Mercurial > repos > iuc > picrust_normalize_by_copy_number

annotate normalize_by_copynumber.xml @ 0:32d13e000a28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
author iuc
date Thu, 08 Dec 2016 06:26:58 -0500
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32d13e000a28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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1 <tool id="picrust_normalize_by_copy_number" name="Normalize" version="@WRAPPER_VERSION@.0">
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2 <description>OTUs by copy number</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="aggressive"><![CDATA[
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9 normalize_by_copy_number.py
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10 -i '$input_data'
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11 -o tempbiom
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12 -c '$gg.precalc'
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13
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14 @OUTPUT_CONVERSION_COMMANDS@
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15 ]]></command>
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16 <inputs>
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17 <param name="input_data" type="data" format="tabular,biom1" label="Input file" help="biom file or legacy QIIME OTU table"/>
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18 <expand macro="otu-reference-precalculated"/>
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19 <expand macro="biom_format_select"/>
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20 </inputs>
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21 <outputs>
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22 <expand macro="biom_output"/>
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23 </outputs>
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24 <tests>
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25 <test> <!-- test with biom input -->
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26 <param name="input_data" value="closed_picked_otus.biom"/>
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27 <param name="source" value="hist"/>
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28 <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
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29 <param name="output_type" value="json"/>
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30 <output name="out_biom" ftype="json">
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31 <assert_contents>
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32 <has_text text="Biological Observation Matrix"/>
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33 <has_text text="generated_by"/>
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34 </assert_contents>
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35 </output>
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36 </test>
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37 <test> <!-- test with QIIME input and classic output -->
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38 <param name="input_data" value="closed_picked_otus.tab"/>
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39 <param name="source" value="hist"/>
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40 <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
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41 <param name="output_type" value="tsv"/>
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42 <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/>
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43 </test>
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44 </tests>
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45 <help>
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46 <![CDATA[
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47 @PICRUST_OVERVIEW@
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48
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49 **Command Documenation**
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50
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51 This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU.
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52
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53 Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_.
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54 A sample file can be downloaded here_
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55
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56 .. _guide: http://picrust.github.com/picrust/methods/constructing_reference_otus.html
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57 .. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab
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58 ]]>
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59 </help>
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60 <expand macro="citations"/>
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61 </tool>