Mercurial > repos > iuc > mothur_cluster_classic

annotate cluster.classic.xml @ 0:872cb4f6fa0b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:04:17 -0400
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children 085625ddf82c
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0
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_cluster_classic" name="Cluster.classic" version="@WRAPPER_VERSION@.0">
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Assign sequences to OTUs (Dotur implementation)</description>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$dist" dist.dat &&
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$name" name.dat &&
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ln -s "$count" count.dat &&
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16
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17 echo 'cluster.classic(
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 phylip=dist.dat,
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19 #if $name:
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 name=name.dat,
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21 #end if
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22 #if $count:
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23 count=count.dat,
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 #end if
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 method=$method,
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 #if $cutoff:
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 cutoff=$cutoff,
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 #end if
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29 hard=$hard,
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 precision=$precision,
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31 sim=$sim
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32 )'
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 | sed 's/ //g' ## mothur trips over whitespace
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 | mothur
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35 | tee mothur.out.log
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 ]]></command>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <inputs>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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41 <param name="method" type="select" label="method - Select a Clustering Method" help="">
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42 <option value="furthest">Furthest neighbor</option>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 <option value="nearest">Nearest neighbor</option>
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44 <option value="average" selected="true">Average neighbor</option>
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45 <option value="weighted">Weighted</option>
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46 </param>
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47 <param name="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold" 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="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
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49 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
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50 <option value="10">.1</option>
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51 <option value="100" selected="true">.01</option>
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52 <option value="1000">.001</option>
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53 <option value="10000">.0001</option>
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54 <option value="100000">.00001</option>
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55 <option value="1000000">.000001</option>
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56 </param>
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57 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
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58 </inputs>
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59 <outputs>
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60 <expand macro="logfile-output"/>
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61 <data name="rabund" format="mothur.rabund" from_work_dir="dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
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62 <data name="sabund" format="mothur.sabund" from_work_dir="dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
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63 <data name="otulist" format="mothur.list" from_work_dir="dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
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64 </outputs>
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65 <tests>
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66 <test><!-- test with phylip and default params-->
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67 <param name="dist" value="env.dist"/>
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68 <output name="rabund" md5="b7f4b5ee46b2c4f5221d487e24dca9db" ftype="mothur.rabund"/>
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69 <output name="sabund" md5="ac2df77e39a106fa65fae3d2132bc4ea" ftype="mothur.sabund"/>
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70 <output name="otulist" ftype="mothur.list">
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71 <assert_contents>
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72 <has_text text="group"/>
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73 <has_text text="unique"/>
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74 <has_line_matching expression="^label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24$"/>
872cb4f6fa0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 </assert_contents>
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76 </output>
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77 <expand macro="logfile-test"/>
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78 </test>
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79 </tests>
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80 <help>
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81 <![CDATA[
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82
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83 @MOTHUR_OVERVIEW@
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84
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85 **Command Documentation**
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86
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87 The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit).
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88
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89 .. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic
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90
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91 ]]>
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92 </help>
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93 <expand macro="citations"/>
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94 </tool>