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comparison macros.xml @ 0:f77f7c426d6f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
author iuc
date Mon, 04 Apr 2022 10:18:21 +0000
parents
children 0feab98f9577
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-1:000000000000 0:f77f7c426d6f
1 <macros>
2 <token name="@TOOL_VERSION@">2.7.17</token>
3 <token name="@VERSION_SUFFIX@">0</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="2.1.1">r-readr</requirement>
12 </requirements>
13 <version_command><![CDATA[
14 echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ")
15 ]]></version_command>
16
17 </xml>
18 <xml name="citations">
19 <citations>
20 <citation type="doi">10.1101/299537</citation>
21 <yield/>
22 </citations>
23 </xml>
24
25 <xml name="rds_input_macro">
26 <param argument="data" type="data" format="ampvis2" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/>
27 </xml>
28
29 <xml name="rds_metadata_input_macro" token_metadata_optional="true">
30 <expand macro="rds_input_macro"/>
31 <param name="metadata_list" type="data" optional="@METADATA_OPTIONAL@" format="tabular" label="Metadata list">
32 <validator type="expression" message="The metadatalist file must have 3 columns"><![CDATA[value.metadata.columns == 4]]></validator>
33 </param>
34 </xml>
35
36 <token name="@SAVE_TAX_LIST@"><![CDATA[
37 for(level in colnames(data\$tax)){
38 for(u in unique(data\$tax[level])){
39 write(u, file="$taxonomy_list_out", append=T)
40 }
41 }
42 ]]></token>
43
44 <token name="@SAVE_METADATA_LIST@"><![CDATA[
45 classes <- sapply(data\$metadata, class)
46 for(name in names(data\$metadata)){
47 ## check if it is the column containing the sample names
48 ## the additional column in the ist file can the be used
49 ## to filter SampleIDs from select inputs
50 ## (check for character columns only .. since data in the column is otherwise converted to the corresponding type .. which fails)
51 if(classes[[name]] == "character" && all(data\$metadata[[name]] == rownames(data\$metadata))){
52 sample_names <- TRUE;
53 }else{
54 sample_names <- FALSE;
55 }
56 for(m in unique(data\$metadata[[name]])){
57 write(paste(name, m, sample_names, classes[[name]], sep="\t"), file="$metadata_list_out", append=T);
58 }
59 }
60 ]]></token>
61
62 <!-- defaults can be set by redefining an on option with selected="true" -->
63 <xml name="taxlevel_macro" token_argument="" token_multiple="false" token_optional="false" token_label="" token_help="">
64 <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
65 <option value="OTU">OTU/ASV</option>
66 <option value="Species">Species</option>
67 <option value="Genus">Genus</option>
68 <option value="Family">Family</option>
69 <option value="Order">Order</option>
70 <option value="Class">Class</option>
71 <option value="Phylum">Phylum</option>
72 <option value="Kingdom">Kingdom</option>
73 <yield/>
74 </param>
75 </xml>
76
77 <xml name="tax_empty_macro">
78 <param argument="tax_empty" type="select" label="How to show OTUs without taxonomic information">
79 <option value="remove">Remove OTUs without taxonomic information</option>
80 <option value="best" selected="true">Use the best classification possible</option>
81 <option value="OTU">Display the OTU name</option>
82 </param>
83 </xml>
84
85 <token name="@TAX_SHOW@"><![CDATA[
86 #if $tax_show_cond.tax_show_sel == "number"
87 tax_show = $tax_show_cond.tax_show,
88 #else
89 #set tax_show_list='c("' + '", "'.join(str($tax_show_cond.tax_show).split(",")) + '")'
90 tax_show = $tax_show_list
91 #end if
92 ]]></token>
93 <xml name="tax_show_macro" token_value="">
94 <conditional name="tax_show_cond">
95 <param name="tax_show_sel" type="select" label="Limit the number of shown taxa">
96 <option value="number">Select a number of taxa to show</option>
97 <option value="explicit">Manually select taxa to show</option>
98 </param>
99 <when value="number">
100 <param argument="tax_show" type="integer" value="@VALUE@" min="1" label="Number of taxa to show"/>
101 </when>
102 <when value="explicit">
103 <param name="taxonomy_list" format="tabular" type="data" optional="false" label="Taxonomy list" help="Generated with ampvis2: load"/>
104 <param argument="tax_show" type="select" multiple="true" optional="false" label="Taxa to show">
105 <options from_dataset="taxonomy_list">
106 <column name="name" index="0"/>
107 <column name="value" index="0"/>
108 <!-- TODO filter by tax_aggregate level? -->
109 </options>
110 </param>
111 </when>
112 </conditional>
113 </xml>
114
115 <xml name="metadata_select" token_quote="__" tokens="argument,label" token_an="argument" token_optional="true" token_multiple="false" token_help="">
116 <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__">
117 <options from_dataset="metadata_list">
118 <column name="name" index="0"/>
119 <column name="value" index="0"/>
120 <filter type="unique_value" column="0"/>
121 <yield name="options"/>
122 </options>
123 <yield/>
124 </param>
125 </xml>
126
127 <xml name="metadata_select_discrete" tokens="argument,label" token_optional="true" token_multiple="false" token_help="">
128 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
129 <token name="options">
130 <filter type="static_value" column="3" value="numeric" keep="false"/>
131 </token>
132 <yield/>
133 </expand>
134 </xml>
135
