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comparison heatmap.xml @ 0:e88112233ce3 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 08:56:04 +0000
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children b95c7b3f411e
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1 <tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="header"/>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$rscript'
9 ]]></command>
10 <configfiles>
11 <configfile name="rscript"><![CDATA[
12 #if $tax_add
13 #set ta='c("' + '", "'.join(str($tax_add).split(",")) + '")'
14 #else
15 #set ta='NULL'
16 #end if
17 library(ampvis2, quietly = TRUE)
18 d <- readRDS("$data")
19 #if $output_options.out_format == "tabular"
20 raw <-
21 #else
22 plot <-
23 #end if
24 amp_heatmap(
25 d
26 ,
27 #if $group_by
28 group_by = "$group_by",
29 #end if
30 #if $facet_by
31 facet_by = "$facet_by",
32 #end if
33 normalise = $normalise,
34 tax_aggregate = "$tax_aggregate",
35 tax_add = $ta,
36 @TAX_SHOW@
37 showRemainingTaxa = $showRemainingTaxa,
38 ## tax_class = NULL,
39 tax_empty = "$tax_empty",
40 ## TODO giving the order of the columns is difficult but "cluster" would be nice I guess
41 ## order_x_by = NULL,
42 ## order_y_by = NULL,
43 plot_values = $plot_values_cond.plot_values,
44 #if $plot_values_cond.plot_values == "TRUE"
45 plot_values_size = $plot_values_cond.plot_values_size,
46 #end if
47 ## plot_legendbreaks = NULL,
48 plot_colorscale = "$plot_colorscale",
49 plot_na = $plot_na,
50 measure = "$measure",
51 #if str($min_abundance) != ''
52 min_abundance = $min_abundance,
53 #end if
54 #if str($max_abundance) != ''
55 max_abundance = $max_abundance,
56 #end if
57 #if $sort_by_cond.sort_by_sel != 'no'
58 sort_by = "$sort_by_cond.sort_by",
59 #end if
60 #if $normalise_by
61 normalise_by = "$normalise_by",
62 #end if
63 #if $scale_by
64 scale_by = "$scale_by",
65 #end if
66 ## color_vector = NULL
67 ## round = 1,
68 #if $output_options.out_format == "tabular"
69 textmap = TRUE,
70 #else
71 textmap = FALSE,
72 #end if
73 #if $plot_functions_cond.plot_functions_sel != "no"
74 plot_functions = TRUE,
75 #if $plot_functions_cond.plot_functions_sel == "file"
76 function_data = read.table("$plot_functions_cond.function_data", header = TRUE, sep = "\t"),
77 #end if
78 #set foo='c("' + '", "'.join(str($plot_functions_cond.functions).split(",")) + '")'
79 functions = $foo,
80 #end if
81 rel_widths = c(0.75, 0.25)
82 )
83 #if $output_options.out_format != "tabular"
84 @OUTPUT_TOKEN@
85 #else
86 write.table(raw, file = "$plot_raw", sep = "\t")
87 #end if
88 ]]></configfile>
89 </configfiles>
90 <inputs>
91 <expand macro="rds_metadata_input_macro"/>
92 <expand macro="metadata_select_discrete" argument="group_by" label="Group samples" help="By a categorical variable in the metadata"/>
93 <expand macro="metadata_select_discrete" argument="facet_by" label="Facet the samples" help="By a categorical variable in the metadata."/>
94 <expand macro="normalise_macro" checked="true"/>
95 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
96 <option value="Phylum" selected="true">Phylum</option>
97 </expand>
98 <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/>
99 <expand macro="tax_show_macro" value="10"/>
100 <param argument="showRemainingTaxa" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Display sum of remaining taxa" help="Add an additional row at the bottom displaying the sum of all remaining taxa that are not part of the top tax_show most abundant taxa."/>
101 <expand macro="tax_empty_macro"/>
102 <conditional name="plot_values_cond">
103 <param argument="plot_values" type="select" label="Plot the values on the heatmap">
104 <option value="TRUE">Yes</option>
105 <option value="FALSE">No</option>
106 </param>
107 <when value="TRUE">
108 <param name="plot_values_size" type="integer" value="4" label="Size of the plotted values"/>
109 </when>
110 <when value="FALSE"/>
111 </conditional>
112 <param argument="plot_colorscale" type="select" label="Type of scale used for coloring abundances">
113 <option value="sqrt">Square root (sqrt)</option>
114 <option value="log10" selected="true">Log (log10)</option>
115 </param>
116 <param argument="plot_na" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Color missing values with the lowest color in the scale"/>
117 <param argument="measure" type="select" label="Value to show across the groups">
118 <option value="mean">Mean</option>
119 <option value="max">Maximum</option>
120 <option value="median">Median</option>
121 </param>
122 <param argument="min_abundance" type="float" value="0.1" min="0" optional="true" label="Maximum abundance" help="All values below this value are given the same color."/>
