Mercurial > repos > iuc > mothur_cluster_classic

annotate cluster.classic.xml @ 7:14e978a6ffdf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"
author iuc
date Thu, 05 Nov 2020 23:46:38 +0000
parents 6ba59950d95c
children 6e6b8dd3b770
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1 <tool profile="16.07" id="mothur_cluster_classic" name="Cluster.classic" version="@WRAPPER_VERSION@.0">
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2 <description>Assign sequences to OTUs (Dotur implementation)</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 '$dist' dist.dat &&
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14 ln -s '$name' name.dat &&
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15 ln -s '$count' count.dat &&
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16
2
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17 echo 'cluster.classic(
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18 phylip=dist.dat,
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19 #if $name:
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20 name=name.dat,
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21 #end if
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22 #if $count:
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23 count=count.dat,
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24 #end if
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25 method=$method,
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26 #if $cutoff:
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27 cutoff=$cutoff,
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28 #end if
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29 precision=$precision,
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30 sim=$sim
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31 )'
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32 | sed 's/ //g' ## mothur trips over whitespace
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33 | mothur
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34 | tee mothur.out.log
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35 ]]></command>
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36 <inputs>
2
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37 <param argument="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"
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38 help="format must be mothur.lower.dist or mothur.square.dist"/>
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39 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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40 <param argument="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 argument="method" type="select" label="method - Select a Clustering Method" help="">
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42 <option value="furthest">Furthest neighbor</option>
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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>
2
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47 <param argument="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold"
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48 help="Ignore pairwise distances larger than this. Default for methods opti,agc,dgc is 0.03, default for the other methods is 0.15"/>
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49 <param argument="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
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50 help="Set higher precision for longer genome scale sequence lengths">
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51 <option value="10">.1</option>
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52 <option value="100" selected="true">.01</option>
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53 <option value="1000">.001</option>
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54 <option value="10000">.0001</option>
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55 <option value="100000">.00001</option>
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56 <option value="1000000">.000001</option>
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57 </param>
2
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58 <param argument="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
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59 <expand macro="param-savelog"/>
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60 </inputs>
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61 <outputs>
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62 <expand macro="logfile-output"/>
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63 <data name="rabund" format="mothur.rabund" from_work_dir="dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
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64 <data name="sabund" format="mothur.sabund" from_work_dir="dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
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65 <data name="otulist" format="mothur.list" from_work_dir="dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
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66 </outputs>
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67 <tests>
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68 <test><!-- test with phylip and default params-->
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69 <param name="dist" value="env.dist"/>
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70 <output name="rabund" md5="b7f4b5ee46b2c4f5221d487e24dca9db" ftype="mothur.rabund"/>
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71 <output name="sabund" md5="ac2df77e39a106fa65fae3d2132bc4ea" ftype="mothur.sabund"/>
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72 <output name="otulist" ftype="mothur.list">
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73 <assert_contents>
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74 <has_text text="group"/>
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75 <has_text text="unique"/>
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76 <has_line_matching expression="^label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24$"/>
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77 </assert_contents>
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78 </output>
2
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79 <param name="savelog" value="true"/>
0
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80 <expand macro="logfile-test"/>
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81 </test>
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82 </tests>
2
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83 <help><![CDATA[
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84
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85 @MOTHUR_OVERVIEW@
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86
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87 **Command Documentation**
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88
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89 The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit).
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90
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91 .. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic
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92
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93 ]]></help>
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94 <expand macro="citations">
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95 <citation type="doi">10.1128/AEM.02810-10</citation>
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96 <citation type="doi">10.1128/AEM.71.3.1501-1506.2005</citation>
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97 </expand>
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98 </tool>