Mercurial > repos > iuc > mothur_mimarks_attributes

annotate mimarks.attributes.xml @ 5:247d1bacbefe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:24:37 -0400
parents 371a522fc3a1
children 5106f3ce22a3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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371a522fc3a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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1 <tool profile="16.07" id="mothur_mimarks_attributes" name="Mimarks.attributes" 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>
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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
371a522fc3a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$biosample_in' biosample_in.dat &&
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15 echo 'mimarks.attributes(
371a522fc3a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 xml=biosample_in.dat
371a522fc3a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 )'
371a522fc3a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 | sed 's/ //g' ## mothur trips over whitespace
371a522fc3a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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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"/>
1a45cc9dc7ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 <!-- TODO: add package type options (currently none described in documentation apart from default)
1a45cc9dc7ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 <param name="package" type="select" label="package - select the mimarks package you would like to use">
1a45cc9dc7ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option>
1a45cc9dc7ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 </param>-->
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371a522fc3a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 <expand macro="param-savelog"/>
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29 </inputs>
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30 <outputs>
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31 <expand macro="logfile-output"/>
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32 <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${tool.name} on ${on_string}: source"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="biosample_in" value="biosample.xml" ftype="xml"/>
1a45cc9dc7ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/>
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371a522fc3a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 <param name="savelog" value="true"/>
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1a45cc9dc7ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <expand macro="logfile-test"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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44 @MOTHUR_OVERVIEW@
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46 **Command Documentation**
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47
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371a522fc3a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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48 The mimarks.attributes_ command reads `BioSample Attributes`_ xml and generates source for get.mimarkspackage_ command.
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50 .. _mimarks.attributes: https://www.mothur.org/w/index.php?search=mimarks.attributes
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51 .. _BioSample Attributes: https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/
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52 .. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage
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54 ]]></help>
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55 <expand macro="citations"/>
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56 </tool>