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comparison phylotype.xml @ 0:61cfe849101c 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 05:59:15 -0400
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children f750e0c2c7f9
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-1:000000000000 0:61cfe849101c
1 <tool profile="16.07" id="mothur_phylotype" name="Phylotype" version="@WRAPPER_VERSION@.0">
2 <description>Assign sequences to OTUs based on taxonomy</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 "$taxonomy" taxonomy.dat &&
14 ln -s "$name" name.dat &&
15
16 echo 'phylotype(
17 taxonomy=taxonomy.dat
18 #if $cutoff:
19 ,cutoff=$cutoff
20 #end if
21 #if $name:
22 ,name=name.dat
23 #end if
24 #if $label:
25 ,label=${ str($label).replace(",","-") }
26 #end if
27 )'
28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur
30 | tee mothur.out.log
31 ]]></command>
32 <inputs>
33 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/>
34 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/>
35 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true">
36 <option value="0">0</option>
37 <option value="1">1</option>
38 <option value="2">2</option>
39 <option value="3">3</option>
40 <option value="4">4</option>
41 <option value="5">5</option>
42 <option value="6">6</option>
43 <option value="7">7</option>
44 <option value="8">8</option>
45 <option value="9">9</option>
46 <option value="10">10</option>
47 </param>
48 <param name="cutoff" type="integer" value="" min="0" max="50" optional="true" label="cutoff - Truncate the taxonomy at depth (Ignored if &lt; 0)"/>
49 </inputs>
50 <outputs>
51 <expand macro="logfile-output"/>
52 <data name="rabund" format="mothur.rabund" from_work_dir="taxonomy*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
53 <data name="sabund" format="mothur.sabund" from_work_dir="taxonomy*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
54 <data name="otulist" format="mothur.list" from_work_dir="taxonomy*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
55 </outputs>
56 <tests>
57 <test>
58 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
59 <output name="rabund" md5="689fb6fd2fb4cd0740fc8b62d7e05556" ftype="mothur.rabund"/>
60 <output name="sabund" md5="62547e84f1d051a16937715433f3d78a" ftype="mothur.sabund"/>
61 <output name="otulist" md5="c808112d524863bbc973dd721ba18a06" ftype="mothur.list"/>
62 <expand macro="logfile-test"/>
63 </test>
64 <test>
65 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
66 <param name="label" value="1,4,5"/>
67 <param name="cutoff" value="5"/>
68 <output name="rabund" md5="3d2e3821bef6ecd7eaf0ea62e8692154" ftype="mothur.rabund"/>
69 <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/>
70 <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/>
71 <expand macro="logfile-test"/>
72 </test>
73 </tests>
74 <help>
75 <![CDATA[
76
77 @MOTHUR_OVERVIEW@
78
79 **Command Documentation**
80
81 The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
82
83 .. _list: https://www.mothur.org/wiki/List_file
84 .. _rabund: https://www.mothur.org/wiki/Rabund_file
85 .. _sabund: https://www.mothur.org/wiki/Sabund_file
86 .. _phylotype: https://www.mothur.org/wiki/Phylotype
87
88 ]]>
89 </help>
90 <expand macro="citations"/>
91 </tool>