Mercurial > repos > iuc > ampvis2_subset_taxa

annotate subset_taxa.xml @ 4:a396cb857098 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 12:56:39 +0000
parents 91c39622b224
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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91c39622b224 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit d92935972ac18906154fadf42bd0c008e3c437e2
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1 <tool id="ampvis2_subset_taxa" name="ampvis2 subset data" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
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2 <description>by taxonomy</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 '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 library(ampvis2, quietly = TRUE)
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13 data <- readRDS("$data")
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15 #if $select_param == "option_input_selected_file"
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16 ## Define the file path (assuming it's a text file with one value per line)
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17 file_path <- "$selected_taxonomy_list"
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19 ## Read the file into a character vector, where each line represents a value
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20 lines <- readLines(file_path)
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22 ## Remove any leading or trailing whitespace (if necessary)
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23 tax_vector <- trimws(lines)
91c39622b224 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit d92935972ac18906154fadf42bd0c008e3c437e2
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24 #else
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25 tax_vector <- unlist(strsplit("$tax_vector", ","))
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26 #end if
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27 data <- amp_subset_taxa(
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28 data,
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29 tax_vector = tax_vector,
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30 normalise = $normalise,
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31 remove = $remove
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32 )
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33
0
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34 saveRDS(data, "$ampvis")
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35 @SAVE_TAX_LIST@
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36 ]]></configfile>
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37 </configfiles>
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38 <inputs>
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39 <expand macro="rds_input_macro"/>
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40 <!-- add validator -->
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41 <conditional name="taxonomy_select_type">
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42 <param name="select_param" type="select" label="Choose taxa input option">
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43 <option value="option_input_file">Select taxa from taxonomy list file</option>
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44 <option value="option_input_selected_file">Provide a file with selected taxa</option>
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45 </param>
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46
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47 <when value="option_input_selected_file">
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48 <param name="selected_taxonomy_list" type="data" optional="false" format="tabular" label="Selected taxonomy list" help="A file containing the taxa to subsample. One taxa per line."/>
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49 </when>
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50
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51 <when value="option_input_file">
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52 <param name="taxonomy_list" type="data" optional="false" format="tabular" label="Taxonomy list" help="Generated with ampvis2: load"/>
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53 <expand macro="taxonomy_select_macro" argument="tax_vector" label="Taxa to keep"/>
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54 </when>
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55 </conditional>
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56
0
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57 <expand macro="normalise_macro"/>
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58 <param argument="remove" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove" help="Selected taxa will be removed instead of being the only ones kept in the data."/>
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59 </inputs>
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60 <outputs>
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61 <data name="ampvis" format="ampvis2"/>
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62 <data name="taxonomy_list_out" format="tabular" label="${tool.name} on ${on_string}: taxonomy list"/>
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63 </outputs>
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64 <!-- Test cases -->
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65 <tests>
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66 <!-- Test case for using comma-separated taxonomy list -->
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67 <test expect_num_outputs="2">
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68 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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69 <param name="select_param" value="option_input_file"/>
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70 <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/>
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71 <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/>
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72 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/>
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73 <output name="taxonomy_list_out" ftype="tabular">
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74 <assert_contents>
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75 <has_text text="f__Caldilineaceae"/>
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76 <has_text text="p__Elusimicrobia"/>
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77 </assert_contents>
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78 </output>
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79 </test>
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80
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81 <!-- Test case for using comma-separated taxonomy list and remove=true -->
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82 <test expect_num_outputs="2">
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83 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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84 <param name="select_param" value="option_input_file"/>
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85 <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/>
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86 <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/>
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87 <param name="remove" value="true"/>
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88 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/>
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89 <output name="taxonomy_list_out" ftype="tabular">
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90 <assert_contents>
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91 <not_has_text text="f__Caldilineaceae"/>
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92 <not_has_text text="p__Elusimicrobia"/>
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93 </assert_contents>
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94 </output>
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95 </test>
1
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96
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97 <!-- Test case for using selected taxonomy list from a file -->
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98 <test expect_num_outputs="2">
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99 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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100 <param name="select_param" value="option_input_selected_file"/>
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101 <param name="selected_taxonomy_list" value="AalborgWWTPs-selected.taxonomy.list"/>
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102 <param name="remove" value="true"/>
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103 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/>
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104 <output name="taxonomy_list_out" ftype="tabular">
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105 <assert_contents>
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106 <not_has_text text="f__Caldilineaceae"/>
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107 <not_has_text text="p__Elusimicrobia"/>
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108 </assert_contents>
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109 </output>
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110 </test>
0
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111 </tests>
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112 <help><![CDATA[
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113 What it does
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114 ============
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115
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116 Subsets the data in ampvis2 objects based on taxonomy and returns the subsetted object.
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117
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118 The Galaxy tool calls the `amp_subset_taxa
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119 <https://kasperskytte.github.io/ampvis2/reference/amp_filter_taxa.html>`_ function
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120 of the ampvis2 package.
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121
1
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122 This tool provides two options for specifying the `subset`:
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123
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124 1. **Provide taxa names matching the taxonomy table**:
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125
0
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126 The taxonomy subset is done by providing a tax_vector of taxa names which are
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127 then matched to the taxonomy table, where all other taxa not matching the
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128 "Taxa to keep" (``tax_vector``) are removed. If "Remove" is enabled, then the
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129 matching taxa are the ones being removed instead. The taxa names
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130 will be matched in all columns of the taxonomy table.
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131
1
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132 2. **Provide a file of selected taxonomies**:
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133
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134 In this option, you can upload a file containing the taxa you wish to subset.
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135 The file should contain one taxon name per line.
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136 This option is useful when you have a pre-defined list of taxa stored in a file.
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137 This is useful if you want to use the tool in a workflow or if you automatically generate
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138 a taxonomy selection e.g. with differential abundance tools like MaAsLi2 and you only want to
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139 plot these taxa.
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140
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141
0
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142 @HELP_RELATIVE_ABUNDANCES@
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143
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144 Input
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145 =====
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146
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147 @HELP_RDS_INPUT@
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148
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149 @HELP_METADATA_LIST_INPUT@
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150
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151 Output
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152 ======
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153
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154 An ampvis2_rds dataset containing subsetted data and an updated taxonomy list dataset.
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155
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156 ]]></help>
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157 <expand macro="citations"/>
1
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158 </tool>