Mercurial > repos > iuc > mothur_get_relabund

comparison get.relabund.xml @ 0:4ad3ea2f8584 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 05:46:09 -0400
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1 <tool profile="16.07" id="mothur_get_relabund" name="Get.relabund" version="@WRAPPER_VERSION@.0">
2 <description>Calculate the relative abundance of each otu</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.relabund(
16 shared=otu.dat,
17 #if $label:
18 label=${ str($label).replace(",","-") },
19 #end if
20 #if $groups:
21 groups=${ str($groups).replace(",","-") },
22 #end if
23 scale=$scale
24 )'
25 | sed 's/ //g' ## mothur trips over whitespace
26 | mothur
27 | tee mothur.out.log
28 ]]></command>
29 <inputs>
30 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared" help="Use Make.shared to create a shared file from a list and a group file"/>
31 <param name="label" type="select" label="label - OTU Labels" multiple="true">
32 <expand macro="labeloptions"/>
33 </param>
34 <param name="groups" type="select" multiple="true" label="groups - Groups to consider">
35 <options>
36 <filter type="data_meta" ref="otu" key="groups"/>
37 </options>
38 </param>
39 <param name="scale" type="select" label="scale - Scale by">
40 <option value="totalgroup" selected="true">Total Groups</option>
41 <option value="totalotu">Total OTUs</option>
42 <option value="averagegroup">Average Groups</option>
43 <option value="averageotu">Average OTUs</option>
44 </param>
45 </inputs>
46 <outputs>
47 <expand macro="logfile-output"/>
48 <data name="relabund" format="mothur.relabund" from_work_dir="otu*.relabund" label="${tool.name} on ${on_string}: relabund"/>
49 </outputs>
50 <tests>
51 <test>
52 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
53 <output name="relabund" file="amazon.an.relabund" ftype="mothur.relabund"/>
54 <expand macro="logfile-test"/>
55 </test>
56 <test>
57 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
58 <param name="label" value="0.03,0.05,0.22"/>
59 <param name="groups" value="forest"/>
60 <output name="relabund" md5="3f91820ebdf2d4c640b7d1489fd67936" ftype="mothur.relabund"/>
61 <expand macro="logfile-test"/>
62 </test>
63 </tests>
64 <help>
65 <![CDATA[
66
67 @MOTHUR_OVERVIEW@
68
69 **Command Documentation**
70
71 The get.relabund_ command calculates the relative abundance of each otu in a sample from a shared_ file. It outputs a .relabund_ file.
72
73 .. _shared: https://www.mothur.org/wiki/Shared_file
74 .. _get.relabund: https://www.mothur.org/wiki/Get.relabund
75
76 v.1.21.0: Updated to Mothur 1.33
77 ]]>
78 </help>
79 <expand macro="citations"/>
80 </tool>