Mercurial > repos > iuc > mothur_get_group

annotate get.group.xml @ 6:081d0fbf9751 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author iuc
date Mon, 02 Dec 2019 06:06:09 -0500
parents 0aa74388e4fc
children d26de4fffac5
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200b088eaf93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_get_group" name="Get.group" version="@WRAPPER_VERSION@.0">
200b088eaf93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>group names from shared or from list and group</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
200b088eaf93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$shared' shared.dat &&
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14
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15 echo 'get.group(
0aa74388e4fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 shared=shared.dat
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17 )'
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18 | sed 's/ //g' ## mothur trips over whitespace
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19 | mothur
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20 | tee mothur.out.log &&
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21
2
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22 ## parse relevant output from logfile to file
0aa74388e4fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 cat mothur.*.logfile
0aa74388e4fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 | head -n-6
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25 | sed '1,30d'
0aa74388e4fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 > "$bootgroups"
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27 ]]></command>
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28 <inputs>
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29 <param argument="shared" type="data" format="mothur.shared" label="shared - OTU Shared"/>
0aa74388e4fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 <expand macro="param-savelog"/>
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31 </inputs>
200b088eaf93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 <outputs>
200b088eaf93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <expand macro="logfile-output"/>
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34 <data name="bootgroups" format="mothur.groups" label="${tool.name} on ${on_string}: bootGroups"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="shared" value="amazon.an.shared" ftype="mothur.shared"/>
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39 <output name="bootgroups" md5="93b9f7ead2ee04f056e77b5bb94ea0dd"/>
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40 <param name="savelog" value="true"/>
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41 <expand macro="logfile-test"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45
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46 @MOTHUR_OVERVIEW@
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47
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48 **Command Documentation**
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49
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50 The get.group_ command generate principle components plot data.
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51
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52 .. _get.group: https://www.mothur.org/wiki/Get.group
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53
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54 v.1.20.0: Updated to Mothur 1.33
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56 ]]></help>
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57 <expand macro="citations"/>
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58 </tool>