Mercurial > repos > iuc > ampvis2_alpha_diversity

annotate alpha_diversity.xml @ 5:a2f72e76fd90 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 commit e0ad9ce8f508215ec6af69be2682a0faf38415da
author iuc
date Mon, 10 Nov 2025 12:54:09 +0000
parents 647f9058075a
children
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647f9058075a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
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1 <tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
0
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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 '$rscript'
3108287dcf47 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 #set m='"' + '", "'.join(str($measure).split(",")) + '"'
3108287dcf47 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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13 library(ampvis2, quietly = TRUE)
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14
0
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15 d <- readRDS("$data")
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16 table <- amp_alphadiv(d,
647f9058075a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
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17 measure = c($m),
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18 richness = $richness
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19 @RAREFY_TOKEN@,
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20 )
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21 plot <- amp_alphadiv(d,
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22 measure = c($m),
3108287dcf47 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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23 richness = $richness
2
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24 @RAREFY_TOKEN@,
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25 plot = TRUE,
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26 plot_group_by = "$group_by",
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27 plot_scatter = $plot_scatter
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28 )
2
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29 write.table(table, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE)
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30 ggsave("$alphadiv_plot",
647f9058075a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
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31 plot = plot,
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32 device = "$output_options.out_format"
647f9058075a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
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33 #if str($output_options.plot_width) != ''
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34 , width = $output_options.plot_width
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35 #end if
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36 #if str($output_options.plot_height) != ''
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37 , height = $output_options.plot_height
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38 #end if
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39 )
0
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40 ]]></configfile>
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41 </configfiles>
3108287dcf47 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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42 <inputs>
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43 <expand macro="rds_input_macro"/>
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44 <param argument="measure" type="select" multiple="true" optional="false" label="Alpha-diversity measure(s) to be included">
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45 <option value="observed" selected="true">observed</option>
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46 <option value="shannon" selected="true">shannon</option>
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47 <option value="simpson" selected="true">simpson</option>
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48 <option value="invsimpson" selected="true">invsimpson</option>
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49 </param>
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50 <param argument="richness" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Calculate sample richness estimates" help="Chao1 and ACE"/>
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51 <expand macro="rarefy_macro" help="before calculating alpha diversity and/or richnes"/>
2
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52 <param argument="group_by" type="text" label="Group by metadata field (for plotting)" help="Specify the metadata field to group the plot by"/>
647f9058075a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
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53 <param argument="plot_scatter" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scatter plot instead of boxplot?" help="Select to generate a scatter plot instead of a boxplot"/>
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54 <expand macro="out_format_macro"/>
0
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55 </inputs>
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56 <outputs>
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57 <data name="alphadiv" format="tabular"/>
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58 <expand macro="out_macro" name="alphadiv_plot" label=": plot"/>
0
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59 </outputs>
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60 <tests>
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61 <test>
2
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62 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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63 <param name="group_by" value="Plant"/>
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64 <param name="plot_scatter" value="false"/>
0
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65 <output name="alphadiv">
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66 <assert_contents>
1
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67 <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;Reads&#9;uniqueOTUs&#9;Shannon&#9;Simpson&#9;invSimpson"/>
0
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68 <has_text text="16SAMP-536&#9;"/>
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69 <has_text text="&#9;Aalborg West&#9;"/>
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70 <has_n_lines n="68"/>
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71 <has_n_columns n="10"/>
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72 </assert_contents>
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73 </output>
2
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74 <output name="alphadiv_plot" ftype="pdf">
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75 <assert_contents>
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76 <has_size min="1"/>
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77 </assert_contents>
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78 </output>
0
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79 </test>
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80 <test>
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81 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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82 <param name="measure" value="observed,shannon"/>
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83 <param name="richness" value="true"/>
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84 <param name="rarefy" value="500"/>
2
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85 <param name="group_by" value="Plant"/>
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86 <param name="plot_scatter" value="true"/>
0
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87 <output name="alphadiv">
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88 <assert_contents>
1
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89 <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;RawReads&#9;Reads&#9;uniqueOTUs&#9;Shannon&#9;Simpson&#9;invSimpson&#9;Chao1&#9;ACE"/>
0
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90 <has_text text="16SAMP-536&#9;"/>
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91 <has_text text="&#9;Aalborg West&#9;"/>
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92 <has_n_lines n="68"/>
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93 <has_n_columns n="13"/>
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94 <has_text text="&#9;500&#9;"/>
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95 </assert_contents>
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96 </output>
2
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97 <output name="alphadiv_plot">
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98 <assert_contents>
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99 <has_size min="1"/>
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100 </assert_contents>
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101 </output>
0
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102 </test>
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103 </tests>
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104 <help><![CDATA[
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105
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106 What it does
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107 ============
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108
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109 Calculate alpha-diversity indices for each sample and combines with the metadata.
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110
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111 The Galaxy tool calls the `amp_alpha_diversity
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112 <https://kasperskytte.github.io/ampvis2/reference/amp_alphadiv.html>`_ function
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113 of the ampvis2 package.
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114
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115 Usage
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116 =====
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117
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118 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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119 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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120 Refer to the vegan documentation for details about the different indices and how they are
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121 calculated.
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122
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123
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124 Input
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125 =====
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126
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127 @HELP_RDS_INPUT@
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128
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129 Output
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130 ======
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131
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132 A tabular dataset containing the chosen alpha-diversity measures per sample.
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133
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134 ]]></help>
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135 <expand macro="citations">
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136 <citation type="doi">10.1371/journal.pcbi.1003531</citation>
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137 </expand>
1
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138 </tool>