annotate mothur/tools/mothur/phylotype.xml @ 36:040410b8167e default tip

Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author galaxyuser <galaxy_user@agr.g.ca>
date Mon, 10 Nov 2014 15:40:02 -0500
parents 95d75b35e4d2
children
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95d75b35e4d2 Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
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1 <tool id="mothur_phylotype" name="Phylotype" version="1.20.0">
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2 <description>Assign sequences to OTUs based on taxonomy</description>
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3 <command interpreter="python">
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4 mothur_wrapper.py
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5 --cmd='phylotype'
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist
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7 --outputdir='$logfile.extra_files_path'
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8 --taxonomy=$taxonomy
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9 #if 50 >= int($cutoff.__str__) > 0:
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10 --cutoff=$cutoff
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11 #end if
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12 #if $name.__str__ != "None" and len($name.__str__) > 0:
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13 --name='$name'
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14 #end if
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15 #if $label.__str__ != "None" and len($label.__str__) > 0:
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16 --label='$label'
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17 #end if
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18 </command>
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19 <inputs>
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20 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/>
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21 <param name="name" type="data" format="names" optional="true" label="name - Names reference file for the taxonomy"/>
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22 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true">
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23 <option value="0">0</option>
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24 <option value="1">1</option>
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25 <option value="2">2</option>
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26 <option value="3">3</option>
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27 <option value="4">4</option>
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28 <option value="5">5</option>
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29 <option value="6">6</option>
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30 <option value="7">7</option>
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31 <option value="8">8</option>
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32 <option value="9">9</option>
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33 <option value="10">10</option>
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34 </param>
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35 <param name="cutoff" type="integer" value="-1" label="cutoff - Truncate the taxonomy at depth (Ignored if &lt; 0)"/>
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36 </inputs>
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37 <outputs>
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38 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
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39 <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
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40 <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
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41 <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
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42 </outputs>
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43 <requirements>
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44 <requirement type="package" version="1.33">mothur</requirement>
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45 </requirements>
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46 <tests>
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47 </tests>
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48 <help>
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49 **Mothur Overview**
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50
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51 Mothur_, initiated by Dr. Patrick Schloss and his software development team
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52 in the Department of Microbiology and Immunology at The University of Michigan,
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53 provides bioinformatics for the microbial ecology community.
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54
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55 .. _Mothur: http://www.mothur.org/wiki/Main_Page
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56
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57 **Command Documenation**
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58
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59 The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
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61 .. _list: http://www.mothur.org/wiki/List_file
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62 .. _rabund: http://www.mothur.org/wiki/Rabund_file
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63 .. _sabund: http://www.mothur.org/wiki/Sabund_file
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64 .. _phylotype: http://www.mothur.org/wiki/Phylotype
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66
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67 </help>
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68 </tool>