Mercurial > repos > iuc > picrust_normalize_by_copy_number

annotate macros.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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children 842ff6c25a77
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1 <macros>
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2 <token name="@WRAPPER_VERSION@">1.0.1</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="1.0.1">picrust</requirement>
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6 </requirements>
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7 </xml>
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8
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9 <xml name="version_command">
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10 <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>
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11 </xml>
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12
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13 <xml name="otu-reference-precalculated">
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14 <!-- selection of "gg" picrust parameter reference data file -->
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15 <conditional name="gg">
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16 <param name="source" type="select" label="Select precalculated file from" help="">
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17 <option value="ref">Cached Reference</option>
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18 <option value="hist">History</option>
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19 </param>
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20 <when value="ref">
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21 <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis">
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22 <options from_data_table="picrust_precalculated"/>
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23 </param>
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24 </when>
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25 <when value="hist">
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26 <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis"
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27 help="files may be downloaded from PICRUSt website (see tool help below)" />
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28 </when>
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29 </conditional>
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30 </xml>
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31
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32 <xml name="biom_format_select">
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33 <param name="output_type" type="select" label="Format of the output BIOM file">
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34 <option value="json" selected="true">JSON</option>
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35 <option value="hdf5">HDF5</option>
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36 <option value="tsv">Classic (tab-separated text)</option>
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37 </param>
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38 </xml>
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39
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40 <xml name="biom_output">
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41 <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
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42 <change_format>
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43 <when input="output_type" value="json" format="json"/>
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44 <when input="output_type" value="tsv" format="tabular"/>
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45 <when input="output_type" value="hdf5" format="hdf5"/>
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46 </change_format>
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47 </data>
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48 </xml>
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49
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50 <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
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51 #if $output_type == "json":
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52 && biom convert -i tempbiom -o '$out_biom' --to-json
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53 #elif $output_type == "tsv":
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54 && biom convert -i tempbiom -o '$out_biom' --to-tsv
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55 #else
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56 && biom convert -i tempbiom -o '$out_biom' --to-hdf5
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57 #end if
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58 ]]></token>
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59
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60 <token name="@PICRUST_OVERVIEW@">
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61 <![CDATA[
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62 **PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States**
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63
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64 The PICRUSt project aims to support prediction of the unobserved character states in a community of
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65 organisms from phylogenetic information about the organisms in that community. The primary application
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66 is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only
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67 marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
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68 bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.
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69
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70 For more information please visit:
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71
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72 - Picrust Documentation: https://picrust.github.io/picrust/
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73 - Picrust GitHub: http://picrust.github.com/
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74 - Picrust Support: https://groups.google.com/d/forum/picrust-users
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75
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76 **Reference Data**
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77
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78 Precalculated files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/
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79
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80 ]]>
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81 </token>
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82
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83 <xml name="citations">
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84 <citations>
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85 <citation type="doi">10.1038/nbt.2676</citation>
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86 <yield/>
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87 </citations>
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88 </xml>
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89
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90 </macros>