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comparison get.label.xml @ 0:8dd86660e447 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:32:11 -0400
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1 <tool profile="16.07" id="mothur_get_label" name="Get.label" version="@WRAPPER_VERSION@.0">
2 <description>label names from list, sabund, or rabund file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11
12 echo 'get.label(
13 #if $otu.is_of_type("mothur.rabund"):
14 rabund=otu.dat
15 #elif $otu.is_of_type("mothur.sabund"):
16 sabund=otu.dat
17 #else
18 list=otu.dat
19 #end if
20 )'
21 | sed 's/ //g' ## mothur trips over whitespace
22 | mothur &&
23
24 ## parse relevant output from logfile to file
25 cat mothur.*.logfile
26 | head -n-3
27 | sed '1,29d'
28 > "$labels_list"
29 ]]></command>
30 <inputs>
31 <param name="otu" type="data" format="mothur.list,motur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/>
32 </inputs>
33 <outputs>
34 <expand macro="logfile-output"/>
35 <data name="labels_list" format="tabular" label="${tool.name} on ${on_string}: labels"/>
36 </outputs>
37 <tests>
38 <test><!-- test with sabund -->
39 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
40 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
41 <expand macro="logfile-test"/>
42 </test>
43 <test><!-- test with rabund -->
44 <param name="otu" value="amazon.an.rabund2" ftype="mothur.rabund"/>
45 <output name="labels_list" md5="0c3fab5bdfa8588c7244048ddd4eac3c" ftype="tabular"/>
46 <expand macro="logfile-test"/>
47 </test>
48 <test><!-- test with list -->
49 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
50 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
51 <expand macro="logfile-test"/>
52 </test>
53 </tests>
54 <help>
55 <![CDATA[
56
57 @MOTHUR_OVERVIEW@
58
59 **Command Documenation**
60
61 The get.label_ command generate principle components plot data.
62
63 .. _get.label: http://www.mothur.org/wiki/Get.label
64
65 v.1.20.0: Updated to Mothur 1.33
66 ]]>
67 </help>
68 <expand macro="citations"/>
69 </tool>