Mercurial > repos > iuc > mothur_rarefaction_single

annotate rarefaction.single.xml @ 14:943c69757b9c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 22:48:02 +0000
parents 8ccd6a1a7ff8
children
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4e53dc9d5e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_rarefaction_single" name="Rarefaction.single" version="@WRAPPER_VERSION@.0">
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2 <description>Generate intra-sample rarefaction curves for OTUs</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[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
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13 ln -s '$otu' otu.dat &&
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14
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15 echo 'rarefaction.single(
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16 #if $otu.is_of_type("mothur.rabund"):
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17 rabund=otu.dat,
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18 #elif $otu.is_of_type("mothur.sabund"):
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19 sabund=otu.dat,
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20 #elif $otu.is_of_type("mothur.shared"):
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21 shared=otu.dat,
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22 #elif $otu.is_of_type("mothur.list"):
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23 list=otu.dat,
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24 #end if
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25 #if $label:
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26 label=${ str($label).replace(",","-") },
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27 #end if
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28 calc=${ str($calc).replace(",","-") },
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29 abund=$abund,
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30 iters=$iters,
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31 freq=$freq,
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32 processors='\${GALAXY_SLOTS:-8}'
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33 )'
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34 | sed 's/ //g' ## mothur trips over whitespace
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35 | mothur
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36 | tee mothur.out.log
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37
5
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38 ## rename output from sobs calculator to be consistent with others
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39 #if 'sobs' in str($calc).split(','):
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40 && mv otu\.*rarefaction otu.r_sobs
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41 #end if
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42 ]]></command>
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43 <inputs>
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44 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
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45 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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46 <expand macro="labeloptions"/>
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47 </param>
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48 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
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49 <option value="ace">ace - Community richness the ACE estimator</option>
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50 <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
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51 <option value="chao">chao - Community richness the Chao1 estimator</option>
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52 <option value="jack">jack - Community richness the jackknife estimator</option>
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53 <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
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54 <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
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55 <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
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56 <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
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57 <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
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58 <option value="coverage">coverage - Community diversity the sampling coverage </option>
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59 <option value="simpson">simpson - Community diversity the Simpson index</option>
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60 <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
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61 <option value="shannon">shannon - Community diversity the Shannon index</option>
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62 <option value="npshannon">npshannon - Community diversity the non-parametric Shannon index</option>
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63 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
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64 </param>
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65 <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
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66 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations"/>
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67 <param name="freq" type="float" value="100" min="0" max="100" label="freq - Reporting frequency" help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/>
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68 <expand macro="param-savelog"/>
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69 </inputs>
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70 <outputs>
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71 <expand macro="logfile-output"/>
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72 <collection name="rarefactioncurves" type="list" label="${tool.name} on ${on_string}: rarefaction curves">
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73 <discover_datasets pattern=".*?(\.groups)?\.r_(?P&lt;designation&gt;.*)" format="tabular"/>
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74 </collection>
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75 </outputs>
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76 <tests>
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77 <test><!-- test with default values -->
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78 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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79 <output_collection name="rarefactioncurves" count="1">
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80 <element name="sobs" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/>
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81 </output_collection>
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82 <param name="savelog" value="true"/>
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83 <expand macro="logfile-test"/>
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84 </test>
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85 <test><!-- test with all calculators and subset of labels -->
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86 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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87 <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,coverage,simpson,invsimpson,shannon,npshannon,nseqs"/>
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88 <param name="label" value="0.03,0.05,0.36,0.55"/>
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89 <output_collection name="rarefactioncurves" count="15">
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90 <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/>
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91 </output_collection>
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92 <param name="savelog" value="true"/>
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93 <expand macro="logfile-test"/>
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94 </test>
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95 </tests>
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96 <help><![CDATA[
0
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97
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98 @MOTHUR_OVERVIEW@
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99
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100 **Command Documentation**
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101
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102 The rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
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103
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104 .. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single
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105
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106 ]]></help>
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107 <expand macro="citations">
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108 <citation type="bibtex"><![CDATA[
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109 @book{magurran2013measuring,
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110 title={Measuring biological diversity},
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111 author={Magurran, Anne E},
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112 year={2013},
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113 publisher={John Wiley \& Sons}
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114 }
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115 ]]></citation>
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116 </expand>
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117 </tool>