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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9fe04d29ea604a152144908dbd20c0754695a025
author | iuc |
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date | Sat, 16 Nov 2024 19:56:46 +0000 |
parents | 4289db874e3c |
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<tool id="ampvis2_octave" name="ampvis2 octave 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 '$rscript' ]]></command> <configfiles> <configfile name="rscript"><![CDATA[ library(ampvis2, quietly = TRUE) d <- readRDS("$data") plot <- amp_octave( d, tax_aggregate = "$tax_aggregate", #if $group_by group_by = "$group_by", #if $scales scales = "$scales", #end if #end if num_threads = 1 ) @OUTPUT_TOKEN@ ]]></configfile> </configfiles> <inputs> <expand macro="rds_metadata_input_macro"/> <expand macro="taxlevel_macro" argument="tax_aggregate" label="Aggregate (sum) OTU's to a taxonomic level initially." help="OTU's that have not been assigned at the chosen level will be removed with a message."> <option value="OTU" selected="true">OTU/ASV</option> </expand> <expand macro="metadata_select" argument="group_by" label="Group the samples based on a metadata variable." help="Variable needs to be categorical/discrete"/> <expand macro="facet_scales_macro" argument="scales" help="Only relevant if for group_by a value is selected"/> <expand macro="out_format_macro"/> </inputs> <outputs> <expand macro="out_macro"/> </outputs> <tests> <test> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <output name="plot" value="AalborgWWTPs-octave.pdf" ftype="pdf" compare="sim_size"/> </test> <test> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <param name="tax_aggregate" value="Class"/> <param name="out_format" value="png"/> <output name="plot" value="AalborgWWTPs-octave.png" ftype="png" compare="sim_size"/> </test> <test> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> <param name="group_by" value="Year"/> <param name="scales" value="free"/> <param name="out_format" value="svg"/> <output name="plot" value="AalborgWWTPs-octave.svg" ftype="svg" compare="sim_size"/> </test> </tests> <help><![CDATA[ What it does ============ Generates an octave plot to assess alpha diversity. An octave plot is a histogram of the number of taxa observed by bins of read counts, where the bin ranges increase exponentially, see details. The Galaxy tool calls the `amp_octave <https://kasperskytte.github.io/ampvis2/reference/amp_octave.html>`_ function of the ampvis2 package. Details ======= The n-th bin in the histogram has the range ``r(n)=2n...2n+1-1``. The height of the bars then reflect the number of unique taxa with read counts in each bin. By judging the distribution one can assess whether the samples have been sequenced deeply enough at the chosen taxonomic level. A full symmetrical bell-shaped distribution with the left part far from the y-axis is the ideal. A high amount of OTU's with a low amount of reads indicates noise, chimeras, and even cross talk. Aggregating OTU's using ``tax_aggregate`` is useful to assess whether the samples have been sequenced deep enough to capture the full diversity at the given level, but ONLY applies to OTU's that have assigned taxonomy at the given level. It is recommended to look at samples individually as grouping samples will almost always look ideal. It is better to identify "bad" samples individually and remove them. Input ===== @HELP_RDS_INPUT@ @HELP_METADATA_LIST_INPUT@ Output ====== Octave plot in the chosen output format. ]]></help> <expand macro="citations"/> </tool>