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comparison subset_taxa.xml @ 7:20a62b3a3038 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit d92935972ac18906154fadf42bd0c008e3c437e2
author iuc
date Fri, 25 Oct 2024 14:15:04 +0000
parents 1332619ad9ec
children
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6:cf579d6919e8 7:20a62b3a3038
1 <tool id="ampvis2_subset_taxa" name="ampvis2 subset data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> 1 <tool id="ampvis2_subset_taxa" name="ampvis2 subset data" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
2 <description>by taxonomy</description> 2 <description>by taxonomy</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="header"/> 6 <expand macro="header"/>
9 ]]></command> 9 ]]></command>
10 <configfiles> 10 <configfiles>
11 <configfile name="rscript"><![CDATA[ 11 <configfile name="rscript"><![CDATA[
12 library(ampvis2, quietly = TRUE) 12 library(ampvis2, quietly = TRUE)
13 data <- readRDS("$data") 13 data <- readRDS("$data")
14 #set tax_vector = 'c("' + '", "'.join(str($tax_vector).split(",")) + '")' 14
15 data <- amp_subset_taxa( 15 #if $select_param == "option_input_selected_file"
16 ## Define the file path (assuming it's a text file with one value per line)
17 file_path <- "$selected_taxonomy_list"
18
19 ## Read the file into a character vector, where each line represents a value
20 lines <- readLines(file_path)
21
22 ## Remove any leading or trailing whitespace (if necessary)
23 tax_vector <- trimws(lines)
24 #else
25 tax_vector <- unlist(strsplit("$tax_vector", ","))
26 #end if
27 data <- amp_subset_taxa(
16 data, 28 data,
17 tax_vector = $tax_vector, 29 tax_vector = tax_vector,
18 normalise = $normalise, 30 normalise = $normalise,
19 remove = $remove 31 remove = $remove
20 ) 32 )
33
21 saveRDS(data, "$ampvis") 34 saveRDS(data, "$ampvis")
22 @SAVE_TAX_LIST@ 35 @SAVE_TAX_LIST@
23 ]]></configfile> 36 ]]></configfile>
24 </configfiles> 37 </configfiles>
25 <inputs> 38 <inputs>
26 <expand macro="rds_input_macro"/> 39 <expand macro="rds_input_macro"/>
27 <!-- add validator --> 40 <!-- add validator -->
28 <param name="taxonomy_list" type="data" optional="false" format="tabular" label="Taxonomy list" help="Generated with ampvis2: load"/> 41 <conditional name="taxonomy_select_type">
29 <expand macro="taxonomy_select_macro" argument="tax_vector" label="Taxa to keep"/> 42 <param name="select_param" type="select" label="Choose taxa input option">
43 <option value="option_input_file">Select taxa from taxonomy list file</option>
44 <option value="option_input_selected_file">Provide a file with selected taxa</option>
45 </param>
46
47 <when value="option_input_selected_file">
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."/>
49 </when>
50
51 <when value="option_input_file">
52 <param name="taxonomy_list" type="data" optional="false" format="tabular" label="Taxonomy list" help="Generated with ampvis2: load"/>
53 <expand macro="taxonomy_select_macro" argument="tax_vector" label="Taxa to keep"/>
54 </when>
55 </conditional>
56
30 <expand macro="normalise_macro"/> 57 <expand macro="normalise_macro"/>
31 <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."/> 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."/>
32 </inputs> 59 </inputs>
33 <outputs> 60 <outputs>
34 <data name="ampvis" format="ampvis2"/> 61 <data name="ampvis" format="ampvis2"/>
35 <data name="taxonomy_list_out" format="tabular" label="${tool.name} on ${on_string}: taxonomy list"/> 62 <data name="taxonomy_list_out" format="tabular" label="${tool.name} on ${on_string}: taxonomy list"/>
36 </outputs> 63 </outputs>
64 <!-- Test cases -->
37 <tests> 65 <tests>
38 <!-- defaults --> 66 <!-- Test case for using comma-separated taxonomy list -->
39 <test expect_num_outputs="2"> 67 <test expect_num_outputs="2">
40 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 68 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
69 <param name="select_param" value="option_input_file"/>
41 <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/> 70 <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/>