136 <xml name="metadata_select_numeric" tokens="argument,label" token_optional="true" token_multiple="false" token_help="">
137 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
138 <token name="options">
139 <filter type="static_value" column="3" value="character" keep="false"/>
140 <filter type="static_value" column="3" value="Date" keep="false"/>
141 </token>
142 <yield/>
143 </expand>
144 </xml>
145
146 <xml name="metadata_select_date" tokens="argument,label" token_optional="true" token_multiple="false" token_help="">
147 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
148 <token name="options">
149 <filter type="static_value" column="3" value="Date" keep="true"/>
150 </token>
151 <yield/>
152 </expand>
153 </xml>
154
155 <xml name="metadata_sample_select" token_argument="">
156 <conditional name="@ARGUMENT@_cond">
157 <param name="@ARGUMENT@_sel" type="select">
158 <option value="no">No</option>
159 <option value="variable">Metadata variable</option>
160 <option value="sample">Specific sample</option>
161 </param>
162 <when value="no"/>
163 <when value="variable">
164 <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/>
165 </when>
166 <when value="sample">
167 <param argument="@ARGUMENT@" type="select" optional="true">
168 <options from_dataset="metadata_list">
169 <column name="name" index="1"/>
170 <column name="value" index="1"/>
171 <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
172 <filter type="unique_value" column="1"/>
173 </options>
174 </param>
175 </when>
176 </conditional>
177 </xml>
178
179 <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true">
180 <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@">
181 <options from_dataset="taxonomy_list">
182 <column name="name" index="0"/>
183 <column name="value" index="0"/>
184 <filter type="unique_value" column="0"/>
185 </options>
186 <yield/>
187 </param>
188 </xml>
189
190 <xml name="facet_scales_macro" token_argument="" token_label="Scales of the facets" token_help="">
191 <param argument="@ARGUMENT@" type="select" optional="true" label="@LABEL@" help="@HELP@">
192 <option value="fixed">Same scale</option>
193 <option value="free">Free scale</option>
194 <option value="free_x">Free x-scale</option>
195 <option value="free_y">Free y-scale</option>
196 </param>
197 </xml>
198
199 <token name="@OUTPUT_TOKEN@">
200 ggsave("$plot",
201 print(plot),
202 device="$output_options.out_format"
203 #if str($output_options.plot_width) != ''
204 , width = $output_options.plot_width
205 #end if
206 #if str($output_options.plot_height) != ''
207 , height = $output_options.plot_height
208 #end if
209 )
210 </token>
211 <xml name="out_macro" token_name="plot" token_label="">
212 <data name="@NAME@" format="pdf" label="${tool.name} on ${on_string}@LABEL@">
213 <yield/>
214 <change_format>
215 <when input="output_options.out_format" value="png" format="png" />
216 <when input="output_options.out_format" value="svg" format="svg" />
217 </change_format>
218 </data>
219 </xml>
220 <xml name="out_format_macro">
221 <section name="output_options" title="Output options" expanded="false">
222 <param name="out_format" type="select" label="Output format">
223 <option value="pdf" selected="true">PDF</option>
224 <option value="png">PNG</option>
225 <option value="svg">SVG</option>
226 <yield/>
227 </param>
228 <param name="plot_width" type="float" value="" min="1" optional="true" label="Plot width in cm"/>
229 <param name="plot_height" type="float" value="" min="1" optional="true" label="Plot height in cm"/>
230 </section>
231 </xml>
232
233 <token name="@RAREFY_TOKEN@">
234 #if str($rarefy) != ""
235 , rarefy = $rarefy
236 #end if
237 </token>
238 <xml name="rarefy_macro" token_help="">
239 <param argument="rarefy" type="integer" optional="true" value="" min="0" label="Rarefy species richness to this value" help="@HELP@"/>
240 </xml>
241
242 <xml name="normalise_macro" token_checked="false">
243 <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."/>
244 </xml>
245
246 <token name="@HELP_RDS_INPUT@">
247 An ampvis2 RDS dataset obtained by the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or one of the
248 ``ampvis2: subset ...`` tools).
249 </token>
250 <token name="@HELP_METADATA_LIST_INPUT@">
251 The metadata list output of the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or the
252 ``ampvis2: subset sample`` tool). This input is only used for providing
253 values to the parameters alowing to select metadata variables or values.
254 </token>
255
256 <token name="@HELP_RELATIVE_ABUNDANCES@">
257 Preserving relative abundances in a subset of larger data
258 =========================================================
259
260 By default the raw read counts in the abundance matrix are normalised
261 (transformed to percentages) by some ampvis2 plotting tools (for
262 example ``ampvis2: heatmap``, ``ampvis2: timeseries``, and more).
263 If this is applied to data generated by one of the ``ampvis2: subset ...`` tools
264 this means that the relative
265 abundances shown will be calculated based on the remaining taxa after the
266 subset, not including the removed taxa, if any. To circumvent this, enable
267 ``normalise`` when subsetting with the ``ampvis2: subset ...``` tools,
268 and then disable ``normalise`` in the plotting tool. This will
269 transform the OTU counts to relative abundances BEFORE the subset.
270 </token>
271 </macros>