Mercurial > repos > iuc > mothur_mimarks_attributes

annotate 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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children 7de47b23e7f9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_mimarks_attributes" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0">
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2 <description>Reads bioSample Attributes xml and generates source for get.mimarkspackage command</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
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10 ln -s "$biosample_in" biosample_in.dat &&
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 echo 'mimarks.attributes(
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 xml=biosample_in.dat
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14 )'
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15 | sed 's/ //g' ## mothur trips over whitespace
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 | mothur
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17 ]]></command>
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18 <inputs>
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19 <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/>
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20 <!-- TODO: add package type options (currently none described in documentation apart from default)
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 <param name="package" type="select" label="package - select the mimarks package you would like to use">
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 </param>-->
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24 </inputs>
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25 <outputs>
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26 <expand macro="logfile-output"/>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${tool.name} on ${on_string}: source"/>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 </outputs>
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29 <tests>
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30 <test>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 <param name="biosample_in" value="biosample.xml" ftype="xml"/>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <expand macro="logfile-test"/>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 </test>
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35 </tests>
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36 <help>
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37 <![CDATA[
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38
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39 @MOTHUR_OVERVIEW@
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40
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 **Command Documenation**
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42
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 The mimarks.attributes_ Reads bioSample Attributes xml and generates source for get.mimarkspackage command.
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44
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45 .. _mimarks.attributes: http://www.mothur.org/wiki/Mimarks.attributes
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46
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47 ]]>
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48 </help>
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49 <citations>
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50 <citation type="doi">10.1128/AEM.01541-09</citation>
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51 </citations>
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52 </tool>