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comparison macros.xml @ 0:a3b0b2a42460 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
author iuc
date Sat, 20 Jan 2018 03:38:23 -0500
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children 025049cb66eb
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-1:000000000000 0:a3b0b2a42460
1 <macros>
2 <token name="@WRAPPER_VERSION@">1.1.1</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="1.1.1">picrust</requirement>
6 </requirements>
7 </xml>
8
9 <xml name="version_command">
10 <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>
11 </xml>
12
13 <xml name="otu-reference-precalculated">
14 <!-- selection of "gg" picrust parameter reference data file -->
15 <conditional name="gg">
16 <param name="source" type="select" label="Select precalculated file from" help="">
17 <option value="ref">Cached Reference</option>
18 <option value="hist">History</option>
19 </param>
20 <when value="ref">
21 <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis">
22 <options from_data_table="picrust_precalculated"/>
23 </param>
24 </when>
25 <when value="hist">
26 <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis"
27 help="files may be downloaded from PICRUSt website (see tool help below)" />
28 </when>
29 </conditional>
30 </xml>
31
32 <xml name="biom_format_select">
33 <param name="output_type" type="select" label="Format of the output BIOM file">
34 <option value="hdf5" selected="true">HDF5</option>
35 <option value="json">JSON</option>
36 <option value="tsv">Classic (tab-separated text)</option>
37 </param>
38 </xml>
39
40 <xml name="biom_format_select_no_json">
41 <param name="output_type" type="select" label="Format of the output BIOM file">
42 <option value="hdf5" selected="true">HDF5</option>
43 <option value="tsv">Classic (tab-separated text)</option>
44 </param>
45 </xml>
46
47 <xml name="biom_output">
48 <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
49 <change_format>
50 <when input="output_type" value="json" format="biom1"/>
51 <when input="output_type" value="tsv" format="tabular"/>
52 <when input="output_type" value="hdf5" format="h5"/>
53 </change_format>
54 </data>
55 </xml>
56
57 <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
58 #if $output_type == "hdf5":
59 && mv tempbiom '$out_biom'
60 #elif $output_type == "tsv":
61 && biom convert -i tempbiom -o '$out_biom' --to-tsv
62 #else:
63 && biom convert -i tempbiom -o '$out_biom' --to-json
64 #end if
65 ]]></token>
66
67 <token name="@PICRUST_OVERVIEW@">
68 <![CDATA[
69 **PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States**
70
71 The PICRUSt project aims to support prediction of the unobserved character states in a community of
72 organisms from phylogenetic information about the organisms in that community. The primary application
73 is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only
74 marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
75 bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.
76
77 For more information please visit:
78
79 - PICRUSt Documentation: https://picrust.github.io/picrust/
80 - PICRUSt GitHub: http://picrust.github.com/
81 - PICRUSt Support: https://groups.google.com/d/forum/picrust-users
82
83 **Reference Data**
84
85 Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/
86
87 ]]>
88 </token>
89
90 <xml name="citations">
91 <citations>
92 <citation type="doi">10.1038/nbt.2676</citation>
93 <yield/>
94 </citations>
95 </xml>
96
97 </macros>