Mercurial > repos > iuc > biom_normalize_table

annotate biom_normalize_table.xml @ 0:a900ebd4a533 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
author iuc
date Wed, 31 May 2017 11:20:30 -0400
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a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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1 <tool id="biom_normalize_table" name="Normalize" version="@VERSION@.1">
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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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>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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5 </macros>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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6 <expand macro="requirements" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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7 <expand macro="version_command" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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8 <command detect_errors="exit_code">
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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9 <![CDATA[
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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10 biom normalize-table
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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11 --input-fp '$input_fp'
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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12 --output-fp '$output_fp'
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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13 $relative_abund
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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14 $presence_absence
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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15 --axis '$axis'
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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16 ]]>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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17 </command>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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18 <inputs>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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19 <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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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" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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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" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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22 <param argument="--axis" type="select" label="The axis to normalize over">
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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23 <option value="sample" selected="True">Sample</option>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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24 <option value="observation">Observation</option>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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25 </param>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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26 </inputs>
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27 <outputs>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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28 <data format="biom1" name="output_fp"/>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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29 </outputs>
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30 <tests>
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31 <test>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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32 <param name="input_fp" value="input_abundance_1.biom1" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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33 <param name="relative_abund" value="--relative-abund" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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34 <param name="presence_absence" value="" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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35 <param name="axis" value="sample" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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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>
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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39 <param name="input_fp" value="input_abundance_1.biom1" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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40 <param name="relative_abund" value="" />
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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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[
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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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.
a900ebd4a533 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>