Mercurial > repos > iuc > mothur_get_otulist

comparison get.otulist.xml @ 0:2e6fb8f23d5e 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 05:52:08 -0400
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-1:000000000000 0:2e6fb8f23d5e
1 <tool profile="16.07" id="mothur_get_otulist" name="Get.otulist" version="@WRAPPER_VERSION@.0">
2 <description>Get otus for each distance in a otu list</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 'get.otulist(
16 list=otu.dat,
17 #if $label:
18 label=${ str($label).replace(",","-") },
19 #end if
20 sort=$sort
21 )'
22 | sed 's/ //g' ## mothur trips over whitespace
23 | mothur
24 | tee mothur.out.log
25 ]]></command>
26 <inputs>
27 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
28 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected.">
29 <expand macro="labeloptions"/>
30 </param>
31 <param name="sort" type="select" label="sort - select the output format" help="If otu is selected the output will be otu number followed by the list of names in that otu. If name is selected the output will be a sequence name followed by its otu number">
32 <option value="otu" selected="true">otu</option>
33 <option value="name">name</option>
34 </param>
35 </inputs>
36 <outputs>
37 <expand macro="logfile-output"/>
38 <collection name="otufiles" type="list" label="${tool.name} on ${on_string}: OTUs per label">
39 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu" format="mothur.list"/>
40 </collection>
41 </outputs>
42 <tests>
43 <test>
44 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
45 <output_collection name="otufiles" count="36">
46 <element name="0.22" md5="9dfa8c449a45d66e7ae6b30b34a821cb" ftype="mothur.list"/>
47 </output_collection>
48 <expand macro="logfile-test"/>
49 </test>
50 <test>
51 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
52 <param name="label" value="0.03,0.38,0.41,0.45"/>
53 <output_collection name="otufiles" count="4">
54 <element name="0.41" md5="b40486b3739a6d5b86459dc17a23c253" ftype="mothur.list"/>
55 </output_collection>
56 <expand macro="logfile-test"/>
57 </test>
58 </tests>
59 <help>
60 <![CDATA[
61
62 @MOTHUR_OVERVIEW@
63
64
65 **Command Documentation**
66
67 The get.otulist_ command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU.
68
69 .. _get.otulist: https://www.mothur.org/wiki/Get.otulist
70
71 v.1.20.0: Updated to Mothur 1.33
72 ]]>
73 </help>
74 <expand macro="citations"/>
75 </tool>