Mercurial > repos > iuc > mothur_get_group

comparison get.group.xml @ 2:0aa74388e4fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:08:52 -0400
parents 200b088eaf93
children d26de4fffac5
comparison
equal deleted inserted replaced
1:57b51d6db607 2:0aa74388e4fc
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$shared' shared.dat &&
14 14
15 echo 'get.group( 15 echo 'get.group(
16 shared=otu.dat 16 shared=shared.dat
17 )' 17 )'
18 | sed 's/ //g' ## mothur trips over whitespace 18 | sed 's/ //g' ## mothur trips over whitespace
19 | mothur 19 | mothur
20 | tee mothur.out.log && 20 | tee mothur.out.log &&
21 21
22 ## parse relevant output from logfile to file 22 ## parse relevant output from logfile to file
23 cat mothur.*.logfile 23 cat mothur.*.logfile
24 | head -n-6 24 | head -n-6
25 | sed '1,29d' 25 | sed '1,30d'
26 > "$bootgroups" 26 > "$bootgroups"
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 29 <param argument="shared" type="data" format="mothur.shared" label="shared - OTU Shared"/>
30 <expand macro="param-savelog"/>
30 </inputs> 31 </inputs>
31 <outputs> 32 <outputs>
32 <expand macro="logfile-output"/> 33 <expand macro="logfile-output"/>
33 <data name="bootgroups" format="mothur.groups" label="${tool.name} on ${on_string}: bootGroups"/> 34 <data name="bootgroups" format="mothur.groups" label="${tool.name} on ${on_string}: bootGroups"/>
34 </outputs> 35 </outputs>
35 <tests> 36 <tests>
36 <test> 37 <test>
37 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 38 <param name="shared" value="amazon.an.shared" ftype="mothur.shared"/>
38 <output name="bootgroups" md5="93b9f7ead2ee04f056e77b5bb94ea0dd"/> 39 <output name="bootgroups" md5="93b9f7ead2ee04f056e77b5bb94ea0dd"/>
40 <param name="savelog" value="true"/>
39 <expand macro="logfile-test"/> 41 <expand macro="logfile-test"/>
40 </test> 42 </test>
41 </tests> 43 </tests>
42 <help> 44 <help><![CDATA[
43 <![CDATA[
44 45
45 @MOTHUR_OVERVIEW@ 46 @MOTHUR_OVERVIEW@
46 47
47 **Command Documentation** 48 **Command Documentation**
48 49
49 The get.group_ command generate principle components plot data. 50 The get.group_ command generate principle components plot data.
50 51
51 .. _get.group: https://www.mothur.org/wiki/Get.group 52 .. _get.group: https://www.mothur.org/wiki/Get.group
52 53
53 v.1.20.0: Updated to Mothur 1.33 54 v.1.20.0: Updated to Mothur 1.33
54 ]]> 55
55 </help> 56 ]]></help>
56 <expand macro="citations"/> 57 <expand macro="citations"/>
57 </tool> 58 </tool>