Mercurial > repos > iuc > mothur_get_label

comparison get.label.xml @ 3:44c7d48a6819 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 22:02:42 -0400
parents d8409b4a2aec
children 7f479eedd900
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2:d8409b4a2aec 3:44c7d48a6819
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 > '$labels_list'
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <param name="otu" type="data" format="mothur.list,mothur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/> 35 <param name="otu" type="data" format="mothur.list,mothur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/>
36 <expand macro="param-savelog"/>
36 </inputs> 37 </inputs>
37 <outputs> 38 <outputs>
38 <expand macro="logfile-output"/> 39 <expand macro="logfile-output"/>
39 <data name="labels_list" format="tabular" label="${tool.name} on ${on_string}: labels"/> 40 <data name="labels_list" format="tabular" label="${tool.name} on ${on_string}: labels"/>
40 </outputs> 41 </outputs>
41 <tests> 42 <tests>
42 <test><!-- test with sabund --> 43 <test><!-- test with sabund -->
43 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> 44 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
44 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/> 45 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
46 <param name="savelog" value="true"/>
45 <expand macro="logfile-test"/> 47 <expand macro="logfile-test"/>
46 </test> 48 </test>
47 <test><!-- test with rabund --> 49 <test><!-- test with rabund -->
48 <param name="otu" value="amazon.an.rabund2" ftype="mothur.rabund"/> 50 <param name="otu" value="amazon.an.rabund2" ftype="mothur.rabund"/>
49 <output name="labels_list" md5="0c3fab5bdfa8588c7244048ddd4eac3c" ftype="tabular"/> 51 <output name="labels_list" md5="0c3fab5bdfa8588c7244048ddd4eac3c" ftype="tabular"/>
52 <param name="savelog" value="true"/>
50 <expand macro="logfile-test"/> 53 <expand macro="logfile-test"/>
51 </test> 54 </test>
52 <test><!-- test with list --> 55 <test><!-- test with list -->
53 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 56 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
54 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/> 57 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
58 <param name="savelog" value="true"/>
55 <expand macro="logfile-test"/> 59 <expand macro="logfile-test"/>
56 </test> 60 </test>
57 </tests> 61 </tests>
58 <help> 62 <help><![CDATA[
59 <![CDATA[
60 63
61 @MOTHUR_OVERVIEW@ 64 @MOTHUR_OVERVIEW@
62 65
63 **Command Documentation** 66 **Command Documentation**
64 67
65 The get.label_ command generate principle components plot data. 68 The get.label_ command generate principle components plot data.
66 69
67 .. _get.label: https://www.mothur.org/wiki/Get.label 70 .. _get.label: https://www.mothur.org/wiki/Get.label
68 71
69 v.1.20.0: Updated to Mothur 1.33 72 v.1.20.0: Updated to Mothur 1.33
70 ]]> 73
71 </help> 74 ]]></help>
72 <expand macro="citations"/> 75 <expand macro="citations"/>
73 </tool> 76 </tool>