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comparison normalize.shared.xml @ 0:042fba3006e9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:57:49 -0400
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-1:000000000000 0:042fba3006e9
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat &&
14
15 echo 'normalize.shared(
16 #if $otu.is_of_type("mothur.relabund"):
17 relabund=otu.dat
18 #elif $otu.is_of_type("mothur.shared"):
19 shared=otu.dat,
20 makerelabund=$makerelabund
21 #end if
22 #if $label:
23 ,label=${ str($label).replace(",","-") }
24 #end if
25 #if $groups:
26 ,groups=${ str($groups).replace(",","-") }
27 #end if
28 #if $method:
29 ,method=${ str($method).replace(",","-") }
30 #end if
31 )'
32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur
34 | tee mothur.out.log
35 ]]></command>
36 <inputs>
37 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
38 <param name="label" type="select" multiple="true" label="label - OTU Labels">
39 <expand macro="labeloptions"/>
40 </param>
41 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
42 <options>
43 <filter type="data_meta" ref="otu" key="groups"/>
44 </options>
45 </param>
46 <param name="method" type="select" label="method - Normalization method">
47 <option value="totalgroup" selected="true">Total Group</option>
48 <option value="zscore">Z Score</option>
49 </param>
50 <param name="makerelabund" type="boolean" truevalue="true" falsevalue="false" checked="false" label="makerelabund - convert a shared file to a relabund file before you normalize"/>
51 </inputs>
52 <outputs>
53 <expand macro="logfile-output"/>
54 <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: norm.shared files collection">
55 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>
56 </collection>
57 </outputs>
58 <tests>
59 <test><!-- test default settings -->
60 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
61 <output_collection name="sharedfiles" count="36">
62 <element name="0.26.norm" md5="73ad51ce74e5b3efbc1d9ec8ed6e1c07" ftype="mothur.shared"/>
63 </output_collection>
64 <expand macro="logfile-test"/>
65 </test>
66 <test><!-- test default settings -->
67 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
68 <param name="label" value="0.03,0.05,0.22,0.26"/>
69 <param name="groups" value="forest,pasture"/>
70 <param name="method" value="zscore"/>
71 <output_collection name="sharedfiles" count="4">
72 <element name="0.26.norm" md5="1204d65c732fd880585180e956610026" ftype="mothur.shared"/>
73 </output_collection>
74 <expand macro="logfile-test"/>
75 </test>
76 </tests>
77 <help>
78 <![CDATA[
79
80 @MOTHUR_OVERVIEW@
81
82 **Command Documentation**
83
84 The normalize.shared_ command normalizes the number of sequences per group to a specified level. The input is a shared_ or relabund_ file.
85
86 .. _shared: https://www.mothur.org/wiki/Shared_file
87 .. _relabund: https://www.mothur.org/wiki/Get.relabund
88 .. _normalize.shared: https://www.mothur.org/wiki/Normalize.shared
89 ]]>
90 </help>
91 <expand macro="citations"/>
92 </tool>