Mercurial > repos > iuc > picrust_normalize_by_copy_number
annotate normalize_by_copy_number.xml @ 4:2e62e32d4f33 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author | iuc |
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date | Thu, 28 Nov 2019 15:53:49 -0500 |
parents | 76c040c8b9fc |
children | 3bd5f5afb9b1 |
rev | line source |
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1
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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1 <tool id="picrust_normalize_by_copy_number" name="Normalize" version="@WRAPPER_VERSION@.0"> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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2 <description>the relative abundance of each OTU by the predicted number of 16S copies</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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4 <import>macros.xml</import> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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5 </macros> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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6 <expand macro="requirements"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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7 <expand macro="version_command"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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8 <command detect_errors="aggressive"><![CDATA[ |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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9 normalize_by_copy_number.py |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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10 -i '$input_data' |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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11 -o tempbiom |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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12 -c '$gg.precalc' |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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13 |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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14 @OUTPUT_CONVERSION_COMMANDS@ |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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15 ]]></command> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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16 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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17 <param name="input_data" type="data" format="biom1,h5" label="Input file" help="biom file"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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18 <expand macro="otu-reference-precalculated"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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19 <expand macro="biom_format_select"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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20 </inputs> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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21 <outputs> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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22 <expand macro="biom_output"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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23 </outputs> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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24 <tests> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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25 <test> <!-- test with biom input --> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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26 <param name="input_data" value="closed_picked_otus.biom"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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27 <param name="source" value="hist"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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28 <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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29 <param name="output_type" value="json"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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30 <output name="out_biom" ftype="biom1"> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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31 <assert_contents> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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32 <has_text text="Biological Observation Matrix"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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33 <has_text text="generated_by"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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34 </assert_contents> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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35 </output> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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36 </test> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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37 <test> <!-- test with QIIME input and classic output --> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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38 <param name="input_data" value="closed_picked_otus.tab"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
parents:
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39 <param name="source" value="hist"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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40 <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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41 <param name="output_type" value="tsv"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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42 <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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43 </test> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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44 </tests> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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45 <help> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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46 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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47 @PICRUST_OVERVIEW@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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48 |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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49 **Command Documenation** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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50 |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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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. |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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52 |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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53 Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_. |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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54 A sample file can be downloaded here_ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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55 |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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56 Make sure that you specify an appropriate 16S database for this command (usually 16S 13_5). |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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57 |
4
2e62e32d4f33
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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58 .. _guide: http://picrust.github.io/picrust/tutorials/quickstart.html#quickstart-guide |
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76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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59 .. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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60 ]]> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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61 </help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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62 <expand macro="citations"/> |
76c040c8b9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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63 </tool> |