Mercurial > repos > iuc > ampvis2_venn
view macros.xml @ 5:6acf30f0d9fa draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author | iuc |
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date | Fri, 16 Aug 2024 09:03:46 +0000 |
parents | 338f47a9e25c |
children | bbb4a531d80b |
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<macros> <token name="@TOOL_VERSION@">2.8.6</token> <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.01</token> <xml name="header"> <xrefs> <xref type="bio.tools">ampvis</xref> </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement> <requirement type="package" version="2.1.5">r-readr</requirement> <requirement type="package" version="1.46.0">bioconductor-phyloseq</requirement> </requirements> <version_command><![CDATA[ echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ") ]]></version_command> </xml> <xml name="citations"> <citations> <citation type="doi">10.1101/299537</citation> <yield/> </citations> </xml> <xml name="rds_input_macro" token_multiple="false"> <param argument="data" type="data" format="ampvis2" multiple="@MULTIPLE@" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/> </xml> <xml name="rds_metadata_input_macro" token_metadata_optional="true"> <expand macro="rds_input_macro"/> <param name="metadata_list" type="data" optional="@METADATA_OPTIONAL@" format="tabular" label="Metadata list"> <validator type="expression" message="The metadatalist file must have 3 columns"><![CDATA[value.metadata.columns == 4]]></validator> </param> </xml> <token name="@SAVE_TAX_LIST@"><![CDATA[ for(level in colnames(data\$tax)){ for(u in unique(data\$tax[level])){ write(paste(u, level, sep="\t"), file="$taxonomy_list_out", append=T) } } ]]></token> <token name="@SAVE_METADATA_LIST@"><![CDATA[ classes <- sapply(data\$metadata, class) data\$metadata[is.na(data\$metadata)] <- "NA" ##the comparison below fails if NA values are present, see https://stackoverflow.com/questions/7355187/error-in-if-while-condition-missing-value-where-true-false-needed for(name in names(data\$metadata)){ ## check if it is the column containing the sample names ## the additional column in the ist file can the be used ## to filter SampleIDs from select inputs ## (check for character columns only .. since data in the column is otherwise converted to the corresponding type .. which fails) if(classes[[name]] == "character" && all(data\$metadata[[name]] == rownames(data\$metadata))){ sample_names <- TRUE; }else{ sample_names <- FALSE; } for(m in unique(data\$metadata[[name]])){ write(paste(name, m, sample_names, classes[[name]], sep="\t"), file="$metadata_list_out", append=T); } } ]]></token> <!-- defaults can be set by redefining an on option with selected="true" --> <xml name="taxlevel_macro" token_argument="" token_multiple="false" token_optional="false" token_label="" token_help=""> <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> <option value="OTU">OTU/ASV</option> <option value="Species">Species</option> <option value="Genus">Genus</option> <option value="Family">Family</option> <option value="Order">Order</option> <option value="Class">Class</option> <option value="Phylum">Phylum</option> <option value="Kingdom">Kingdom</option> <yield/> </param> </xml> <xml name="tax_empty_macro"> <param argument="tax_empty" type="select" label="How to show OTUs without taxonomic information"> <option value="remove">Remove OTUs without taxonomic information</option> <option value="best" selected="true">Use the best classification possible</option> <option value="OTU">Display the OTU name</option> </param> </xml> <token name="@TAX_SHOW@"><![CDATA[ #if $tax_show_cond.tax_show_sel == "number" tax_show = $tax_show_cond.tax_show, #else #set tax_show_list='c("' + '", "'.join(str($tax_show_cond.tax_show).split(",")) + '")' tax_show = $tax_show_list #end if ]]></token> <xml name="tax_show_macro" token_value=""> <conditional name="tax_show_cond"> <param name="tax_show_sel" type="select" label="Limit the number of shown taxa"> <option value="number">Select a number of taxa to show</option> <option value="explicit">Manually select taxa to show</option> </param> <when value="number"> <param argument="tax_show" type="integer" value="@VALUE@" min="1" label="Number of taxa to show"/> </when> <when value="explicit"> <param name="taxonomy_list" format="tabular" type="data" optional="false" label="Taxonomy list" help="Generated with ampvis2: load"/> <param argument="tax_show" type="select" multiple="true" optional="false" label="Taxa to show"> <options from_dataset="taxonomy_list"> <column name="name" index="0"/> <column name="value" index="0"/> <!-- TODO filter by tax_aggregate level? --> </options> </param> </when> </conditional> </xml> <xml name="metadata_select" token_quote="__" tokens="argument,label" token_an="argument" token_optional="true" token_multiple="false" token_help=""> <param __AN__="__ARGUMENT__" type="select" optional="__OPTIONAL__" multiple="__MULTIPLE__" label="__LABEL__" help="In order to select values a metadata list needs to be selected first. __HELP__"> <options from_dataset="metadata_list"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="unique_value" column="0"/> <yield name="options"/> </options> <yield/> </param> </xml> <xml name="metadata_select_discrete" tokens="argument,label" token_optional="true" token_multiple="false" token_help=""> <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> <token name="options"> <filter type="static_value" column="3" value="numeric" keep="false"/> </token> <yield/> </expand> </xml> <xml name="metadata_select_numeric" tokens="argument,label" token_optional="true" token_multiple="false" token_help=""> <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> <token name="options"> <filter type="static_value" column="3" value="character" keep="false"/> <filter type="static_value" column="3" value="Date" keep="false"/> </token> <yield/> </expand> </xml> <xml name="metadata_select_date" tokens="argument,label" token_optional="true" token_multiple="false" token_help=""> <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> <token name="options"> <filter type="static_value" column="3" value="Date" keep="true"/> </token> <yield/> </expand> </xml> <!