Mercurial > repos > iuc > ampvis2_subset_taxa
changeset 7:20a62b3a3038 draft
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 | cf579d6919e8 |
| children | 76cb398e9110 |
| files | subset_taxa.xml test-data/AalborgWWTPs-selected.taxonomy.list |
| diffstat | 2 files changed, 72 insertions(+), 10 deletions(-) [+] |
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--- a/subset_taxa.xml Mon Aug 26 16:18:57 2024 +0000 +++ b/subset_taxa.xml Fri Oct 25 14:15:04 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="ampvis2_subset_taxa" name="ampvis2 subset data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> +<tool id="ampvis2_subset_taxa" name="ampvis2 subset data" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT"> <description>by taxonomy</description> <macros> <import>macros.xml</import> @@ -11,13 +11,26 @@ <configfile name="rscript"><![CDATA[ library(ampvis2, quietly = TRUE) data <- readRDS("$data") - #set tax_vector = 'c("' + '", "'.join(str($tax_vector).split(",")) + '")' - data <- amp_subset_taxa( + + #if $select_param == "option_input_selected_file" + ## Define the file path (assuming it's a text file with one value per line) + file_path <- "$selected_taxonomy_list" + + ## Read the file into a character vector, where each line represents a value + lines <- readLines(file_path) + + ## Remove any leading or trailing whitespace (if necessary) + tax_vector <- trimws(lines) + #else + tax_vector <- unlist(strsplit("$tax_vector", ",")) + #end if + data <- amp_subset_taxa( data, - tax_vector = $tax_vector, + tax_vector = tax_vector, normalise = $normalise, remove = $remove - ) + ) + saveRDS(data, "$ampvis") @SAVE_TAX_LIST@ ]]></configfile> @@ -25,8 +38,22 @@ <inputs> <expand macro="rds_input_macro"/> <!-- add validator --> - <param name="taxonomy_list" type="data" optional="false" format="tabular" label="Taxonomy list" help="Generated with ampvis2: load"/> - <expand macro="taxonomy_select_macro" argument="tax_vector" label="Taxa to keep"/> + <conditional name="taxonomy_select_type"> + <param name="select_param" type="select" label="Choose taxa input option"> + <option value="option_input_file">Select taxa from taxonomy list file</option> + <option value="option_input_selected_file">Provide a file with selected taxa</option> + </param> + + <when value="option_input_selected_file"> + <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."/> + </when> + + <when value="option_input_file"> + <param name="taxonomy_list" type="data" optional="false" format="tabular" label="Taxonomy list" help="Generated with ampvis2: load"/> + <expand macro="taxonomy_select_macro" argument="tax_vector" label="Taxa to keep"/> + </when> + </conditional> + <expand macro="normalise_macro"/> <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."/> </inputs> @@ -34,10 +61,12 @@ <data name="ampvis" format="ampvis2"/> <data name="taxonomy_list_out" format="tabular" label="${tool.name} on ${on_string}: taxonomy list"/> </outputs> + <!-- Test cases --> <tests> - <!-- defaults --> + <!-- Test case for using comma-separated taxonomy list --> <test expect_num_outputs="2"> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="select_param" value="option_input_file"/> <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/> <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/> <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/> @@ -48,9 +77,11 @@ </assert_contents> </output> </test> - <!-- defaults --> + + <!-- Test case for using comma-separated taxonomy list and remove=true --> <test expect_num_outputs="2"> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="select_param" value="option_input_file"/> <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/> <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/> <param name="remove" value="true"/> @@ -62,6 +93,21 @@ </assert_contents> </output> </test> + + <!-- Test case for using selected taxonomy list from a file --> + <test expect_num_outputs="2"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="select_param" value="option_input_selected_file"/> + <param name="selected_taxonomy_list" value="AalborgWWTPs-selected.taxonomy.list"/> + <param name="remove" value="true"/> + <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/> + <output name="taxonomy_list_out" ftype="tabular"> + <assert_contents> + <not_has_text text="f__Caldilineaceae"/> + <not_has_text text="p__Elusimicrobia"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ What it does @@ -73,12 +119,26 @@ <https://kasperskytte.github.io/ampvis2/reference/amp_filter_taxa.html>`_ function of the ampvis2 package. +This tool provides two options for specifying the `subset`: + +1. **Provide taxa names matching the taxonomy table**: + The taxonomy subset is done by providing a tax_vector of taxa names which are then matched to the taxonomy table, where all other taxa not matching the "Taxa to keep" (``tax_vector``) are removed. If "Remove" is enabled, then the matching taxa are the ones being removed instead. The taxa names will be matched in all columns of the taxonomy table. +2. **Provide a file of selected taxonomies**: + +In this option, you can upload a file containing the taxa you wish to subset. +The file should contain one taxon name per line. +This option is useful when you have a pre-defined list of taxa stored in a file. +This is useful if you want to use the tool in a workflow or if you automatically generate +a taxonomy selection e.g. with differential abundance tools like MaAsLi2 and you only want to +plot these taxa. + + @HELP_RELATIVE_ABUNDANCES@ Input @@ -95,4 +155,4 @@ ]]></help> <expand macro="citations"/> -</tool> \ No newline at end of file +</tool>