Mercurial > repos > iuc > ampvis2_alpha_diversity
changeset 8:77000428c613 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
| author | iuc |
|---|---|
| date | Fri, 01 Nov 2024 17:09:34 +0000 |
| parents | c14c7fd4d1be |
| children | |
| files | alpha_diversity.xml |
| diffstat | 1 files changed, 42 insertions(+), 5 deletions(-) [+] |
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--- a/alpha_diversity.xml Fri Oct 25 14:13:48 2024 +0000 +++ b/alpha_diversity.xml Fri Nov 01 17:09:34 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> +<tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT"> <description></description> <macros> <import>macros.xml</import> @@ -11,13 +11,32 @@ <configfile name="rscript"><![CDATA[ #set m='"' + '", "'.join(str($measure).split(",")) + '"' library(ampvis2, quietly = TRUE) + d <- readRDS("$data") - a <- amp_alphadiv(d, + table <- amp_alphadiv(d, + measure = c($m), + richness = $richness + @RAREFY_TOKEN@, + ) + plot <- amp_alphadiv(d, measure = c($m), richness = $richness - @RAREFY_TOKEN@ + @RAREFY_TOKEN@, + plot = TRUE, + plot_group_by = "$group_by", + plot_scatter = $plot_scatter ) - write.table(a, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) + write.table(table, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) + ggsave("$alphadiv_plot", + plot = plot, + device = "$output_options.out_format" + #if str($output_options.plot_width) != '' + , width = $output_options.plot_width + #end if + #if str($output_options.plot_height) != '' + , height = $output_options.plot_height + #end if + ) ]]></configfile> </configfiles> <inputs> @@ -30,13 +49,19 @@ </param> <param argument="richness" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Calculate sample richness estimates" help="Chao1 and ACE"/> <expand macro="rarefy_macro" help="before calculating alpha diversity and/or richnes"/> + <param argument="group_by" type="text" label="Group by metadata field (for plotting)" help="Specify the metadata field to group the plot by"/> + <param argument="plot_scatter" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scatter plot instead of boxplot?" help="Select to generate a scatter plot instead of a boxplot"/> + <expand macro="out_format_macro"/> </inputs> <outputs> <data name="alphadiv" format="tabular"/> + <expand macro="out_macro" name="alphadiv_plot" label=": plot"/> </outputs> <tests> <test> - <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="group_by" value="Plant"/> + <param name="plot_scatter" value="false"/> <output name="alphadiv"> <assert_contents> <has_line line="SampleID	Plant	Date	Year	Period	Reads	uniqueOTUs	Shannon	Simpson	invSimpson"/> @@ -46,12 +71,19 @@ <has_n_columns n="10"/> </assert_contents> </output> + <output name="alphadiv_plot" ftype="pdf"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </output> </test> <test> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <param name="measure" value="observed,shannon"/> <param name="richness" value="true"/> <param name="rarefy" value="500"/> + <param name="group_by" value="Plant"/> + <param name="plot_scatter" value="true"/> <output name="alphadiv"> <assert_contents> <has_line line="SampleID	Plant	Date	Year	Period	RawReads	Reads	uniqueOTUs	Shannon	Simpson	invSimpson	Chao1	ACE"/> @@ -62,6 +94,11 @@ <has_text text="	500	"/> </assert_contents> </output> + <output name="alphadiv_plot"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[