123 <param argument="max_abundance" type="float" value="" min="0" optional="true" label="Maximum abundance" help="All values above this value are given the same color." />
124
125 <conditional name="sort_by_cond">
126 <param name="sort_by_sel" type="select" label="Sort heatmap by most abundant taxa">
127 <option value="no">No</option>
128 <option value="group">in a group of samples</option>
129 <option value="sample">in a specific sample</option>
130 </param>
131 <when value="no"/>
132 <when value="group">
133 <param argument="sort_by" type="select" optional="true" label="Group to sort by">
134 <options from_dataset="metadata_list">
135 <column name="name" index="1"/>
136 <column name="value" index="1"/>
137 <filter type="param_value" column="0" ref="group_by"/>
138 <filter type="unique_value" column="1"/>
139 </options>
140 </param>
141 </when>
142 <when value="sample">
143 <param argument="sort_by" type="select" optional="true" label="Sample to sort by">
144 <options from_dataset="metadata_list">
145 <column name="name" index="1"/>
146 <column name="value" index="1"/>
147 <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
148 <filter type="unique_value" column="1"/>
149 </options>
150 </param>
151 </when>
152 </conditional>
153 <!-- https://github.com/KasperSkytte/ampvis2/issues/168
154 if this is possible again reuse: metadata_sample_or_variable_select ? -->
155 <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/>
156 <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/>
157
158 <conditional name="plot_functions_cond">
159 <param name="plot_functions_sel" type="select" label="Show functional information about the Genus-level OTUs" help="Produces a 2-column grid plot, showing known functional information about the Genus-level OTUs next to the heatmap. When using this feature, make sure that either tax_aggregate or tax_add is set to Genus and that Genus is the lowest level in either.">
160 <option value="no">No</option>
161 <option value="midasfieldguide">Use data from midasfieldguide.org</option>
162 <option value="file">Use data from a dataset in the history</option>
163 </param>
164 <when value="no"/>
165 <when value="file">
166 <!-- neeed tsv here since tabular does not fill the column_names
167 metadata and therefore the data_meta filter in the functions
168 select would not work-->
169 <param argument="function_data" type="data" format="tsv" label="Tabular dataset with functional information at Genus level" help="See help"/>
170 <param argument="functions" type="select" multiple="true" label="Function(s) to include">
171 <options>
172 <filter type="data_meta" ref="function_data" key="column_names"/>
173 <filter type="remove_value" value="Genus"/>
174 </options>
175 </param>
176 </when>
177 <when value="midasfieldguide">
178 <param name="functions" type="select" multiple="true" label="Function(s) to include">
179 <option value="MiDAS" selected="true">MiDAS</option>
180 <option value="Filamentous" selected="true">Filamentous</option>
181 <option value="AOB" selected="true">AOB</option>
182 <option value="NOB" selected="true">PAO</option>
183 <option value="GAO" selected="true">GAO</option>
184 </param>
185 </when>
186 </conditional>
187 <expand macro="out_format_macro">
188 <option value="tabular">Table</option>
189 </expand>
190 </inputs>
191 <outputs>
192 <expand macro="out_macro">
193 <filter>output_options["out_format"] != "tabular"</filter>
194 </expand>
195 <data name="plot_raw" format="tabular" label="${tool.name} on ${on_string}: Table">
196 <filter>output_options["out_format"] == "tabular"</filter>
197 </data>
198 </outputs>
199 <tests>
200 <!-- defaults -->
201 <test expect_num_outputs="1">
202 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
203 <output name="plot" value="AalborgWWTPs-heatmap.pdf" ftype="pdf" compare="sim_size"/>
204 </test>
205 <!-- group and facet-->
206 <test expect_num_outputs="1">
207 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
208 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
209 <param name="group_by" value="Plant"/>
210 <param name="facet_by" value="Year"/>
211 <output name="plot_raw" value="AalborgWWTPs-heatmap-group-facet.pdf" ftype="pdf" compare="sim_size"/>
212 </test>
213 <!-- group and facet and test raw output -->
214 <test expect_num_outputs="1">
215 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
216 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
217 <param name="group_by" value="Plant"/>
218 <param name="facet_by" value="Year"/>
219 <param name="out_format" value="tabular"/>
220 <output name="plot_raw" value="AalborgWWTPs-heatmap-group-facet.tsv" ftype="tabular"/>
