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annotate biom_normalize_table.xml @ 3:ea1936aa2d98 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4ca0a67fd4126f8b2a135b6cb7894042e980b39a"
author iuc
date Sat, 23 Oct 2021 21:26:40 +0000
parents a900ebd4a533
children 9443ac1f7108
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ea1936aa2d98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4ca0a67fd4126f8b2a135b6cb7894042e980b39a"
iuc
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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 name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" />
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20 <param name="relative_abund" argument="--relative-abund" type="boolean" checked="True" truevalue="--relative-abund" falsevalue="" label="Convert table to relative abundance" />
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21 <param name="presence_absence" 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>