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comparison get.label.xml @ 0:6c4190485910 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 05:02:01 -0400
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children d8409b4a2aec
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-1:000000000000 0:6c4190485910
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="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.label(
16 #if $otu.is_of_type("mothur.rabund"):
17 rabund=otu.dat
18 #elif $otu.is_of_type("mothur.sabund"):
19 sabund=otu.dat
20 #else
21 list=otu.dat
22 #end if
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 | tee mothur.out.log &&
27
28 ## parse relevant output from logfile to file
29 cat mothur.*.logfile
30 | head -n-3
31 | sed '1,29d'
32 > "$labels_list"
33 ]]></command>
34 <inputs>
35 <param name="otu" type="data" format="mothur.list,motur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/>
36 </inputs>
37 <outputs>
38 <expand macro="logfile-output"/>
39 <data name="labels_list" format="tabular" label="${tool.name} on ${on_string}: labels"/>
40 </outputs>
41 <tests>
42 <test><!-- test with sabund -->
43 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
44 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
45 <expand macro="logfile-test"/>
46 </test>
47 <test><!-- test with rabund -->
48 <param name="otu" value="amazon.an.rabund2" ftype="mothur.rabund"/>
49 <output name="labels_list" md5="0c3fab5bdfa8588c7244048ddd4eac3c" ftype="tabular"/>
50 <expand macro="logfile-test"/>
51 </test>
52 <test><!-- test with list -->
53 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
54 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
55 <expand macro="logfile-test"/>
56 </test>
57 </tests>
58 <help>
59 <![CDATA[
60
61 @MOTHUR_OVERVIEW@
62
63 **Command Documentation**
64
65 The get.label_ command generate principle components plot data.
66
67 .. _get.label: https://www.mothur.org/wiki/Get.label
68
69 v.1.20.0: Updated to Mothur 1.33
70 ]]>
71 </help>
72 <expand macro="citations"/>
73 </tool>