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comparison macros.xml @ 0:797603efc62d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author iuc
date Fri, 16 Aug 2024 08:50:10 +0000
parents
children 74b728bd018f
comparison
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-1:000000000000 0:797603efc62d
1 <macros>
2 <token name="@TOOL_VERSION@">2.8.6</token>
3 <token name="@VERSION_SUFFIX@">2</token>
4 <token name="@PROFILE@">22.01</token>
5 <xml name="header">
6 <xrefs>
7 <xref type="bio.tools">ampvis</xref>
8 </xrefs>
9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement>
11 <requirement type="package" version="2.1.5">r-readr</requirement>
12 <requirement type="package" version="1.46.0">bioconductor-phyloseq</requirement>
13 </requirements>
14 <version_command><![CDATA[
15 echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ")
16 ]]></version_command>
17
18 </xml>
19 <xml name="citations">
20 <citations>
21 <citation type="doi">10.1101/299537</citation>
22 <yield/>
23 </citations>
24 </xml>
25
26 <xml name="rds_input_macro" token_multiple="false">
27 <param argument="data" type="data" format="ampvis2" multiple="@MULTIPLE@" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/>
28 </xml>
29
30 <xml name="rds_metadata_input_macro" token_metadata_optional="true">
31 <expand macro="rds_input_macro"/>
32 <param name="metadata_list" type="data" optional="@METADATA_OPTIONAL@" format="tabular" label="Metadata list">
33 <validator type="expression" message="The metadatalist file must have 3 columns"><![CDATA[value.metadata.columns == 4]]></validator>
34 </param>
35 </xml>
36
37 <token name="@SAVE_TAX_LIST@"><![CDATA[
38 for(level in colnames(data\$tax)){
39 for(u in unique(data\$tax[level])){
40 write(paste(u, level, sep="\t"), file="$taxonomy_list_out", append=T)
41 }
42 }
43 ]]></token>
44
45 <token name="@SAVE_METADATA_LIST@"><![CDATA[
46 classes <- sapply(data\$metadata, class)
47 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
48 for(name in names(data\$metadata)){
49 ## check if it is the column containing the sample names
50 ## the additional column in the ist file can the be used
51 ## to filter SampleIDs from select inputs
52 ## (check for character columns only .. since data in the column is otherwise converted to the corresponding type .. which fails)
53 if(classes[[name]] == "character" && all(data\$metadata[[name]] == rownames(data\$metadata))){
54 sample_names <- TRUE;
55 }else{
56 sample_names <- FALSE;
57 }
58 for(m in unique(data\$metadata[[name]])){
59 write(paste(name, m, sample_names, classes[[name]], sep="\t"), file="$metadata_list_out", append=T);
60 }
61 }
62 ]]></token>
63
64 <!-- defaults can be set by redefining an on option with selected="true" -->
65 <xml name="taxlevel_macro" token_argument="" token_multiple="false" token_optional="false" token_label="" token_help="">
66 <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
67 <option value="OTU">OTU/ASV</option>
68 <option value="Species">Species</option>
69 <option value="Genus">Genus</option>
70 <option value="Family">Family</option>
71 <option value="Order">Order</option>
72 <option value="Class">Class</option>
73 <option value="Phylum">Phylum</option>
74 <option value="Kingdom">Kingdom</option>
75 <yield/>
76 </param>
77 </xml>
78
79 <xml name="tax_empty_macro">
80 <param argument="tax_empty" type="select" label="How to show OTUs without taxonomic information">
81 <option value="remove">Remove OTUs without taxonomic information</option>
82 <option value="best" selected="true">Use the best classification possible</option>
83 <option value="OTU">Display the OTU name</option>
84 </param>
85 </xml>
86
87 <token name="@TAX_SHOW@"><![CDATA[
88 #if $tax_show_cond.tax_show_sel == "number"
89 tax_show = $tax_show_cond.tax_show,
90 #else
91 #set tax_show_list='c("' + '", "'.join(str($tax_show_cond.tax_show).split(",")) + '")'
92 tax_show = $tax_show_list
93 #end if
94 ]]></token>
95 <xml name="tax_show_macro" token_value="">
96 <conditional name="tax_show_cond">
97 <param name="tax_show_sel" type="select" label="Limit the number of shown taxa">
98 <option value="number">Select a number of taxa to show</option>
99 <option value="explicit">Manually select taxa to show</option>
100 </param>
101 <when value="number">
102 <param argument="tax_show" type="integer" value="@VALUE@" min="1" label="Number of taxa to show"/>
103 </when>
104 <when value="explicit">
105 <param name="taxonomy_list" format="tabular" type="data" optional="false" label="Taxonomy list" help="Generated with ampvis2: load"/>
106 <param argument="tax_show" type="select" multiple="true" optional="false" label="Taxa to show">
107 <options from_dataset="taxonomy_list">
108 <column name="name" index="0"/>
109 <column name="value" index="0"/>
110 <!-- TODO filter by tax_aggregate level? -->
111 </options>
112 </param>
113 </when>
114 </conditional>
115 </xml>
116
117 <xml name="metadata_select" token_quote="__" tokens="argument,label" token_an="argument" token_optional="true" token_multiple="false" token_help="">
118 <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__">
119 <options from_dataset="metadata_list">
120 <column name="name" index="0"/>
121 <column name="value" index="0"/>
122 <filter type="unique_value" column="0"/>
123 <yield name="options"/>
124 </options>
125 <yield/>
126 </param>
127 </xml>
128
129 <xml name="metadata_select_discrete" tokens="argument,label" token_optional="true" token_multiple="false" token_help="">
130 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
131 <token name="options">
132 <filter type="static_value" column="3" value="numeric" keep="false"/>
133 </token>
134 <yield/>
135 </expand>
136 </xml>
137
138 <xml name="metadata_select_numeric" tokens="argument,label" token_optional="true" token_multiple="false" token_help="">
