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comparison normalize.shared.xml @ 0:ed349f5c32fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:42:45 -0400
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-1:000000000000 0:ed349f5c32fe
1 <tool profile="16.07" id="mothur_normalize_shared" name="Normalize.shared" version="@WRAPPER_VERSION@.0">
2 <description>Normalize the number of sequences per group to a specified level</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 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11
12 echo 'normalize.shared(
13 #if $otu.is_of_type("mothur.relabund"):
14 relabund=otu.dat
15 #elif $otu.is_of_type("mothur.shared"):
16 shared=otu.dat,
17 makerelabund=$makerelabund
18 #end if
19 #if $label:
20 ,label=${ str($label).replace(",","-") }
21 #end if
22 #if $groups:
23 ,groups=${ str($groups).replace(",","-") }
24 #end if
25 #if $method:
26 ,method=${ str($method).replace(",","-") }
27 #end if
28 )'
29 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur
31 ]]></command>
32 <inputs>
33 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
34 <param name="label" type="select" multiple="true" label="label - OTU Labels">
35 <expand macro="labeloptions"/>
36 </param>
37 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
38 <options>
39 <filter type="data_meta" ref="otu" key="groups"/>
40 </options>
41 </param>
42 <param name="method" type="select" label="method - Normalization method">
43 <option value="totalgroup" selected="true">Total Group</option>
44 <option value="zscore">Z Score</option>
45 </param>
46 <param name="makerelabund" type="boolean" truevalue="true" falsevalue="false" checked="false" label="makerelabund - convert a shared file to a relabund file before you normalize"/>
47 </inputs>
48 <outputs>
49 <expand macro="logfile-output"/>
50 <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: norm.shared files collection">
51 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>
52 </collection>
53 </outputs>
54 <tests>
55 <test><!-- test default settings -->
56 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
57 <output_collection name="sharedfiles" count="36">
58 <element name="0.26.norm" md5="73ad51ce74e5b3efbc1d9ec8ed6e1c07" ftype="mothur.shared"/>
59 </output_collection>
60 <expand macro="logfile-test"/>
61 </test>
62 <test><!-- test default settings -->
63 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
64 <param name="label" value="0.03,0.05,0.22,0.26"/>
65 <param name="groups" value="forest,pasture"/>
66 <param name="method" value="zscore"/>
67 <output_collection name="sharedfiles" count="4">
68 <element name="0.26.norm" md5="1204d65c732fd880585180e956610026" ftype="mothur.shared"/>
69 </output_collection>
70 <expand macro="logfile-test"/>
71 </test>
72 </tests>
73 <help>
74 <![CDATA[
75
76 @MOTHUR_OVERVIEW@
77
78 **Command Documenation**
79
80 The normalize.shared_ command normalizes the number of sequences per group to a specified level. The input is a shared_ or relabund_ file.
81
82 .. _shared: http://www.mothur.org/wiki/Shared_file
83 .. _relabund: http://www.mothur.org/wiki/Get.relabund
84 .. _normalize.shared: http://www.mothur.org/wiki/Normalize.shared
85 ]]>
86 </help>
87 <expand macro="citations"/>
88 </tool>