Mercurial > repos > iuc > biom_normalize_table

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4d77c1e4bd9f6876ee338858a8cd4c7e9528d54c
author iuc
date Wed, 13 Sep 2023 09:39:15 +0000
parents ea1936aa2d98
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ea1936aa2d98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4ca0a67fd4126f8b2a135b6cb7894042e980b39a"
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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="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 biom normalize-table
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11 --input-fp '$input_fp'
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12 --output-fp '$output_fp'
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13 $relative_abund
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14 $presence_absence
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15 --axis '$axis'
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" />
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20 <param argument="--relative-abund" type="boolean" checked="True" truevalue="--relative-abund" falsevalue="" label="Convert table to relative abundance" />
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21 <param argument="--presence-absence" type="boolean" checked="True" truevalue="--presence-absence" falsevalue="" label="Convert table to presence/absence" />
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22 <param argument="--axis" type="select" label="The axis to normalize over">
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23 <option value="sample" selected="True">Sample</option>
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24 <option value="observation">Observation</option>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <data format="biom1" name="output_fp"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_fp" value="input_abundance_1.biom1" />
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33 <param name="relative_abund" value="--relative-abund" />
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34 <param name="presence_absence" value="" />
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35 <param name="axis" value="sample" />
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36 <output name="output_fp" value="normalized_relative_abund_samples.biom" ftype="biom1" compare="sim_size"/>
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37 </test>
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38 <test>
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39 <param name="input_fp" value="input_abundance_1.biom1" />
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40 <param name="relative_abund" value="" />
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41 <param name="presence_absence" value="--presence-absence" />
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42 <param name="axis" value="observation" />
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43 <output name="output_fp" value="normalized_presence_absence_observations.biom" ftype="biom1" compare="sim_size"/>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 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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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>