Mercurial > repos > iuc > ampvis2_timeseries
view timeseries.xml @ 4:9de032723f5b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit ab75ba7665d7fb5c18ad08dfbba92b273f991dfc
author | iuc |
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date | Sat, 16 Mar 2024 11:40:38 +0000 |
parents | 3c16699f39d6 |
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<tool id="ampvis2_timeseries" name="ampvis2 timeseries plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="header"/> <command detect_errors="exit_code"><![CDATA[ Rscript '$rscript' ]]></command> <configfiles> <configfile name="rscript"><![CDATA[ library(ampvis2, quietly = TRUE) #if $tax_add #set ta='c("' + '", "'.join(str($tax_add).split(",")) + '")' #else #set ta='NULL' #end if data <- readRDS("$data") plot <- amp_timeseries( data, time_variable = "$time_variable", #if $group_by group_by = "$group_by", #end if tax_aggregate = "$tax_aggregate", tax_add = $ta, @TAX_SHOW@ tax_class = NULL, tax_empty = "$tax_empty", split = $split, scales = "free_y", normalise = TRUE, plotly = FALSE, format = "%Y-%m-%d" ) @OUTPUT_TOKEN@ ]]></configfile> </configfiles> <inputs> <expand macro="rds_metadata_input_macro"/> <expand macro="metadata_select_date" argument="time_variable" optional="false" label="Time variable" help="Must be directly compatible with as_date and preferably of the form yyyy-mm-dd or %Y-%m-%d"/> <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by"/> <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs"> <option value="OTU" selected="true">OTU/ASV</option> </expand> <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/> <expand macro="tax_show_macro" value="6"/> <expand macro="tax_empty_macro"/> <param argument="split" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Create a facet for each taxon"/> <expand macro="facet_scales_macro" argument="scales"/> <expand macro="normalise_macro" checked="true"/> <expand macro="out_format_macro"/> </inputs> <outputs> <expand macro="out_macro"/> </outputs> <tests> <!-- defaults --> <test expect_num_outputs="1"> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> <param name="time_variable" value="Date"/> <output name="plot" value="AalborgWWTPs-timeseries.pdf" ftype="pdf" compare="sim_size"/> </test> <!-- group --> <test expect_num_outputs="1"> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> <param name="time_variable" value="Date"/> <param name="group_by" value="Plant"/> <output name="plot" value="AalborgWWTPs-timeseries-group.pdf" ftype="pdf" compare="sim_size"/> </test> <!-- taxlevel --> <test expect_num_outputs="1"> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> <param name="time_variable" value="Date"/> <param name="tax_aggregate" value="Family"/> <param name="tax_add" value="Phylum"/> <output name="plot" value="AalborgWWTPs-timeseries-tax.pdf" ftype="pdf" compare="sim_size"/> </test> </tests> <help><![CDATA[ What it does ============ Generates a timeseries plot showing relative read abundances over time. The Galaxy tool calls the `amp_timeseries <https://kasperskytte.github.io/ampvis2/reference/amp_timeseries.html>`_ function of the ampvis2 package. @HELP_RELATIVE_ABUNDANCES@ Input ===== @HELP_RDS_INPUT@ @HELP_METADATA_LIST_INPUT@ Output ====== A timeseries plot in the chosen output format. ]]></help> <expand macro="citations"/> </tool>