Mercurial > repos > iuc > mothur_get_label

comparison get.label.xml @ 4:2db0ca9ce0d9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:26:19 -0500
parents 6d082f402534
children 5d5df87a14d5
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3:6d082f402534 4:2db0ca9ce0d9
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 "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 14
15 echo 'get.label( 15 echo 'get.label(
16 #if $otu.is_of_type("mothur.rabund"): 16 #if $otu.is_of_type("mothur.rabund"):
17 rabund=otu.dat 17 rabund=otu.dat
18 #elif $otu.is_of_type("mothur.sabund"): 18 #elif $otu.is_of_type("mothur.sabund"):
19 sabund=otu.dat 19 sabund=otu.dat
20 #else 20 #else
21 list=otu.dat 21 list=otu.dat
22 #end if 22 #end if
23 )' 23 )'
24 | sed 's/ //g' ## mothur trips over whitespace 24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur 25 | mothur
26 | tee mothur.out.log && 26 | tee mothur.out.log &&
27 27
28 ## parse relevant output from logfile to file 28 ## parse relevant output from logfile to file
29 cat mothur.*.logfile 29 cat mothur.*.logfile
30 | head -n-3 30 | head -n-3
31 | sed '1,29d' 31 | sed '1,30d'
32 > "$labels_list" 32 > '$labels_list'
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <param name="otu" type="data" format="mothur.list,mothur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/> 35 <param name="otu" type="data" format="mothur.list,mothur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/>
36 </inputs> 36 </inputs>
37 <outputs> 37 <outputs>
53 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 53 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
54 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/> 54 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
55 <expand macro="logfile-test"/> 55 <expand macro="logfile-test"/>
56 </test> 56 </test>
57 </tests> 57 </tests>
58 <help> 58 <help><![CDATA[
59 <![CDATA[
60 59
61 @MOTHUR_OVERVIEW@ 60 @MOTHUR_OVERVIEW@
62 61
63 **Command Documentation** 62 **Command Documentation**
64 63
65 The get.label_ command generate principle components plot data. 64 The get.label_ command generate principle components plot data.
66 65
67 .. _get.label: https://www.mothur.org/wiki/Get.label 66 .. _get.label: https://www.mothur.org/wiki/Get.label
68 67
69 v.1.20.0: Updated to Mothur 1.33 68 v.1.20.0: Updated to Mothur 1.33
70 ]]> 69
71 </help> 70 ]]></help>
72 <expand macro="citations"/> 71 <expand macro="citations"/>
73 </tool> 72 </tool>