Mercurial > repos > iuc > biom_normalize_table

annotate biom_normalize_table.xml @ 9:4ede01f01d20 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 2230d399cc6a526674f192099f00632dcc931e8c
author iuc
date Fri, 09 Feb 2024 21:35:33 +0000
parents e34a4fe24d77
children
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1 <tool id="biom_normalize_table" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>a BIOM table</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 biom normalize-table
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12 --input-fp '$input_fp'
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13 --output-fp '$output_fp'
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14 $relative_abund
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15 $presence_absence
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16 --axis '$axis'
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" />
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21 <param argument="--relative-abund" type="boolean" checked="True" truevalue="--relative-abund" falsevalue="" label="Convert table to relative abundance" />
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22 <param argument="--presence-absence" type="boolean" checked="True" truevalue="--presence-absence" falsevalue="" label="Convert table to presence/absence" />
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23 <param argument="--axis" type="select" label="The axis to normalize over">
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24 <option value="sample" selected="True">Sample</option>
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25 <option value="observation">Observation</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="biom1" name="output_fp"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input_fp" value="input_abundance_1.biom1" />
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34 <param name="relative_abund" value="--relative-abund" />
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35 <param name="presence_absence" value="" />
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36 <param name="axis" value="sample" />
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37 <output name="output_fp" value="normalized_relative_abund_samples.biom" ftype="biom1" compare="sim_size"/>
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38 </test>
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39 <test>
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40 <param name="input_fp" value="input_abundance_1.biom1" />
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41 <param name="relative_abund" value="" />
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42 <param name="presence_absence" value="--presence-absence" />
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43 <param name="axis" value="observation" />
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44 <output name="output_fp" value="normalized_presence_absence_observations.biom" ftype="biom1" compare="sim_size"/>
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 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.
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49 ]]></help>
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50 <expand macro="citations" />
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51 </tool>