221 </test>
222 <!-- normalise -->
223 <test expect_num_outputs="1">
224 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
225 <param name="normalise" value="true"/>
226 <output name="plot" value="AalborgWWTPs-heatmap-normalise.pdf" ftype="pdf" compare="sim_size"/>
227 </test>
228 <!-- normalise by a specific sample -->
229 <test expect_num_outputs="1">
230 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
231 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
232 <param name="normalise" value="true"/>
233 <param name="normalise_by" value="16SAMP-747"/>
234 <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_sample.pdf" ftype="pdf" compare="sim_size"/>
235 </test>
236 <!-- normalise by a metadata variable
237 https://github.com/KasperSkytte/ampvis2/issues/168 -->
238 <!-- <test expect_num_outputs="1">
239 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
240 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
241 <param name="group_by" value="Plant"/>
242 <conditional name="normalise_by_cond">
243 <param name="normalise_by_sel" value="variable"/>
244 <param name="normalise_by" value="Plant"/>
245 </conditional>
246 <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_variable.pdf" ftype="pdf"/>
247 </test> -->
248 <!-- tax options -->
249 <test expect_num_outputs="1">
250 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
251 <param name="tax_aggregate" value="Order"/>
252 <param name="tax_add" value="Class"/>
253 <param name="tax_show" value="5"/>
254 <param name="showRemainingTaxa" value="true"/>
255 <output name="plot" value="AalborgWWTPs-heatmap-tax.pdf" ftype="pdf" compare="sim_size"/>
256 </test>
257 <!-- sort by a specific sample -->
258 <test expect_num_outputs="1">
259 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
260 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
261 <conditional name="sort_by_cond">
262 <param name="sort_by_sel" value="sample"/>
263 <param name="sort_by" value="16SAMP-747"/>
264 </conditional>
265 <output name="plot" value="AalborgWWTPs-heatmap-sort_by_sample.pdf" ftype="pdf" compare="sim_size"/>
266 </test>
267 <!-- sort by a group of samples -->
268 <test expect_num_outputs="1">
269 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
270 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
271 <param name="group_by" value="Period"/>
272 <conditional name="sort_by_cond">
273 <param name="sort_by_sel" value="group"/>
274 <param name="sort_by" value="Winter"/>
275 </conditional>
276 <output name="plot" value="AalborgWWTPs-heatmap-sort_by_group.pdf" ftype="pdf" compare="sim_size"/>
277 </test>
278 <test expect_num_outputs="1">
279 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
280 <param name="tax_aggregate" value="Genus"/>
281 <conditional name="plot_functions_cond">
282 <param name="plot_functions_sel" value="midasfieldguide"/>
283 <param name="functions" value="MiDAS,Filamentous,AOB,NOB,GAO"/>
284 </conditional>
285 <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_midas.pdf" ftype="pdf" compare="sim_size"/>
286 </test>
287 <test expect_num_outputs="1">
288 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
289 <param name="tax_aggregate" value="Genus"/>
290 <conditional name="plot_functions_cond">
291 <param name="plot_functions_sel" value="file"/>
292 <param name="function_data" value="AalborgWWTPs-functions.tsv" ftype="tsv"/>
293 <param name="functions" value="Foo,Bar"/>
294 </conditional>
295 <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf" compare="sim_size"/>
296 </test>
297
298 </tests>
299 <help><![CDATA[
300 What it does
301 ============
302
303 Generates a heatmap of amplicon data by using sample metadata to aggregate
304 samples and taxonomy to aggregate OTUs.
305
306 The Galaxy tool calls the `amp_heatmap
307 <https://kasperskytte.github.io/ampvis2/reference/amp_heatmap.html>`_ function
308 of the ampvis2 package.
309
310 @HELP_RELATIVE_ABUNDANCES@
311
312 Input
313 =====
314
315 @HELP_RDS_INPUT@
316
317 @HELP_METADATA_LIST_INPUT@
318
319 Funtional data at genus level can be added to the plot. By default the
320 information is taken from `midasfieldguide <https://midasfieldguide.org/>`_ but
321 it can also be given by a dataset (parameter function_data):
322
323 - The first column must be the Genus names and
324 - any other column(s) can be any property or metabolic function of the individual Genera.
325
326 Output
327 ======
328
329 Heatmap in the chosen output format.
330 If table output is chosen the data presented in the heatmap is written into a tabular dataset.
331 ]]></help>
332 <expand macro="citations"/>
333 </tool>