-- metadata_sample_or_variable_select is currently unused (heatmap is documented to allow normalize by sample or variable, but only sample seems possible https://github.com/KasperSkytte/ampvis2/issues/168 leaving it for now in case it can be fixed .. then metadata_sample_select could be removed) --> <xml name="metadata_sample_select" token_argument=""> <param argument="@ARGUMENT@" type="select" optional="true"> <options from_dataset="metadata_list"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples --> <filter type="unique_value" column="1"/> </options> </param> </xml> <xml name="metadata_sample_or_variable_select" token_argument=""> <conditional name="@ARGUMENT@_cond"> <param name="@ARGUMENT@_sel" type="select"> <option value="no">No</option> <option value="variable">Metadata variable</option> <option value="sample">Specific sample</option> </param> <when value="no"/> <when value="variable"> <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/> </when> <when value="sample"> <expand macro="metadata_sample_select"/> </when> </conditional> </xml> <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true"> <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@"> <options from_dataset="taxonomy_list"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="unique_value" column="0"/> </options> <yield/> </param> </xml> <xml name="facet_scales_macro" token_argument="" token_label="Scales of the facets" token_help=""> <param argument="@ARGUMENT@" type="select" optional="true" label="@LABEL@" help="@HELP@"> <option value="fixed">Same scale</option> <option value="free">Free scale</option> <option value="free_x">Free x-scale</option> <option value="free_y">Free y-scale</option> </param> </xml> <token name="@OUTPUT_TOKEN@"> ggsave("$plot", print(plot), device="$output_options.out_format" #if str($output_options.plot_width) != '' , width = $output_options.plot_width #end if #if str($output_options.plot_height) != '' , height = $output_options.plot_height #end if ) </token> <xml name="out_macro" token_name="plot" token_label=""> <data name="@NAME@" format="pdf" label="${tool.name} on ${on_string}@LABEL@"> <yield/> <change_format> <when input="output_options.out_format" value="png" format="png" /> <when input="output_options.out_format" value="svg" format="svg" /> </change_format> </data> </xml> <xml name="out_format_macro"> <section name="output_options" title="Output options" expanded="false"> <param name="out_format" type="select" label="Output format"> <option value="pdf" selected="true">PDF</option> <option value="png">PNG</option> <option value="svg">SVG</option> <yield/> </param> <param name="plot_width" type="float" value="" min="1" optional="true" label="Plot width in cm"/> <param name="plot_height" type="float" value="" min="1" optional="true" label="Plot height in cm"/> </section> </xml> <token name="@RAREFY_TOKEN@"> #if str($rarefy) != "" , rarefy = $rarefy #end if </token> <xml name="rarefy_macro" token_help=""> <param argument="rarefy" type="integer" optional="true" value="" min="0" label="Rarefy species richness to this value" help="@HELP@"/> </xml> <xml name="normalise_macro" token_checked="false"> <param argument="normalise" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="@CHECKED@" label="Normalise read counts" help="Transform the OTU read counts to be in percent per sample."/> </xml> <token name="@HELP_RDS_INPUT@"> An ampvis2 RDS dataset obtained by the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or one of the ``ampvis2: subset ...`` tools). </token> <token name="@HELP_METADATA_LIST_INPUT@"> The metadata list output of the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or the ``ampvis2: subset sample`` tool). This input is only used for providing values to the parameters alowing to select metadata variables or values. </token> <token name="@HELP_RELATIVE_ABUNDANCES@"> Preserving relative abundances in a subset of larger data ========================================================= By default the raw read counts in the abundance matrix are normalised (transformed to percentages) by some ampvis2 plotting tools (for example ``ampvis2: heatmap``, ``ampvis2: timeseries``, and more). If this is applied to data generated by one of the ``ampvis2: subset ...`` tools this means that the relative abundances shown will be calculated based on the remaining taxa after the subset, not including the removed taxa, if any. To circumvent this, enable ``normalise`` when subsetting with the ``ampvis2: subset ...``` tools, and then disable ``normalise`` in the plotting tool. This will transform the OTU counts to relative abundances BEFORE the subset. </token> </macros>