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comparison macros.xml @ 1:f5878b9842c7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
author iuc
date Wed, 30 Aug 2017 04:47:26 -0400
parents 98d48a808424
children 750b705e701f
comparison
equal deleted inserted replaced
0:98d48a808424 1:f5878b9842c7
1 <macros> 1 <macros>
2 <token name="@WRAPPER_VERSION@">1.0.1</token> 2 <token name="@WRAPPER_VERSION@">1.1.1</token>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.0.1">picrust</requirement> 5 <requirement type="package" version="1.1.1">picrust</requirement>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 8
9 <xml name="version_command"> 9 <xml name="version_command">
10 <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command> 10 <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>
29 </conditional> 29 </conditional>
30 </xml> 30 </xml>
31 31
32 <xml name="biom_format_select"> 32 <xml name="biom_format_select">
33 <param name="output_type" type="select" label="Format of the output BIOM file"> 33 <param name="output_type" type="select" label="Format of the output BIOM file">
34 <option value="json" selected="true">JSON</option> 34 <option value="hdf5" selected="true">HDF5</option>
35 <option value="hdf5">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>
36 <option value="tsv">Classic (tab-separated text)</option> 43 <option value="tsv">Classic (tab-separated text)</option>
37 </param> 44 </param>
38 </xml> 45 </xml>
39 46
40 <xml name="biom_output"> 47 <xml name="biom_output">
41 <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs"> 48 <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
42 <change_format> 49 <change_format>
43 <when input="output_type" value="json" format="json"/> 50 <when input="output_type" value="json" format="biom1"/>
44 <when input="output_type" value="tsv" format="tabular"/> 51 <when input="output_type" value="tsv" format="tabular"/>
45 <when input="output_type" value="hdf5" format="hdf5"/> 52 <when input="output_type" value="hdf5" format="h5"/>
46 </change_format> 53 </change_format>
47 </data> 54 </data>
48 </xml> 55 </xml>
49 56
50 <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[ 57 <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
51 #if $output_type == "json": 58 #if $output_type == "hdf5":
52 && biom convert -i tempbiom -o '$out_biom' --to-json 59 && mv tempbiom '$out_biom'
53 #elif $output_type == "tsv": 60 #elif $output_type == "tsv":
54 && biom convert -i tempbiom -o '$out_biom' --to-tsv 61 && biom convert -i tempbiom -o '$out_biom' --to-tsv
55 #else 62 #else:
56 && biom convert -i tempbiom -o '$out_biom' --to-hdf5 63 && biom convert -i tempbiom -o '$out_biom' --to-json
57 #end if 64 #end if
58 ]]></token> 65 ]]></token>
59 66
60 <token name="@PICRUST_OVERVIEW@"> 67 <token name="@PICRUST_OVERVIEW@">
61 <![CDATA[ 68 <![CDATA[
67 marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative 74 marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
68 bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs. 75 bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.
69 76
70 For more information please visit: 77 For more information please visit:
71 78
72 - Picrust Documentation: https://picrust.github.io/picrust/ 79 - PICRUSt Documentation: https://picrust.github.io/picrust/
73 - Picrust GitHub: http://picrust.github.com/ 80 - PICRUSt GitHub: http://picrust.github.com/
74 - Picrust Support: https://groups.google.com/d/forum/picrust-users 81 - PICRUSt Support: https://groups.google.com/d/forum/picrust-users
75 82
76 **Reference Data** 83 **Reference Data**
77 84
78 Precalculated files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/ 85 Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/
79 86
80 ]]> 87 ]]>
81 </token> 88 </token>
82 89
83 <xml name="citations"> 90 <xml name="citations">