Mercurial > repos > iuc > mothur_metastats

annotate metastats.xml @ 2:ce49a6e10308 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:26:03 -0400
parents 7c817f668dac
children 10866c1f8e06
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7c817f668dac 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_metastats" name="Metastats" version="@WRAPPER_VERSION@.0">
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>generate principle components plot data</description>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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"/>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
2
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@
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11
2
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$otu' otu.dat &&
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$design' design.dat &&
0
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15
2
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16 echo 'metastats(
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 shared=otu.dat,
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 design=design.dat,
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 #if $label:
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20 label=${ str($label).replace(",","-") },
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #end if
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 #if $groups:
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 groups=${ str($groups).replace(",","-") },
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 #end if
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #if $sets:
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 sets=${ str($sets).replace(",","-") },
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 #end if
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 iters=$iters,
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 threshold=$threshold,
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 processors='\${GALAXY_SLOTS:-8}'
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 )'
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 | sed 's/ //g' ## mothur trips over whitespace
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 | mothur
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34 | tee mothur.out.log
0
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 ]]></command>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 <inputs>
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37 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <param name="label" type="select" label="label - OTU Labels" multiple="true">
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <expand macro="labeloptions"/>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 </param>
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42 <param name="sets" type="select" label="sets - group sets to analyze" multiple="true">
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 <options>
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44 <filter type="data_meta" ref="design" key="groups"/>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 </options>
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46 </param>
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47 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 <options>
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49 <filter type="data_meta" ref="otu" key="groups"/>
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50 </options>
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51 </param>
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52 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations (default 1000)"/>
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53 <param name="threshold" type="float" value="0.05" min="0" max="1" label="threshold - significance level to reject null hypotheses"/>
2
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54 <expand macro="param-savelog"/>
0
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55 </inputs>
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56 <outputs>
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57 <expand macro="logfile-output"/>
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58 <collection name="metastats" type="list" label="${tool.name} on ${on_string}: metastats">
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59 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.metastats" format="txt"/>
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60 </collection>
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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65 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
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66 <output_collection name="metastats" count="36">
2
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67 <element name="0.23.tardis_dalek" ftype="txt">
0
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68 <assert_contents>
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69 <has_text text="group1"/>
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70 <has_text text="group2"/>
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71 <has_text text="OTU"/>
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72 <has_text text="variance"/>
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73 <has_text text="1000 permutations"/>
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74 </assert_contents>
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75 </element>
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76 </output_collection>
2
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77 <param name="savelog" value="true"/>
0
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78 <expand macro="logfile-test"/>
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79 </test>
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80 <test>
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81 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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82 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
7c817f668dac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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83 <param name="iters" value="42"/>
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84 <param name="threshold" value="0.1"/>
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85 <param name="label" value="0.03,0.05,0.23"/>
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86 <param name="groups" value="forest,pasture"/>
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87 <param name="sets" value="tardis,dalek"/>
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88 <output_collection name="metastats" count="3">
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89 <element name="0.23.tardis_dalek" ftype="txt">
0
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90 <assert_contents>
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91 <has_text text="group1"/>
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92 <has_text text="group2"/>
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93 <has_text text="OTU"/>
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94 <has_text text="variance"/>
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95 <has_text text="42 permutations"/>
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96 </assert_contents>
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97 </element>
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98 </output_collection>
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99 <param name="savelog" value="true"/>
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100 <expand macro="logfile-test"/>
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101 </test>
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102 </tests>
2
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103 <help><![CDATA[
0
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104
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105 @MOTHUR_OVERVIEW@
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106
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107 **Command Documentation**
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108
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109 The metastats_ command generate principle components plot data.
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110
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111 .. _metastats: https://www.mothur.org/wiki/Metastats
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112
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113 v.1.21.0: Updated to mothur 1.33
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114
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115 ]]></help>
0
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116 <expand macro="citations"/>
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117 </tool>