Mercurial > repos > iuc > picrust_compare_biom
annotate macros.xml @ 0:43244ad9e7ef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
author | iuc |
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date | Sat, 20 Jan 2018 03:31:34 -0500 |
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children | 9168545e09df |
rev | line source |
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0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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1 <macros> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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2 <token name="@WRAPPER_VERSION@">1.1.1</token> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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3 <xml name="requirements"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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4 <requirements> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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5 <requirement type="package" version="1.1.1">picrust</requirement> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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6 </requirements> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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7 </xml> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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8 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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9 <xml name="version_command"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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10 <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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11 </xml> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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12 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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13 <xml name="otu-reference-precalculated"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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14 <!-- selection of "gg" picrust parameter reference data file --> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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15 <conditional name="gg"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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16 <param name="source" type="select" label="Select precalculated file from" help=""> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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17 <option value="ref">Cached Reference</option> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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18 <option value="hist">History</option> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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19 </param> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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20 <when value="ref"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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21 <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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22 <options from_data_table="picrust_precalculated"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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23 </param> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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24 </when> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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25 <when value="hist"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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26 <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis" |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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27 help="files may be downloaded from PICRUSt website (see tool help below)" /> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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28 </when> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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29 </conditional> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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30 </xml> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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31 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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32 <xml name="biom_format_select"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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33 <param name="output_type" type="select" label="Format of the output BIOM file"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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34 <option value="hdf5" selected="true">HDF5</option> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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35 <option value="json">JSON</option> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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36 <option value="tsv">Classic (tab-separated text)</option> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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37 </param> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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38 </xml> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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39 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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40 <xml name="biom_format_select_no_json"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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41 <param name="output_type" type="select" label="Format of the output BIOM file"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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42 <option value="hdf5" selected="true">HDF5</option> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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43 <option value="tsv">Classic (tab-separated text)</option> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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44 </param> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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45 </xml> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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46 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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47 <xml name="biom_output"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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48 <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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49 <change_format> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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50 <when input="output_type" value="json" format="biom1"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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51 <when input="output_type" value="tsv" format="tabular"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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52 <when input="output_type" value="hdf5" format="h5"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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53 </change_format> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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54 </data> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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55 </xml> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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56 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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57 <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[ |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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58 #if $output_type == "hdf5": |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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59 && mv tempbiom '$out_biom' |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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60 #elif $output_type == "tsv": |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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61 && biom convert -i tempbiom -o '$out_biom' --to-tsv |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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62 #else: |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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63 && biom convert -i tempbiom -o '$out_biom' --to-json |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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64 #end if |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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65 ]]></token> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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66 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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67 <token name="@PICRUST_OVERVIEW@"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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68 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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69 **PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States** |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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70 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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71 The PICRUSt project aims to support prediction of the unobserved character states in a community of |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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72 organisms from phylogenetic information about the organisms in that community. The primary application |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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73 is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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74 marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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75 bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs. |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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76 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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77 For more information please visit: |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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78 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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79 - PICRUSt Documentation: https://picrust.github.io/picrust/ |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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80 - PICRUSt GitHub: http://picrust.github.com/ |
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81 - PICRUSt Support: https://groups.google.com/d/forum/picrust-users |
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82 |
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83 **Reference Data** |
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84 |
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85 Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/ |
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86 |
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87 ]]> |
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88 </token> |
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89 |
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90 <xml name="citations"> |
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91 <citations> |
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92 <citation type="doi">10.1038/nbt.2676</citation> |
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93 <yield/> |
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94 </citations> |
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95 </xml> |
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96 |
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97 </macros> |