Mercurial > repos > iuc > ampvis2_export_fasta
diff macros.xml @ 0:3c3c359d9b85 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
| author | iuc |
|---|---|
| date | Mon, 04 Apr 2022 10:22:24 +0000 |
| parents | |
| children | e10b5eebd415 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Apr 04 10:22:24 2022 +0000 @@ -0,0 +1,271 @@ +<macros> + <token name="@TOOL_VERSION@">2.7.17</token> + <token name="@VERSION_SUFFIX@">0</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="2.1.1">r-readr</requirement> + </requirements> + <version_command><![CDATA[ +echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/299537</citation> + <yield/> + </citations> + </xml> + + <xml name="rds_input_macro"> + <param argument="data" type="data" format="ampvis2" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/> + </xml> + + <xml name="rds_metadata_input_macro" token_metadata_optional="true"> + <expand macro="rds_input_macro"/> + <param name="metadata_list" type="data" optional="@METADATA_OPTIONAL@" format="tabular" label="Metadata list"> + <validator type="expression" message="The metadatalist file must have 3 columns"><![CDATA[value.metadata.columns == 4]]></validator> + </param> + </xml> + + <token name="@SAVE_TAX_LIST@"><![CDATA[ + for(level in colnames(data\$tax)){ + for(u in unique(data\$tax[level])){ + write(u, file="$taxonomy_list_out", append=T) + } + } + ]]></token> + + <token name="@SAVE_METADATA_LIST@"><![CDATA[ + classes <- sapply(data\$metadata, class) + 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> + + <xml name="metadata_sample_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"> + <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> + </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> \ No newline at end of file