Mercurial > repos > iuc > mothur_phylotype
comparison phylotype.xml @ 0:61cfe849101c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:59:15 -0400 |
parents | |
children | f750e0c2c7f9 |
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-1:000000000000 | 0:61cfe849101c |
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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($label).replace(",","-") } | |
26 #end if | |
27 )' | |
28 | sed 's/ //g' ## mothur trips over whitespace | |
29 | mothur | |
30 | tee mothur.out.log | |
31 ]]></command> | |
32 <inputs> | |
33 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/> | |
34 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/> | |
35 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true"> | |
36 <option value="0">0</option> | |
37 <option value="1">1</option> | |
38 <option value="2">2</option> | |
39 <option value="3">3</option> | |
40 <option value="4">4</option> | |
41 <option value="5">5</option> | |
42 <option value="6">6</option> | |
43 <option value="7">7</option> | |
44 <option value="8">8</option> | |
45 <option value="9">9</option> | |
46 <option value="10">10</option> | |
47 </param> | |
48 <param name="cutoff" type="integer" value="" min="0" max="50" optional="true" label="cutoff - Truncate the taxonomy at depth (Ignored if < 0)"/> | |
49 </inputs> | |
50 <outputs> | |
51 <expand macro="logfile-output"/> | |
52 <data name="rabund" format="mothur.rabund" from_work_dir="taxonomy*.rabund" label="${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> |