annotate macros.xml @ 0:6273e2721fa3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
author iuc
date Thu, 08 Dec 2016 06:28:17 -0500
parents
children 76c040c8b9fc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
1 <macros>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
2 <token name="@WRAPPER_VERSION@">1.0.1</token>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
3 <xml name="requirements">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
4 <requirements>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
5 <requirement type="package" version="1.0.1">picrust</requirement>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
6 </requirements>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
7 </xml>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
8
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
9 <xml name="version_command">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
10 <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
11 </xml>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
12
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
13 <xml name="otu-reference-precalculated">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
14 <!-- selection of "gg" picrust parameter reference data file -->
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
15 <conditional name="gg">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
16 <param name="source" type="select" label="Select precalculated file from" help="">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
17 <option value="ref">Cached Reference</option>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
18 <option value="hist">History</option>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
19 </param>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
20 <when value="ref">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
21 <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
22 <options from_data_table="picrust_precalculated"/>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
23 </param>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
24 </when>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
25 <when value="hist">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
26 <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis"
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
27 help="files may be downloaded from PICRUSt website (see tool help below)" />
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
28 </when>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
29 </conditional>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
30 </xml>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
31
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
32 <xml name="biom_format_select">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
33 <param name="output_type" type="select" label="Format of the output BIOM file">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
34 <option value="json" selected="true">JSON</option>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
35 <option value="hdf5">HDF5</option>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
36 <option value="tsv">Classic (tab-separated text)</option>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
37 </param>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
38 </xml>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
39
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
40 <xml name="biom_output">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
41 <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
42 <change_format>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
43 <when input="output_type" value="json" format="json"/>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
44 <when input="output_type" value="tsv" format="tabular"/>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
45 <when input="output_type" value="hdf5" format="hdf5"/>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
46 </change_format>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
47 </data>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
48 </xml>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
49
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
50 <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
51 #if $output_type == "json":
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
52 && biom convert -i tempbiom -o '$out_biom' --to-json
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
53 #elif $output_type == "tsv":
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
54 && biom convert -i tempbiom -o '$out_biom' --to-tsv
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
55 #else
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
56 && biom convert -i tempbiom -o '$out_biom' --to-hdf5
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
57 #end if
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
58 ]]></token>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
59
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
60 <token name="@PICRUST_OVERVIEW@">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
61 <![CDATA[
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
62 **PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States**
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
63
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
64 The PICRUSt project aims to support prediction of the unobserved character states in a community of
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
65 organisms from phylogenetic information about the organisms in that community. The primary application
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
66 is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
67 marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
68 bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
69
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
70 For more information please visit:
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
71
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
72 - Picrust Documentation: https://picrust.github.io/picrust/
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
73 - Picrust GitHub: http://picrust.github.com/
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
74 - Picrust Support: https://groups.google.com/d/forum/picrust-users
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
75
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
76 **Reference Data**
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
77
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
78 Precalculated files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
79
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
80 ]]>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
81 </token>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
82
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
83 <xml name="citations">
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
84 <citations>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
85 <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
iuc
parents:
diff changeset
86 <yield/>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
87 </citations>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
88 </xml>
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
89
6273e2721fa3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
iuc
parents:
diff changeset
90 </macros>