Mercurial > repos > iuc > mothur_list_otulabels

comparison list.otulabels.xml @ 0:e86c535cf4d1 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 05:50:07 -0400
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children 88e8819fb923
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-1:000000000000 0:e86c535cf4d1
1 <tool profile="16.07" id="mothur_list_otulabels" name="List.otulabels" version="@WRAPPER_VERSION@.0">
2 <description>Lists otu labels from shared or relabund file</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 'list.otulabels(
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 #else
21 list=otu.dat
22 #end if
23 #if $label:
24 ,label=${ str($label).replace(",","-") }
25 #end if
26 #if $groups:
27 ,groups=${ str($groups).replace(",","-") }
28 #end if
29 )'
30 | sed 's/ //g' ## mothur trips over whitespace
31 | mothur
32 | tee mothur.out.log
33 ]]></command>
34 <inputs>
35 <param name="otu" type="data" format="mothur.shared,mothur.relabund,mothur.list" label="list or shared or relabund - OTU List or Shared or Relabund"/>
36 <param name="label" type="select" multiple="true" label="label - OTU Labels">
37 <expand macro="labeloptions"/>
38 </param>
39 <param name="groups" type="select" multiple="true" label="groups - Pairwise comparision groups">
40 <options>
41 <filter type="data_meta" ref="otu" key="groups"/>
42 </options>
43 </param>
44 </inputs>
45 <outputs>
46 <expand macro="logfile-output"/>
47 <collection name="otulabels" type="list" label="${tool.name} on ${on_string}: otulabels">
48 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otulabels" format="mothur.otulabels"/>
49 </collection>
50 </outputs>
51 <tests>
52 <test>
53 <param name="infile" value="otulist"/>
54 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
55 <output_collection name="otulabels" count="36">
56 <element name="unique" md5="c901cebfbc87559f1667546111408a22" ftype="mothur.otulabels"/>
57 <element name="0.55" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.otulabels"/>
58 </output_collection>
59 <expand macro="logfile-test"/>
60 </test>
61 <test><!-- test with group select -->
62 <param name="infile" value="otulist"/>
63 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
64 <param name="groups" value="forest"/>
65 <output_collection name="otulabels" count="36">
66 <element name="unique" md5="8a4d85496fdcfdf99337129989350e7e" ftype="mothur.otulabels"/>
67 </output_collection>
68 <expand macro="logfile-test"/>
69 </test>
70 </tests>
71 <help>
72 <![CDATA[
73
74 @MOTHUR_OVERVIEW@
75
76 **Command Documentation**
77
78 The list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otulabels_ or remove.otulabels_ commands.
79
80 .. _list.otulabels: https://www.mothur.org/wiki/List.otulabels
81 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
82 .. _otu.association: https://www.mothur.org/wiki/Otu.association
83 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
84 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels
85 .. _shared: https://www.mothur.org/wiki/Shared_file
86 .. _relabund: https://www.mothur.org/wiki/Get.relabund
87
88 v.1.27.0: Updated to mothur 1.33, added list file for otu
89 ]]>
90 </help>
91 <expand macro="citations"/>
92 </tool>