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comparison mimarks.attributes.xml @ 0:0d6d694d9d18 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 16:42:10 -0400
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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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$biosample_in" biosample_in.dat &&
11
12 echo 'mimarks.attributes(
13 xml=biosample_in.dat
14 )'
15 | sed 's/ //g' ## mothur trips over whitespace
16 | mothur
17 ]]></command>
18 <inputs>
19 <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/>
20 <!-- TODO: add package type options (currently none described in documentation apart from default)
21 <param name="package" type="select" label="package - select the mimarks package you would like to use">
22 <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option>
23 </param>-->
24 </inputs>
25 <outputs>
26 <expand macro="logfile-output"/>
27 <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${tool.name} on ${on_string}: source"/>
28 </outputs>
29 <tests>
30 <test>
31 <param name="biosample_in" value="biosample.xml" ftype="xml"/>
32 <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/>
33 <expand macro="logfile-test"/>
34 </test>
35 </tests>
36 <help>
37 <![CDATA[
38
39 @MOTHUR_OVERVIEW@
40
41 **Command Documenation**
42
43 The mimarks.attributes_ Reads bioSample Attributes xml and generates source for get.mimarkspackage command.
44
45 .. _mimarks.attributes: http://www.mothur.org/wiki/Mimarks.attributes
46
47 ]]>
48 </help>
49 <citations>
50 <citation type="doi">10.1128/AEM.01541-09</citation>
51 </citations>
52 </tool>