Mercurial > repos > iuc > mothur_metastats

annotate metastats.xml @ 10:feb408da0143 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:50:12 +0000
parents 10866c1f8e06
children
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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>
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4 <import>macros.xml</import>
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5 </macros>
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feb408da0143 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
2
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11 @SHELL_OPTIONS@
0
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12
2
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13 ## 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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14 ln -s '$otu' otu.dat &&
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15 ln -s '$design' design.dat &&
0
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16
2
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17 echo 'metastats(
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 shared=otu.dat,
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19 design=design.dat,
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20 #if $label:
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21 label=${ str($label).replace(",","-") },
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 #end if
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23 #if $groups:
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24 groups=${ str($groups).replace(",","-") },
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #end if
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26 #if $sets:
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27 sets=${ str($sets).replace(",","-") },
ce49a6e10308 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 #end if
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29 iters=$iters,
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30 threshold=$threshold,
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31 processors='\${GALAXY_SLOTS:-8}'
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32 )'
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33 | sed 's/ //g' ## mothur trips over whitespace
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34 | mothur
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35 | tee mothur.out.log
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36 ]]></command>
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37 <inputs>
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38 <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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39 <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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40 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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41 <expand macro="labeloptions"/>
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42 </param>
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43 <param name="sets" type="select" label="sets - group sets to analyze" multiple="true">
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44 <options>
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45 <filter type="data_meta" ref="design" key="groups"/>
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46 </options>
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47 </param>
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48 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
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49 <options>
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50 <filter type="data_meta" ref="otu" key="groups"/>
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51 </options>
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52 </param>
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53 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations (default 1000)"/>
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54 <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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55 <expand macro="param-savelog"/>
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56 </inputs>
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57 <outputs>
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58 <expand macro="logfile-output"/>
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59 <collection name="metastats" type="list" label="${tool.name} on ${on_string}: metastats">
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60 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.metastats" format="txt"/>
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61 </collection>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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66 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
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67 <output_collection name="metastats" count="36">
2
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68 <element name="0.23.tardis_dalek" ftype="txt">
0
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69 <assert_contents>
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70 <has_text text="group1"/>
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71 <has_text text="group2"/>
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72 <has_text text="OTU"/>
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73 <has_text text="variance"/>
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74 <has_text text="1000 permutations"/>
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75 </assert_contents>
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76 </element>
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77 </output_collection>
2
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78 <param name="savelog" value="true"/>
0
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79 <expand macro="logfile-test"/>
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80 </test>
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81 <test>
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82 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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83 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
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84 <param name="iters" value="42"/>
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85 <param name="threshold" value="0.1"/>
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86 <param name="label" value="0.03,0.05,0.23"/>
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87 <param name="groups" value="forest,pasture"/>
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88 <param name="sets" value="tardis,dalek"/>
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89 <output_collection name="metastats" count="3">
2
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90 <element name="0.23.tardis_dalek" ftype="txt">
0
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91 <assert_contents>
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92 <has_text text="group1"/>
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93 <has_text text="group2"/>
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94 <has_text text="OTU"/>
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95 <has_text text="variance"/>
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96 <has_text text="42 permutations"/>
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97 </assert_contents>
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98 </element>
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99 </output_collection>
2
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100 <param name="savelog" value="true"/>
0
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101 <expand macro="logfile-test"/>
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102 </test>
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103 </tests>
2
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104 <help><![CDATA[
0
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105
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106 @MOTHUR_OVERVIEW@
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107
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108 **Command Documentation**
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109
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110 The metastats_ command generate principle components plot data.
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111
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112 .. _metastats: https://www.mothur.org/wiki/Metastats
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113
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114 v.1.21.0: Updated to mothur 1.33
2
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115
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116 ]]></help>
5
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117 <expand macro="citations">
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118 <citation type="doi">10.1371/journal.pcbi.1000352</citation>
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119 </expand>
0
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120 </tool>