Mercurial > repos > iuc > mothur_lefse

annotate lefse.xml @ 10:d952b95bafe9 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 12:06:41 +0000
parents 772e6a5b7358
children
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1c04b0449893 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_lefse" name="Lefse" version="@WRAPPER_VERSION@.0">
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>description</description>
1c04b0449893 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>
10
d952b95bafe9 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"/>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$otu' shared.dat &&
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$design' design.dat &&
0
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16
2
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17 echo 'lefse(
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 shared=shared.dat,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 design=design.dat,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 #if $class:
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21 class=$class,
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22 #end if
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23 #if $sclass:
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 subclass=$sclass,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #end if
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #if $label:
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27 label=${ str($label).replace(",","-") },
8c39f704d21a 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 #if $sets:
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 sets=${ str($sets).replace(",","-") },
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 #end if
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 aalpha=$aalpha,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 walpha=$walpha,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 lda=$lda,
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35 iters=$iters,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 fboots=$fboots,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 strict=$strict,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 minc=$minc,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 wilc=$wilc,
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40 curv=$curv,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 norm=$norm
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42 )'
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43 | sed 's/ //g' ## mothur trips over whitespace
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44 | mothur
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45 | tee mothur.out.log
0
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46 ]]></command>
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47 <inputs>
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48 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
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49 <param name="design" type="data" format="mothur.design" label="design - assigns groups to sets" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
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50 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
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51 <expand macro="labeloptions"/>
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52 </param>
2
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53 <param name="sets" type="text" label="sets - Which of the sets in your design file you would like to analyze?" help="separate sets by dashes or commas, e.g. set1,set2 or set1-set2-set3"/>
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54 <!-- TODO: update galaxy datatypes to set metadata for design files, then can switch to a select box
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55 <param argument="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze."
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56 help="The set names are separated by dashes. The defualt is all sets in designfile">
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57 <options>
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58 <filter type="data_meta" ref="design" key="sets"/>
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59 </options>
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60 </param>
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61 -->
0
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62 <param name="class" type="text" optional="true" value="" label="class -indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided first category is used"/>
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63 <param name="sclass" type="text" optional="true" value="" label="subclass - indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided second category is used"/>
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64 <param name="aalpha" type="float" value="0.05" label="aalpha - alpha value for the Krukal Wallis Anova test" help=""/>
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65 <param name="walpha" type="float" value="0.05" label="walpha - alpha value for the Wilcoxon test" help=""/>
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66 <param name="lda" type="float" value="2.0" label="lda - threshold on the absolute value of the logarithmic LDA score" help=""/>
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67 <param name="iters" type="integer" value="30" min="0" label="iters - number of bootstrap iteration for LDA" help=""/>
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68 <param name="fboots" type="float" value="0.67" label="fboots - set the subsampling fraction value for each bootstrap iteration" help=""/>
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69 <param name="strict" type="integer" value="0" min="0" max="2" label="strict - set the multiple testing correction options" help=" 0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for independent comparison"/>
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70 <param name="minc" type="integer" value="10" min="0" label="minc - minimum number of samples per subclass for performing wilcoxon test" help=""/>
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71 <param name="wilc" type="boolean" truevalue="T" falsevalue="F" checked="true" label="wilc - indicate whether to perform the Wilcoxon test" help=""/>
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72 <param name="curv" type="boolean" truevalue="T" falsevalue="F" checked="false" label="curv - whether perform the wilcoxon testing the Curtis's approach (beta)" help=""/>
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73 <param name="norm" type="boolean" truevalue="T" falsevalue="F" checked="true" label="norm - multiply relative abundances by 1000000" help="Recommended when very low values are present"/>
2
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74 <expand macro="param-savelog"/>
0
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75 </inputs>
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76 <outputs>
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77 <expand macro="logfile-output"/>
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78 <data name="summary" format="tabular" from_work_dir="shared.*lefse_summary" label="${tool.name} on ${on_string}: summary"/>
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79 </outputs>
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80 <tests>
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81 <test><!-- test with defaults -->
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82 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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83 <param name="design" value="mouse.design"/>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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84 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
2
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85 <param name="savelog" value="true"/>
0
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 <expand macro="logfile-test"/>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 </test>
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88 <test><!-- test with label and class select -->
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 <param name="design" value="mouse.design"/>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 <param name="label" value="1"/>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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92 <param name="class" value="dpw"/>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
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94 <param name="savelog" value="true"/>
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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95 <expand macro="logfile-test"/>
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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96 </test>
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97 <test><!-- test with sets -->
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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98 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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99 <param name="design" value="mouse.design"/>
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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100 <param name="sets" value="8,142"/>
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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101 <param name="label" value="1"/>
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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102 <param name="class" value="dpw"/>
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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103 <output name="summary" md5="64ebfb48d8c3e0bcd993a7ea8aa60e62" ftype="tabular"/>
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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104 <param name="savelog" value="true"/>
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105 <expand macro="logfile-test"/>
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106 </test>
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107 </tests>
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108 <help><![CDATA[
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109 @MOTHUR_OVERVIEW@
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110
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111
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112 **Command Documentation**
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113
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114
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115 .. _lefse: https://www.mothur.org/wiki/Lefse
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116 ]]></help>
5
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117 <expand macro="citations">
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118 <citation type="doi">10.1186/gb-2011-12-6-r60</citation>
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119 </expand>
0
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120 </tool>