Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/cluster.classic.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
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1 <tool id="mothur_cluster_classic" name="Cluster.classic" version="1.88.0"> |
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2 <description>Assign sequences to OTUs (Dotur implementation)</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='cluster.classic' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist |
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7 --outputdir='$logfile.extra_files_path' |
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8 --phylip=$dist |
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9 #if $name.__str__ != "None" and len($name.__str__) > 0: |
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10 --name=$name |
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11 #end if |
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12 #if $count.__str__ != "None" and len($count.__str__) > 0: |
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13 --count=$count |
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14 #end if |
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15 #if len($method.__str__) > 0: |
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16 --method=$method |
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17 #end if |
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18 #if float($cutoff.__str__) > 0.0: |
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19 --cutoff=$cutoff |
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20 #end if |
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21 $hard |
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22 #if len($precision.__str__) > 0: |
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23 --precision=$precision |
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24 #end if |
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25 $sim |
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26 </command> |
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27 <inputs> |
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28 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
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29 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
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30 <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> |
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31 <!-- ? conditional - to hide complexity --> |
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32 <param name="method" type="select" label="method - Select a Clustering Method" help=""> |
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33 <option value="furthest">Furthest neighbor</option> |
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34 <option value="nearest">Nearest neighbor</option> |
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35 <option value="average" selected="true">Average neighbor</option> |
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36 <option value="weighted">Weighted</option> |
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37 </param> |
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38 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" |
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39 help="Ignore pairwise distances larger than this, a common value would be 0.10"/> |
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40 <param name="hard" type="boolean" checked="true" truevalue="--hard=true" falsevalue="--hard=false" label="hard - Use hard cutoff instead of rounding" |
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41 help=""/> |
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42 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" |
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43 help="Set higher precision for longer genome scale sequence lengths"> |
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44 <option value="10">.1</option> |
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45 <option value="100" selected="true">.01</option> |
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46 <option value="1000">.001</option> |
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47 <option value="10000">.0001</option> |
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48 <option value="100000">.00001</option> |
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49 <option value="1000000">.000001</option> |
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50 </param> |
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51 <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" |
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52 help=""/> |
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53 </inputs> |
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54 <outputs> |
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55 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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56 <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> |
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57 <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> |
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58 <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> |
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59 </outputs> |
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60 <requirements> |
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61 <requirement type="package" version="1.33">mothur</requirement> |
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62 </requirements> |
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63 <tests> |
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64 </tests> |
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65 <help> |
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66 **Mothur Overview** |
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67 |
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68 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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69 in the Department of Microbiology and Immunology at The University of Michigan, |
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70 provides bioinformatics for the microbial ecology community. |
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71 |
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72 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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73 |
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74 **Command Documenation** |
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75 |
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76 The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit). |
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77 |
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78 .. _cluster.classic: http://www.mothur.org/wiki/Cluster.classic |
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79 |
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80 |
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81 </help> |
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82 </tool> |