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Make title and others visible in volcanoplot #5977

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merged 9 commits into from
May 15, 2024
Merged

Make title and others visible in volcanoplot #5977

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79e5a4a
Make title and others visible in volcanoplot.xml
pcm32 Apr 29, 2024
b07709d
Bumps version
pcm32 Apr 29, 2024
18a7b2c
Profile and citation
pcm32 Apr 29, 2024
74a8641
Add homepage URL to .shed.yml
pcm32 Apr 29, 2024
09cd664
Avoid element_blank for legend title
pcm32 Apr 29, 2024
bff1831
Fix legend title handling
pcm32 Apr 30, 2024
893f319
Update test sizes
pcm32 Apr 30, 2024
d558ad0
Hopefully fixes last test
pcm32 Apr 30, 2024
8fd412a
Update test sizes
pcm32 Apr 30, 2024
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1 change: 1 addition & 0 deletions tools/volcanoplot/.shed.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,4 +8,5 @@ long_description: |
name: volcanoplot
owner: iuc
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot
homepage_url: https://ggplot2.tidyverse.org/
type: unrestricted
33 changes: 17 additions & 16 deletions tools/volcanoplot/volcanoplot.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand Down Expand Up @@ -145,29 +145,29 @@ p <- p + geom_text_repel(data = filter(results, labels != ""), aes(label = label
#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
Expand All @@ -191,10 +191,10 @@ sessionInfo()
<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">
Expand Down Expand Up @@ -260,7 +260,7 @@ sessionInfo()
<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>
Expand Down Expand Up @@ -321,5 +321,6 @@ A PDF containing a Volcano plot like below. The R code can be output through *Ou

]]></help>
<citations>
<citation type="doi">doi.org/10.1007/978-3-319-24277-4</citation>
</citations>
</tool>
</tool>