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comparison mimarks.attributes.xml @ 0:1a45cc9dc7ee 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 05:30:43 -0400
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children 371a522fc3a1
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-1:000000000000 0:1a45cc9dc7ee
1 <tool profile="16.07" id="mothur_mimarks_attributes" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0">
2 <description>Reads bioSample Attributes xml and generates source for get.mimarkspackage command</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 "$biosample_in" biosample_in.dat &&
14
15 echo 'mimarks.attributes(
16 xml=biosample_in.dat
17 )'
18 | sed 's/ //g' ## mothur trips over whitespace
19 | mothur
20 | tee mothur.out.log
21 ]]></command>
22 <inputs>
23 <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/>
24 <!-- TODO: add package type options (currently none described in documentation apart from default)
25 <param name="package" type="select" label="package - select the mimarks package you would like to use">
26 <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option>
27 </param>-->
28 </inputs>
29 <outputs>
30 <expand macro="logfile-output"/>
31 <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${tool.name} on ${on_string}: source"/>
32 </outputs>
33 <tests>
34 <test>
35 <param name="biosample_in" value="biosample.xml" ftype="xml"/>
36 <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/>
37 <expand macro="logfile-test"/>
38 </test>
39 </tests>
40 <help>
41 <![CDATA[
42
43 @MOTHUR_OVERVIEW@
44
45 **Command Documentation**
46
47 The mimarks.attributes_ Reads bioSample Attributes xml and generates source for make.sra command.
48
49 ]]>
50 </help>
51 <citations>
52 <citation type="doi">10.1128/AEM.01541-09</citation>
53 </citations>
54 </tool>