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annotate make.design.xml @ 0:78dcf76823de 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 16:37:34 -0400
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78dcf76823de 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_make_design" name="Make Design" version="@WRAPPER_VERSION@.0">
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2 <description>Assign groups to Sets</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"/>
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 #for $grouping in $groupings:
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10 #set grp_str = $grouping.groups.__str__
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11 #if grp_str:
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 #for $grp in grp_str.split(','):
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 echo -e "$grp\t$grouping.name" >> $design;
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #end for
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15 #end if
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #end for
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17 ]]></command>
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18 <inputs>
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19 <param name="source" type="data" format="mothur.shared,mothur.groups" label="Source containing groups"/>
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20 <repeat name="groupings" title="Grouping">
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 <param name="name" type="text" label="Name for a new combined grouping"/>
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 <options>
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24 <filter type="data_meta" ref="source" key="groups"/>
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 </options>
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26 </param>
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27 </repeat>
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 </inputs>
78dcf76823de 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 <data name="design" format="mothur.design" label="${tool.name} on ${on_string}: design"/>
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31 </outputs>
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32 <tests>
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33 <test>
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <param name="source" value="amazon.mothur.shared" ftype="mothur.shared"/>
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <repeat name="groupings">
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36 <param name="name" value="tardis"/>
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37 <param name="groups" value="forest,pasture"/>
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38 </repeat>
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39 <repeat name="groupings">
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40 <param name="name" value="dalek"/>
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <param name="groups" value="pasture"/>
78dcf76823de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 </repeat>
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43 <output name="design" file="toymothur.design" ftype="mothur.design"/>
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44 </test>
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45 </tests>
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46 <help>
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47 <![CDATA[
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48
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49 @MOTHUR_OVERVIEW@
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50
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51 **Command Documenation**
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52
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53 Make Design creates a design file for use in mothur commands: merge.groups_, indicator_, and metastats_.
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54 A design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.
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55
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56 .. _merge.groups: http://www.mothur.org/wiki/Merge.groups
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57 .. _indicator: http://www.mothur.org/wiki/Indicator
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58 .. _metastats: http://www.mothur.org/wiki/Metastats
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59 ]]>
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60 </help>
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61 <expand macro="citations"/>
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62 </tool>