend.title = '$plot_options.legend') +#if $plot_options.legend: +p <- p + guides(color = guide_legend(title = '$plot_options.legend')) #else p <- p + theme(legend.title = element_blank()) #end if @@ -191,10 +191,10 @@ <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)" /> - <param name="pval_col" type="data_column" data_ref="input" label="P value (raw)" /> - <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change" /> - <param name="label_col" type="data_column" data_ref="input" label="Labels" /> + <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="signif_thresh" type="float" max="1" value="0.05" label="Significance threshold" help="Default: 0.05"/> <param name="lfc_thresh" type="float" value="0" label="LogFC threshold to colour" help="Default: 0"/> <conditional name="labels"> @@ -260,7 +260,7 @@ <param name="label_file" ftype="tabular" value="labels.tab" /> <output name="plot"> <assert_contents> - <has_size value= "933832" delta="1000" /> + <has_size value= "933830" delta="1000" /> </assert_contents> </output> </test> @@ -321,5 +321,6 @@ ]]></help> <citations> + <citation type="doi">doi.org/10.1007/978-3-319-24277-4</citation> </citations> -</tool> \ No newline at end of file +</tool>