Mercurial > repos > iuc > picrust_metagenome_contributions
annotate metagenome_contributions.xml @ 0:b0a55e81a3dd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
author | iuc |
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date | Wed, 30 Aug 2017 04:49:13 -0400 |
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children | f0f5028a3393 |
rev | line source |
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b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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1 <tool id="picrust_metagenome_contributions" name="Metagenome Contributions" version="@WRAPPER_VERSION@.0"> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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2 <description>of OTUs to user-specified functions</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> |
b0a55e81a3dd
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> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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5 </macros> |
b0a55e81a3dd
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"/> |
b0a55e81a3dd
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"/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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8 <command detect_errors="aggressive"><![CDATA[ |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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9 metagenome_contributions.py |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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10 -i '$input_data' |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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11 -o '$contrib_table' |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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12 -c '$gg.precalc' |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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13 -l '$limit_gene' |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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14 ]]></command> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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15 <inputs> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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16 <param name="input_data" type="data" format="biom1,h5" label="Input file" help="Biom file, which should be the output of the normalize_by_copy_number command."/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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17 <expand macro="otu-reference-precalculated"/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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18 <param name="limit_gene" type="text" format="txt" label="Function ids" help="Limit to specified function ids (e.g. K00500). If limiting to multiple ids then separate them by commas with no spaces between them." /> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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19 </inputs> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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20 <outputs> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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21 <data name="contrib_table" format="tabular"/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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22 </outputs> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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23 <tests> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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24 <test> |
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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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25 <param name="input_data" value="otu_table_for_custom_trait_table.biom"/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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26 <param name="source" value="hist"/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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27 <param name="precalc" value="custom_trait_table.tab"/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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28 <output name="contrib_table" ftype="tabular"> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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29 <assert_contents> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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30 <has_text text="GeneCountPerGenome"/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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31 <has_text text="OTUAbundanceInSample"/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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32 </assert_contents> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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33 </output> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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34 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
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35 </tests> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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36 <help> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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37 <![CDATA[ |
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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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38 @PICRUST_OVERVIEW@ |
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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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39 |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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40 **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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41 |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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42 This module outputs the relative contribution of OTUs to the predicted abundances of functions in your samples. The input biom file should be the output of normalize_by_copy_number. One output text file will be generated. |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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43 |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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44 Make sure that you specify an appropriate functional database for this command (usually the ko, cog, or rfam v13_5 database). |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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45 |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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46 ]]> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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47 </help> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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48 <expand macro="citations"/> |
b0a55e81a3dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
iuc
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49 </tool> |