Mercurial > repos > iuc > ampvis2_alpha_diversity

annotate alpha_diversity.xml @ 2:21b85417e4c3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:41:01 +0000
parents b54f72135f58
children 289d6299bd2e
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1 <tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description></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="header"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 #set m='"' + '", "'.join(str($measure).split(",")) + '"'
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13 library(ampvis2, quietly = TRUE)
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14 d <- readRDS("$data")
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15 a <- amp_alphadiv(d,
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16 measure = c($m),
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17 richness = $richness
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18 @RAREFY_TOKEN@
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19 )
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20 write.table(a, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE)
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21 ]]></configfile>
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22 </configfiles>
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23 <inputs>
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24 <expand macro="rds_input_macro"/>
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25 <param argument="measure" type="select" multiple="true" optional="false" label="Alpha-diversity measure(s) to be included">
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26 <option value="observed" selected="true">observed</option>
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27 <option value="shannon" selected="true">shannon</option>
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28 <option value="simpson" selected="true">simpson</option>
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29 <option value="invsimpson" selected="true">invsimpson</option>
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30 </param>
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31 <param argument="richness" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Calculate sample richness estimates" help="Chao1 and ACE"/>
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32 <expand macro="rarefy_macro" help="before calculating alpha diversity and/or richnes"/>
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33 </inputs>
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34 <outputs>
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35 <data name="alphadiv" format="tabular"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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40 <output name="alphadiv">
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41 <assert_contents>
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42 <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;Reads&#9;ObservedOTUs&#9;Shannon&#9;Simpson&#9;invSimpson"/>
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43 <has_text text="16SAMP-536&#9;"/>
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44 <has_text text="&#9;Aalborg West&#9;"/>
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45 <has_n_lines n="68"/>
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46 <has_n_columns n="10"/>
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47 </assert_contents>
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48 </output>
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49 </test>
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50 <test>
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51 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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52 <param name="measure" value="observed,shannon"/>
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53 <param name="richness" value="true"/>
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54 <param name="rarefy" value="500"/>
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55 <output name="alphadiv">
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56 <assert_contents>
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57 <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;RawReads&#9;Reads&#9;ObservedOTUs&#9;Shannon&#9;Chao1&#9;ACE"/>
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58 <has_text text="16SAMP-536&#9;"/>
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59 <has_text text="&#9;Aalborg West&#9;"/>
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60 <has_n_lines n="68"/>
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61 <has_n_columns n="11"/>
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62 <has_text text="&#9;500&#9;"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68
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69 What it does
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70 ============
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71
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72 Calculate alpha-diversity indices for each sample and combines with the metadata.
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73
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74 The Galaxy tool calls the `amp_alpha_diversity
2
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75 <https://kasperskytte.github.io/ampvis2/reference/amp_alphadiv.html>`_ function
0
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76 of the ampvis2 package.
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77
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78 Usage
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79 =====
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80
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81 The alpha-diversity indices are calculated per sample using the vegan function `diversity <https://rdrr.io/pkg/vegan/man/diversity.html>`_,
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82 where the read abundances are first rarefied using `rrarefy <https://rdrr.io/pkg/vegan/man/rarefy.html>`_ by the size of the rarefy argument.
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83 Refer to the vegan documentation for details about the different indices and how they are
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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84 calculated.
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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85
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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86
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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87 Input
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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88 =====
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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89
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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90 @HELP_RDS_INPUT@
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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91
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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92 Output
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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93 ======
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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94
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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95 A tabular dataset containing the chosen alpha-diversity measures per sample.
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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96
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97 ]]></help>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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98 <expand macro="citations">
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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99 <citation type="doi">10.1371/journal.pcbi.1003531</citation>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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100 </expand>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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101 </tool>