Mercurial > repos > iuc > mothur_mimarks_attributes

annotate mimarks.attributes.xml @ 1:7de47b23e7f9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:42:46 -0400
parents 0d6d694d9d18
children b708a003d02e
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1 <tool profile="16.07" id="mothur_mimarks_attributes" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0">
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 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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15 echo 'mimarks.attributes(
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 xml=biosample_in.dat
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17 )'
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18 | sed 's/ //g' ## mothur trips over whitespace
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19 | mothur
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20 | tee mothur.out.log
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21 ]]></command>
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22 <inputs>
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23 <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 <!-- 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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25 <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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26 <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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27 </param>-->
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 </inputs>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 <outputs>
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30 <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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31 <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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32 </outputs>
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33 <tests>
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34 <test>
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35 <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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36 <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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37 <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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38 </test>
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39 </tests>
0d6d694d9d18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <help>
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41 <![CDATA[
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42
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43 @MOTHUR_OVERVIEW@
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44
1
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45 **Command Documentation**
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46
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47 The mimarks.attributes_ Reads bioSample Attributes xml and generates source for make.sra command.
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48
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49 ]]>
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50 </help>
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51 <citations>
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52 <citation type="doi">10.1128/AEM.01541-09</citation>
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53 </citations>
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54 </tool>