139 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
140 <token name="options">
141 <filter type="static_value" column="3" value="character" keep="false"/>
142 <filter type="static_value" column="3" value="Date" keep="false"/>
143 </token>
144 <yield/>
145 </expand>
146 </xml>
147
148 <xml name="metadata_select_date" tokens="argument,label" token_optional="true" token_multiple="false" token_help="">
149 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
150 <token name="options">
151 <filter type="static_value" column="3" value="Date" keep="true"/>
152 </token>
153 <yield/>
154 </expand>
155 </xml>
156
157 <!-- metadata_sample_or_variable_select is currently unused (heatmap is documented to allow normalize by
158 sample or variable, but only sample seems possible https://github.com/KasperSkytte/ampvis2/issues/168
159 leaving it for now in case it can be fixed .. then metadata_sample_select could be removed) -->
160 <xml name="metadata_sample_select" token_argument="">
161 <param argument="@ARGUMENT@" type="select" optional="true">
162 <options from_dataset="metadata_list">
163 <column name="name" index="1"/>
164 <column name="value" index="1"/>
165 <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
166 <filter type="unique_value" column="1"/>
167 </options>
168 </param>
169 </xml>
170 <xml name="metadata_sample_or_variable_select" token_argument="">
171 <conditional name="@ARGUMENT@_cond">
172 <param name="@ARGUMENT@_sel" type="select">
173 <option value="no">No</option>
174 <option value="variable">Metadata variable</option>
175 <option value="sample">Specific sample</option>
176 </param>
177 <when value="no"/>
178 <when value="variable">
179 <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/>
180 </when>
181 <when value="sample">
182 <expand macro="metadata_sample_select"/>
183 </when>
184 </conditional>
185 </xml>
186
187 <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true">
188 <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@">
189 <options from_dataset="taxonomy_list">
190 <column name="name" index="0"/>
191 <column name="value" index="0"/>
192 <filter type="unique_value" column="0"/>
193 </options>
194 <yield/>
195 </param>
196 </xml>
197
198 <xml name="facet_scales_macro" token_argument="" token_label="Scales of the facets" token_help="">
199 <param argument="@ARGUMENT@" type="select" optional="true" label="@LABEL@" help="@HELP@">
200 <option value="fixed">Same scale</option>
201 <option value="free">Free scale</option>
202 <option value="free_x">Free x-scale</option>
203 <option value="free_y">Free y-scale</option>
204 </param>
205 </xml>
206
207 <token name="@OUTPUT_TOKEN@">
208 ggsave("$plot",
209 print(plot),
210 device="$output_options.out_format"
211 #if str($output_options.plot_width) != ''
212 , width = $output_options.plot_width
213 #end if
214 #if str($output_options.plot_height) != ''
215 , height = $output_options.plot_height
216 #end if
217 )
218 </token>
219 <xml name="out_macro" token_name="plot" token_label="">
220 <data name="@NAME@" format="pdf" label="${tool.name} on ${on_string}@LABEL@">
221 <yield/>
222 <change_format>
223 <when input="output_options.out_format" value="png" format="png" />
224 <when input="output_options.out_format" value="svg" format="svg" />
225 </change_format>
226 </data>
227 </xml>
228 <xml name="out_format_macro">
229 <section name="output_options" title="Output options" expanded="false">
230 <param name="out_format" type="select" label="Output format">
231 <option value="pdf" selected="true">PDF</option>
232 <option value="png">PNG</option>
233 <option value="svg">SVG</option>
234 <yield/>
235 </param>
236 <param name="plot_width" type="float" value="" min="1" optional="true" label="Plot width in cm"/>
237 <param name="plot_height" type="float" value="" min="1" optional="true" label="Plot height in cm"/>
238 </section>
239 </xml>
240
241 <token name="@RAREFY_TOKEN@">
242 #if str($rarefy) != ""
243 , rarefy = $rarefy
244 #end if
245 </token>
246 <xml name="rarefy_macro" token_help="">
247 <param argument="rarefy" type="integer" optional="true" value="" min="0" label="Rarefy species richness to this value" help="@HELP@"/>
248 </xml>
249
250 <xml name="normalise_macro" token_checked="false">
251 <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."/>
252 </xml>
253
254 <token name="@HELP_RDS_INPUT@">
255 An ampvis2 RDS dataset obtained by the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or one of the
256 ``ampvis2: subset ...`` tools).
257 </token>
258 <token name="@HELP_METADATA_LIST_INPUT@">
259 The metadata list output of the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or the
260 ``ampvis2: subset sample`` tool). This input is only used for providing
261 values to the parameters alowing to select metadata variables or values.
262 </token>
263
264 <token name="@HELP_RELATIVE_ABUNDANCES@">
265 Preserving relative abundances in a subset of larger data
266 =========================================================
267
268 By default the raw read counts in the abundance matrix are normalised
269 (transformed to percentages) by some ampvis2 plotting tools (for
270 example ``ampvis2: heatmap``, ``ampvis2: timeseries``, and more).
271 If this is applied to data generated by one of the ``ampvis2: subset ...`` tools
272 this means that the relative
273 abundances shown will be calculated based on the remaining taxa after the
274 subset, not including the removed taxa, if any. To circumvent this, enable
275 ``normalise`` when subsetting with the ``ampvis2: subset ...``` tools,
276 and then disable ``normalise`` in the plotting tool. This will
277 transform the OTU counts to relative abundances BEFORE the subset.
278 </token>
279 </macros>