42 <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/> 71 <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/>
43 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/> 72 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/>
44 <output name="taxonomy_list_out" ftype="tabular"> 73 <output name="taxonomy_list_out" ftype="tabular">
45 <assert_contents> 74 <assert_contents>
46 <has_text text="f__Caldilineaceae"/> 75 <has_text text="f__Caldilineaceae"/>
47 <has_text text="p__Elusimicrobia"/> 76 <has_text text="p__Elusimicrobia"/>
48 </assert_contents> 77 </assert_contents>
49 </output> 78 </output>
50 </test> 79 </test>
51 <!-- defaults --> 80
81 <!-- Test case for using comma-separated taxonomy list and remove=true -->
52 <test expect_num_outputs="2"> 82 <test expect_num_outputs="2">
53 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 83 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
84 <param name="select_param" value="option_input_file"/>
54 <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/> 85 <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/>
55 <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/> 86 <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/>
87 <param name="remove" value="true"/>
88 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/>
89 <output name="taxonomy_list_out" ftype="tabular">
90 <assert_contents>
91 <not_has_text text="f__Caldilineaceae"/>
92 <not_has_text text="p__Elusimicrobia"/>
93 </assert_contents>
94 </output>
95 </test>
96
97 <!-- Test case for using selected taxonomy list from a file -->
98 <test expect_num_outputs="2">
99 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
100 <param name="select_param" value="option_input_selected_file"/>
101 <param name="selected_taxonomy_list" value="AalborgWWTPs-selected.taxonomy.list"/>
56 <param name="remove" value="true"/> 102 <param name="remove" value="true"/>
57 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/> 103 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/>
58 <output name="taxonomy_list_out" ftype="tabular"> 104 <output name="taxonomy_list_out" ftype="tabular">
59 <assert_contents> 105 <assert_contents>
60 <not_has_text text="f__Caldilineaceae"/> 106 <not_has_text text="f__Caldilineaceae"/>
71 117
72 The Galaxy tool calls the `amp_subset_taxa 118 The Galaxy tool calls the `amp_subset_taxa
73 <https://kasperskytte.github.io/ampvis2/reference/amp_filter_taxa.html>`_ function 119 <https://kasperskytte.github.io/ampvis2/reference/amp_filter_taxa.html>`_ function
74 of the ampvis2 package. 120 of the ampvis2 package.
75 121
122 This tool provides two options for specifying the `subset`:
123
124 1. **Provide taxa names matching the taxonomy table**:
125
76 The taxonomy subset is done by providing a tax_vector of taxa names which are 126 The taxonomy subset is done by providing a tax_vector of taxa names which are
77 then matched to the taxonomy table, where all other taxa not matching the 127 then matched to the taxonomy table, where all other taxa not matching the
78 "Taxa to keep" (``tax_vector``) are removed. If "Remove" is enabled, then the 128 "Taxa to keep" (``tax_vector``) are removed. If "Remove" is enabled, then the
79 matching taxa are the ones being removed instead. The taxa names 129 matching taxa are the ones being removed instead. The taxa names
80 will be matched in all columns of the taxonomy table. 130 will be matched in all columns of the taxonomy table.
131
132 2. **Provide a file of selected taxonomies**:
133
134 In this option, you can upload a file containing the taxa you wish to subset.
135 The file should contain one taxon name per line.
136 This option is useful when you have a pre-defined list of taxa stored in a file.
137 This is useful if you want to use the tool in a workflow or if you automatically generate
138 a taxonomy selection e.g. with differential abundance tools like MaAsLi2 and you only want to
139 plot these taxa.
140
81 141
82 @HELP_RELATIVE_ABUNDANCES@ 142 @HELP_RELATIVE_ABUNDANCES@
83 143
84 Input 144 Input
85 ===== 145 =====