Mercurial > repos > iuc > mothur_otu_hierarchy

annotate otu.hierarchy.xml @ 8:98abd0047263 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
author iuc
date Tue, 08 Dec 2020 13:39:16 +0000
parents 058e6e36f6e5
children 2e82b56377d8
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1 <tool profile="16.07" id="mothur_otu_hierarchy" name="Otu.hierarchy" version="@WRAPPER_VERSION@.0">
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2 <description>Relate OTUs at different distances</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[
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 '$otu' otu.dat &&
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15 echo 'otu.hierarchy(
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16 list=otu.dat,
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17 label=$label1-$label2,
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18 output=$output
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19 )'
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20 | sed 's/ //g' ## mothur trips over whitespace
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21 | mothur
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22 | tee mothur.out.log
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23 ]]></command>
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24 <inputs>
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25 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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26 <param name="label1" type="select" label="label - OTU Label 1">
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27 <expand macro="labeloptions"/>
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28 </param>
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29 <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1">
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30 <expand macro="labeloptions"/>
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31 </param>
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32 <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers">
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33 <option value="name" selected="true">OTU sequence names</option>
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34 <option value="number">OTU numbers</option>
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35 </param>
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36 <expand macro="param-savelog"/>
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37 </inputs>
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38 <outputs>
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39 <expand macro="logfile-output"/>
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40 <data name="hierarchy" format="tabular" from_work_dir="otu*.hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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45 <param name="label1" value="0.05"/>
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46 <param name="label2" value="0.03"/>
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47 <output name="hierarchy" file="amazon.an.0.03.-.0.05.otu.hierarchy" ftype="tabular"/>
2
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48 <param name="savelog" value="true"/>
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49 <expand macro="logfile-test"/>
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50 </test>
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51 </tests>
2
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52 <help><![CDATA[
0
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53
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54 @MOTHUR_OVERVIEW@
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56 **Command Documentation**
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57
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58 The otu.hierarchy_ command relates OTUs from a list_ at different distances.
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59
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60 .. _list: https://www.mothur.org/wiki/List_file
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61 .. _otu.hierarchy: https://www.mothur.org/wiki/Otu.hierarchy
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62
2
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63 ]]></help>
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64 <expand macro="citations"/>
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65 </tool>