Mercurial > repos > iuc > ampvis2_export_otu

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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 12:50:02 +0000
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f92f6cb141fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 commit e0ad9ce8f508215ec6af69be2682a0faf38415da
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1 <tool id="ampvis2_export_otu" name="ampvis2 export otu" 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' &&
adab1cdb8811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit f32c3d9a92dca8a60504824fc7bcee290c30a211
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9 mv tmp_otu.tsv $otu_long
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="rscript"><![CDATA[
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13 library(ampvis2, quietly = TRUE)
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14 library(phyloseq)
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15 library(tibble)
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16
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17 ## read the data
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18 data <- readRDS("$data")
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20 ## Export otutable (including taxonomy) from an ampvis2 object as TSV
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21 amp_export_otutable(data, filename = "tmp_otu", sep = "\t", extension = "tsv", normalise = "$norm")
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23 ## get only tax table (first column OTU ID)
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24 tax_table <- data\$tax
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25 tax_table <- tax_table[,c(8,(ncol(tax_table)-6):(ncol(tax_table) - 1))]
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26 write.table(tax_table, "$tax", sep = "\t", row.names=FALSE, quote = FALSE)
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27
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28 ## get only otu table (first column OTU ID)
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29 #if $norm
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30 data_norm <- normaliseTo100(data)
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31 otu_table <- data_norm\$abund
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32 #else
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33 otu_table <- data\$abund
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34 #end if
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36 otu_table <- cbind(OTU = rownames(otu_table), otu_table)
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37
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38 ## add index col manually: https://stackoverflow.com/questions/2478352/write-table-writes-unwanted-leading-empty-column-to-header-when-has-rownames
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39 write.table(otu_table, "$otu_short", sep = "\t", row.names=FALSE, quote = FALSE)
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41 ## get metadata
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42 meta_data = data\$metadata
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43 write.table(meta_data, "$meta", sep = "\t", row.names = FALSE, quote = FALSE)
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45 ## needs to be numeric
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46 otu_table <- apply(otu_table, 2, as.numeric)
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47
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48 ## needs to be character so that reupload as ampvis object works
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49 meta_data[] <- lapply(meta_data, as.character)
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50
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51 OTU <- otu_table(otu_table, taxa_are_rows = TRUE)
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52 TAX <- tax_table(tax_table)
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53 META <- sample_data(meta_data)
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54
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55 ## we always assume this names and order
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56 colnames(TAX) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
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58 physeq <- phyloseq(OTU, TAX, META)
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59
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60 ## Save the Phyloseq object
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61 saveRDS(physeq, "$phyloseq")
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62
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63 ]]></configfile>
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64 </configfiles>
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65 <inputs>
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66 <expand macro="rds_input_macro"/>
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67 <param argument="norm" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Transform the OTU read counts to be in percent per sample"/>
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68 <param name="output_selection" type="select" multiple="true" label="Output files selection" min="1">
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69 <option value="otu_long" selected="false">
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70 Long OTU with Taxonomy at the end
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71 </option>
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72 <option value="otu_short" selected="true">
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73 Short OTU
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74 </option>
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75 <option value="tax" selected="true">
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76 Taxonomy mapping
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77 </option>
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78 <option value="meta" selected="true">
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79 Metadata mapping
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80 </option>
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81 <option value="phyloseq" selected="false">
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82 Phyloseq object
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83 </option>
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84 </param>
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85 </inputs>
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86 <outputs>
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87 <data name="otu_long" format="tabular" label="${tool.name}: Long OTU" >
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88 <filter>"otu_long" in output_selection</filter>
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89 </data>
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90 <data name="otu_short" format="tabular" label="${tool.name}: Short OTU">
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91 <filter>"otu_short" in output_selection</filter>
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92 </data>
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93 <data name="tax" format="tabular" label="${tool.name}: Taxonomy mapping" >
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94 <filter>"tax" in output_selection</filter>
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95 </data>
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96 <data name="meta" format="tabular" label="${tool.name}: Metadata mapping" >
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97 <filter>"meta" in output_selection</filter>
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98 </data>
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99 <data name="phyloseq" format="phyloseq" label="${tool.name}: Phyloseq object" >
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100 <filter>"phyloseq" in output_selection</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <!-- defaults -->
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105 <test expect_num_outputs="3">
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106 <param name="data" value="AalborgWWTPs-complete.rds" ftype="ampvis2"/>
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107 <output name="otu_short" value="output_otu_short.tsv" ftype="tabular" />
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108 <output name="tax" value="output_otu_taxonomy_mapping.tsv" ftype="tabular" />
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109 <output name="meta" value="output_metadata.tsv" ftype="tabular" />
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110 </test>
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111 <test expect_num_outputs="5">
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112 <param name="data" value="AalborgWWTPs-complete.rds" ftype="ampvis2"/>
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113 <param name="output_selection" value="otu_long,otu_short,tax,meta,phyloseq" />
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114 <output name="otu_long" value="output_otu_long.tsv" ftype="tabular" />
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115 <output name="otu_short" value="output_otu_short.tsv" ftype="tabular" />
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116 <output name="tax" value="output_otu_taxonomy_mapping.tsv" ftype="tabular" />
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117 <output name="meta" value="output_metadata.tsv" ftype="tabular" />
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118 <output name="phyloseq" ftype="phyloseq" >
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119 <assert_contents>
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120 <has_size value="12684" delta="10"/>
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121 </assert_contents>
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122 </output>
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123 </test>
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124 </tests>
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125 <help><![CDATA[
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126 What it does
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127 ============
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128
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129 Exports OTU/ASV, Taxonomy table, Metadata, or phyloseq object from an ampvis2 object.
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130 The taxonomy table in the phyloseq object always uses the following headers:
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131 ``Kingdom, Phylum, Class, Order, Family, Genus, Species``.
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132
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133 This can be changed using the `Add Rank Names to Phyloseq Object <toolshed.g2.bx.psu.edu/repos/iuc/phyloseq_add_rank_names/phyloseq_add_rank_names/1.50.0+galaxy2>`_ tool.
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134
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135 The Galaxy tool calls the `amp_export_otutable <https://kasperskytte.github.io/ampvis2/reference/amp_export_otutable.html>`_ function
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136 from the ampvis2 package.
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137
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138 Input
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139 =====
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140
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141 @HELP_RDS_INPUT@
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142
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143 Use case
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144 ========
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145
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146 Load your OTU into a ampvis object with ampvis load. Subset based on metadata and/or taxonomy. Export the OTU table / phyloseq object.
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147 Perform downstream analysis such as differential analysis and/or phyloseq visualization.
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148
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149 ]]></help>
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150 <expand macro="citations"/>
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151 </tool>