Mercurial > repos > iuc > biom_normalize_table
view biom_normalize_table.xml @ 8:77174295b6f4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 94b799bfabff7127794b8ed43d6d278f3f961222
author | iuc |
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date | Thu, 26 Oct 2023 07:28:12 +0000 |
parents | e34a4fe24d77 |
children | 4ede01f01d20 |
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<tool id="biom_normalize_table" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>a BIOM table</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"> <![CDATA[ biom normalize-table --input-fp '$input_fp' --output-fp '$output_fp' $relative_abund $presence_absence --axis '$axis' ]]> </command> <inputs> <param argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" /> <param argument="--relative-abund" type="boolean" checked="True" truevalue="--relative-abund" falsevalue="" label="Convert table to relative abundance" /> <param argument="--presence-absence" type="boolean" checked="True" truevalue="--presence-absence" falsevalue="" label="Convert table to presence/absence" /> <param argument="--axis" type="select" label="The axis to normalize over"> <option value="sample" selected="True">Sample</option> <option value="observation">Observation</option> </param> </inputs> <outputs> <data format="biom1" name="output_fp"/> </outputs> <tests> <test> <param name="input_fp" value="input_abundance_1.biom1" /> <param name="relative_abund" value="--relative-abund" /> <param name="presence_absence" value="" /> <param name="axis" value="sample" /> <output name="output_fp" value="normalized_relative_abund_samples.biom" ftype="biom1" compare="sim_size"/> </test> <test> <param name="input_fp" value="input_abundance_1.biom1" /> <param name="relative_abund" value="" /> <param name="presence_absence" value="--presence-absence" /> <param name="axis" value="observation" /> <output name="output_fp" value="normalized_presence_absence_observations.biom" ftype="biom1" compare="sim_size"/> </test> </tests> <help><![CDATA[ Normalize the values of a BIOM table through various methods. Relative abundance will take the relative abundance of each observation in terms of samples or observations. Presence absensece will convert observations to 1's and 0's based on presence of the observation. ]]></help> <expand macro="citations" /> </tool>