Mercurial > repos > iuc > picrust_normalize_by_copy_number

comparison normalize_by_copy_number.xml @ 1:76c040c8b9fc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
author iuc
date Wed, 30 Aug 2017 04:49:31 -0400
parents
children 2e62e32d4f33
comparison
equal deleted inserted replaced
0:6273e2721fa3 1:76c040c8b9fc
1 <tool id="picrust_normalize_by_copy_number" name="Normalize" version="@WRAPPER_VERSION@.0">
2 <description>the relative abundance of each OTU by the predicted number of 16S copies</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 normalize_by_copy_number.py
10 -i '$input_data'
11 -o tempbiom
12 -c '$gg.precalc'
13
14 @OUTPUT_CONVERSION_COMMANDS@
15 ]]></command>
16 <inputs>
17 <param name="input_data" type="data" format="biom1,h5" label="Input file" help="biom file"/>
18 <expand macro="otu-reference-precalculated"/>
19 <expand macro="biom_format_select"/>
20 </inputs>
21 <outputs>
22 <expand macro="biom_output"/>
23 </outputs>
24 <tests>
25 <test> <!-- test with biom input -->
26 <param name="input_data" value="closed_picked_otus.biom"/>
27 <param name="source" value="hist"/>
28 <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
29 <param name="output_type" value="json"/>
30 <output name="out_biom" ftype="biom1">
31 <assert_contents>
32 <has_text text="Biological Observation Matrix"/>
33 <has_text text="generated_by"/>
34 </assert_contents>
35 </output>
36 </test>
37 <test> <!-- test with QIIME input and classic output -->
38 <param name="input_data" value="closed_picked_otus.tab"/>
39 <param name="source" value="hist"/>
40 <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
41 <param name="output_type" value="tsv"/>
42 <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/>
43 </test>
44 </tests>
45 <help>
46 <![CDATA[
47 @PICRUST_OVERVIEW@
48
49 **Command Documenation**
50
51 This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU.
52
53 Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_.
54 A sample file can be downloaded here_
55
56 Make sure that you specify an appropriate 16S database for this command (usually 16S 13_5).
57
58 .. _guide: http://picrust.github.com/picrust/methods/constructing_reference_otus.html
59 .. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab
60 ]]>
61 </help>
62 <expand macro="citations"/>
63 </tool>