Mercurial > repos > iuc > mothur_lefse

annotate lefse.xml @ 2:8c39f704d21a 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 21:58:54 -0400
parents 1c04b0449893
children 772e6a5b7358
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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>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
1c04b0449893 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"/>
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9 <command><![CDATA[
2
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@
0
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11
2
8c39f704d21a 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
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$otu' shared.dat &&
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$design' design.dat &&
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15
2
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16 echo 'lefse(
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 shared=shared.dat,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 design=design.dat,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 #if $class:
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 class=$class,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #end if
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 #if $sclass:
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23 subclass=$sclass,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 #end if
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #if $label:
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 label=${ str($label).replace(",","-") },
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 #end if
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 #if $sets:
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 sets=${ str($sets).replace(",","-") },
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 #end if
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 aalpha=$aalpha,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 walpha=$walpha,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 lda=$lda,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 iters=$iters,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 fboots=$fboots,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 strict=$strict,
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37 minc=$minc,
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38 wilc=$wilc,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 curv=$curv,
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 norm=$norm
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 )'
8c39f704d21a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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42 | sed 's/ //g' ## mothur trips over whitespace
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43 | mothur
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44 | tee mothur.out.log
0
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 ]]></command>
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46 <inputs>
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47 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
1c04b0449893 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 <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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49 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
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50 <expand macro="labeloptions"/>
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51 </param>
2
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52 <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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53 <!-- TODO: update galaxy datatypes to set metadata for design files, then can switch to a select box
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54 <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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55 help="The set names are separated by dashes. The defualt is all sets in designfile">
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56 <options>
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57 <filter type="data_meta" ref="design" key="sets"/>
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58 </options>
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59 </param>
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60 -->
0
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61 <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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62 <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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63 <param name="aalpha" type="float" value="0.05" label="aalpha - alpha value for the Krukal Wallis Anova test" help=""/>
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64 <param name="walpha" type="float" value="0.05" label="walpha - alpha value for the Wilcoxon test" help=""/>
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65 <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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66 <param name="iters" type="integer" value="30" min="0" label="iters - number of bootstrap iteration for LDA" help=""/>
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67 <param name="fboots" type="float" value="0.67" label="fboots - set the subsampling fraction value for each bootstrap iteration" help=""/>
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68 <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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69 <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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70 <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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71 <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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72 <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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73 <expand macro="param-savelog"/>
0
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74 </inputs>
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75 <outputs>
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76 <expand macro="logfile-output"/>
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77 <data name="summary" format="tabular" from_work_dir="shared.*lefse_summary" label="${tool.name} on ${on_string}: summary"/>
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78 </outputs>
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79 <tests>
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80 <test><!-- test with defaults -->
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81 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
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82 <param name="design" value="mouse.design"/>
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83 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
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84 <param name="savelog" value="true"/>
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85 <expand macro="logfile-test"/>
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86 </test>
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87 <test><!-- test with label and class select -->
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88 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
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89 <param name="design" value="mouse.design"/>
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90 <param name="label" value="1"/>
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91 <param name="class" value="dpw"/>
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92 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
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93 <param name="savelog" value="true"/>
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94 <expand macro="logfile-test"/>
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95 </test>
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96 <test><!-- test with sets -->
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97 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
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98 <param name="design" value="mouse.design"/>
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99 <param name="sets" value="8,142"/>
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100 <param name="label" value="1"/>
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101 <param name="class" value="dpw"/>
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102 <output name="summary" md5="64ebfb48d8c3e0bcd993a7ea8aa60e62" ftype="tabular"/>
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103 <param name="savelog" value="true"/>
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104 <expand macro="logfile-test"/>
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 @MOTHUR_OVERVIEW@
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109
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110
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111 **Command Documentation**
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112
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113
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114 .. _lefse: https://www.mothur.org/wiki/Lefse
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115 ]]></help>
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116 <expand macro="citations"/>
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117 </tool>