Mercurial > repos > iuc > picrust_normalize_by_copy_number

annotate macros.xml @ 6:65e5f9caefcc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 899e24f2aecad79c80667fb6c938dd4573a98820
author iuc
date Fri, 09 Feb 2024 21:41:38 +0000
parents 3bd5f5afb9b1
children
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1 <macros>
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3bd5f5afb9b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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2 <token name="@TOOL_VERSION@">1.1.1</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="1.1.1">picrust</requirement>
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6 </requirements>
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7 </xml>
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9 <xml name="bio_tools">
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10 <xrefs>
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11 <xref type="bio.tools">picrust</xref>
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12 </xrefs>
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13 </xml>
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15 <xml name="version_command">
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16 <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>
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17 </xml>
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19 <xml name="otu-reference-precalculated">
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20 <!-- selection of "gg" picrust parameter reference data file -->
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21 <conditional name="gg">
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22 <param name="source" type="select" label="Select precalculated file from" help="">
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23 <option value="ref">Cached Reference</option>
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24 <option value="hist">History</option>
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25 </param>
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26 <when value="ref">
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27 <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis">
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28 <options from_data_table="picrust_precalculated"/>
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29 </param>
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30 </when>
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31 <when value="hist">
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32 <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis"
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33 help="files may be downloaded from PICRUSt website (see tool help below)" />
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34 </when>
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35 </conditional>
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36 </xml>
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37
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38 <xml name="biom_format_select">
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39 <param name="output_type" type="select" label="Format of the output BIOM file">
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40 <option value="hdf5" selected="true">HDF5</option>
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41 <option value="json">JSON</option>
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42 <option value="tsv">Classic (tab-separated text)</option>
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43 </param>
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44 </xml>
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45
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46 <xml name="biom_format_select_no_json">
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47 <param name="output_type" type="select" label="Format of the output BIOM file">
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48 <option value="hdf5" selected="true">HDF5</option>
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49 <option value="tsv">Classic (tab-separated text)</option>
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50 </param>
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51 </xml>
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52
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53 <xml name="biom_output">
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54 <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
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55 <change_format>
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56 <when input="output_type" value="json" format="biom1"/>
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57 <when input="output_type" value="tsv" format="tabular"/>
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58 <when input="output_type" value="hdf5" format="h5"/>
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59 </change_format>
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60 </data>
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61 </xml>
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62
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63 <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
1
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64 #if $output_type == "hdf5":
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65 && mv tempbiom '$out_biom'
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66 #elif $output_type == "tsv":
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67 && biom convert -i tempbiom -o '$out_biom' --to-tsv
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68 #else:
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69 && biom convert -i tempbiom -o '$out_biom' --to-json
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70 #end if
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71 ]]></token>
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72
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73 <token name="@PICRUST_OVERVIEW@">
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74 <![CDATA[
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75 **PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States**
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76
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77 The PICRUSt project aims to support prediction of the unobserved character states in a community of
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78 organisms from phylogenetic information about the organisms in that community. The primary application
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79 is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only
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80 marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
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81 bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.
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82
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83 For more information please visit:
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84
1
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85 - PICRUSt Documentation: https://picrust.github.io/picrust/
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3bd5f5afb9b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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86 - PICRUSt GitHub: https://github.com/picrust/picrust/
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87 - PICRUSt Support: https://groups.google.com/d/forum/picrust-users
0
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88
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89 **Reference Data**
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90
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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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91 Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/
0
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92
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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93 ]]>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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94 </token>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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95
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96 <xml name="citations">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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97 <citations>
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98 <citation type="doi">10.1038/nbt.2676</citation>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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99 <yield/>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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100 </citations>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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101 </xml>
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102
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103 </macros>