Mercurial > repos > iuc > ampvis2_subset_samples
diff subset_samples.xml @ 0:03b77eb5ed68 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
| author | iuc |
|---|---|
| date | Mon, 04 Apr 2022 10:25:42 +0000 |
| parents | |
| children | 0b0214cbe38b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/subset_samples.xml Mon Apr 04 10:25:42 2022 +0000 @@ -0,0 +1,112 @@ +<tool id="ampvis2_subset_samples" name="ampvis2 subset samples" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description>by sample metadata</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="header"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$rscript' + ]]></command> + <configfiles> + <configfile name="rscript"><![CDATA[ + library(ampvis2, quietly = TRUE) + data <- readRDS("$data") + #set vals = 'c("' + '", "'.join(str($vals).split(",")) + '")' + data <- amp_subset_samples( + data, + $invert $var %in% $vals, + minreads = $minreads + @RAREFY_TOKEN@, + normalise = $normalise, + removeAbsents = $removeAbsents + ) + saveRDS(data, "$ampvis") + @SAVE_METADATA_LIST@ + ]]></configfile> + </configfiles> + <inputs> + <expand macro="rds_metadata_input_macro"/> + <expand macro="metadata_select" an="name" argument="var" optional="false" multiple="false" label="Metadata variable"/> + <param name="vals" type="select" optional="false" multiple="true" label="Metadata value(s)"> + <options from_dataset="metadata_list"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="param_value" ref="var" column="0"/> + <filter type="unique_value" column="1"/> + </options> + </param> + <param name="invert" type="boolean" truevalue="!" falsevalue="" checked="false"/> + <param argument="minreads" type="integer" value="0" min="0" label="Minimum number of reads" help="Per sample. Samples below this value will be removed initially"/> + <expand macro="rarefy_macro" help="This is done initially, but after filtering based on the minreads value, if set."/> + <expand macro="normalise_macro"/> + <param argument="removeAbsents" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"/> + </inputs> + <outputs> + <data name="ampvis" format="ampvis2"/> + <data name="metadata_list_out" format="tabular" label="${tool.name} on ${on_string}: metadata list"/> + </outputs> + <tests> + <!-- defaults --> + <test expect_num_outputs="2"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> + <param name="var" value="Plant"/> + <param name="vals" value="Aalborg East"/> + <output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/> + <output name="metadata_list_out" ftype="tabular"> + <assert_contents> + <has_line line="Plant	Aalborg East	FALSE	character"/> + <not_has_text text="Plant	Aalborg West	FALSE	character"/> + <has_n_lines n="85"/> + <has_n_columns n="4"/> + </assert_contents> + </output> + </test> + <!-- invert --> + <test expect_num_outputs="2"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> + <param name="var" value="Plant"/> + <param name="vals" value="Aalborg East"/> + <param name="invert" value="true"/> + <output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/> + <output name="metadata_list_out" ftype="tabular"> + <assert_contents> + <not_has_text text="Plant	Aalborg East	FALSE	character"/> + <has_line line="Plant	Aalborg West	FALSE	character"/> + <has_n_lines n="79"/> + <has_n_columns n="4"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +What it does +============ + +Subsets the data in ampvis2 objects based on metadata and returns the subsetted object. + +The Galaxy tool calls the `amp_subset_samples +<https://madsalbertsen.github.io/ampvis2/reference/amp_subset_samples.html>`_ function +of the ampvis2 package. + +The subset is performed on the metadata by ``subset()`` and the abundance- and taxonomy +tables are then adjusted accordingly. + +@HELP_RELATIVE_ABUNDANCES@ + +Input +===== + +@HELP_RDS_INPUT@ + +@HELP_METADATA_LIST_INPUT@ + +Output +====== + +An ampvis2_rds dataset containing subsetted data and an updated metadata list dataset. + + ]]></help> + <expand macro="citations"/> +</tool> \ No newline at end of file