annotate mothur/tools/mothur/hcluster.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:35:35 -0400
parents 3202a38e44d9
children e990ac8a0f58
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fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_hcluster" name="Hcluster" version="1.16.0">
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2 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
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3 <command interpreter="python">
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4 mothur_wrapper.py
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5 --cmd='hcluster'
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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 #if $matrix.format == "column":
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9 --column=$matrix.dist
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10 --name=$matrix.name
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11 #elif $matrix.format == "phylip":
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12 --phylip=$matrix.dist
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13 #if $matrix.name.__str__ != "None" and len($matrix.name.__str__) > 0:
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14 --name=$matrix.name
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15 #end if
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16 #end if
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17 #if len($method.__str__) > 0:
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18 --method=$method
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19 #end if
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20 #if float($cutoff.__str__) > 0.0:
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21 --READ_cutoff=$cutoff
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22 #end if
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23 #if len($precision.__str__) > 0:
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24 --READ_precision=$precision
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25 #end if
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26 $hard
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27 $sorted
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28 $showabund
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29 </command>
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30 <inputs>
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31 <conditional name="matrix">
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32 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
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33 <option value="column">Pairwise Column Matrix</option>
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34 <option value="phylip">Phylip Distance Matrix</option>
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35 </param>
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36 <when value="column">
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37 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
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38 <param name="name" type="data" format="names" label="name - Names"/>
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39 </when>
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40 <when value="phylip">
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41 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
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42 <param name="name" type="data" format="names" optional="true" label="name - Names"/>
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43 </when>
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44 </conditional>
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45 <!-- ? conditional - to hide complexity -->
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46 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0"
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47 help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
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48 <param name="hard" type="boolean" checked="false" truevalue="--hard=true" falsevalue="" label="hard - Use hard cutoff instead of rounding"
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49 help=""/>
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50 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
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51 help="Set higher precision for longer genome scale sequence lengths">
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52 <option value="10">.1</option>
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53 <option value="100" selected="true">.01</option>
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54 <option value="1000">.001</option>
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55 <option value="10000">.0001</option>
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56 <option value="100000">.00001</option>
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57 <option value="1000000">.000001</option>
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58 </param>
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59
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60 <param name="method" type="select" label="method - Select a Clustering Method" help="">
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61 <option value="furthest" selected="true">Furthest neighbor</option>
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62 <option value="nearest">Nearest neighbor</option>
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63 <option value="average">Average neighbor</option>
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64 <option value="weighted">Weighted</option>
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65 </param>
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66 <param name="sorted" type="boolean" checked="false" truevalue="--sorted=true" falsevalue="" label="sorted - The input matrix is already sorted"
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67 help=""/>
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68 <param name="showabund" type="boolean" checked="true" truevalue="" falsevalue="--showabund=false" label="showabund - Verbose ouput"
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69 help=""/>
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70
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71 </inputs>
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72 <outputs>
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73 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
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74 <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
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75 <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
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76 <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
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77 </outputs>
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78 <requirements>
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79 <requirement type="binary">mothur</requirement>
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80 </requirements>
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81 <tests>
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82 </tests>
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83 <help>
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84 **Mothur Overview**
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85
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86 Mothur_, initiated by Dr. Patrick Schloss and his software development team
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87 in the Department of Microbiology and Immunology at The University of Michigan,
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88 provides bioinformatics for the microbial ecology community.
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89
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90 .. _Mothur: http://www.mothur.org/wiki/Main_Page
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91
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92 **Command Documenation**
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93
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94 The cluster_ command assign sequences to OTUs (Operational Taxonomy Unit).
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95
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96 .. _cluster: http://www.mothur.org/wiki/Cluster
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97
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98
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99 </help>
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100 </tool>