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comparison plot_muon.xml @ 0:04f784475be4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/muon commit fef10e0d450018d1e6ba4cbbda76c7686edc8aae
author iuc
date Sat, 25 Oct 2025 21:00:22 +0000
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-1:000000000000 0:04f784475be4
1 <tool id="plot_muon" name="muon plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="bio_tools"/>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[
9 @COPY_MUDATA@
10 @CMD@
11 ]]></command>
12 <configfiles>
13 <configfile name="script_file"><![CDATA[
14 @CMD_imports@
15 @CMD_read_inputs@
16
17 #if $method.method == "pl.embedding"
18 plot = mu.pl.embedding(
19 mdata,
20 basis='$method.basis',
21 @CMD_params_embedding@
22 return_fig=True
23 )
24 plot.savefig("plot.$plot_ext")
25
26 #else if $method.method == "pl.histogram"
27 plot = mu.pl.histogram(
28 mdata,
29 #if $method.key_variables.type == "var_names"
30 #set $key_list = mdata.var_names
31 #else if $method.key_variables.type == "obs"
32 #set $key_list = mdata.obs.select_dtypes(exclude=['category']).columns
33 #else if $method.key_variables.type == "custom"
34 #set $key_list=([x.strip() for x in str($method.key_variables.keys).split(',')])
35 #end if
36 keys=$key_list,
37 #if $method.groupby
38 groupby='$method.groupby',
39 #end if
40 save='plot.$plot_ext'
41 )
42 os.rename(os.path.join('figures', 'histogram_plot.$plot_ext'), 'plot.$plot_ext')
43
44 #else if $method.method == "pl.mofa"
45 plot = mu.pl.mofa(
46 mdata,
47 @CMD_params_embedding@
48 return_fig=True
49 )
50 plot.savefig("plot.$plot_ext")
51
52 #else if $method.method == "pl.mofa_loadings"
53 plot = mu.pl.mofa_loadings(
54 mdata,
55 #if $method.factors
56 factors='$method.factors',
57 #end if
58 include_lowest=$method.include_lowest,
59 #if str($method.n_points)
60 n_points=$method.n_points,
61 #end if
62 save='plot.$plot_ext'
63 )
64 os.rename(os.path.join('figures', 'mofa_loadings_plot.$plot_ext'), 'plot.$plot_ext')
65
66 #else if $method.method == "pl.umap"
67 plot = mu.pl.umap(
68 mdata,
69 @CMD_params_embedding@
70 return_fig=True
71 )
72 plot.savefig("plot.$plot_ext")
73
74 #end if
75
76 ]]></configfile>
77 </configfiles>
78 <inputs>
79 <expand macro="inputs_mudata"/>
80 <conditional name="method">
81 <param name="method" type="select" label="Method used for plotting">
82 <option value="pl.embedding">Scatter: Scatter plot along observations (.obs column), using 'muon.pl.embedding'</option>
83 <option value="pl.histogram">Histogram: Plot Histogram of Fragment lengths within specified region, using 'muon.pl.histogram'</option>
84 <option value="pl.mofa">Scatter: Scatter plot in MOFA factor coordinates, using 'muon.pl.mofa'</option>
85 <option value="pl.mofa_loadings">Ranking: Rank genes according to contributions to MOFA factors, using 'muon.pl.mofa_loadings'</option>
86 <option value="pl.umap">Scatter: UMAP scatter plot, using 'muon.pl.umap'</option>
87 </param>
88 <when value="pl.embedding">
89 <param argument="basis" type="text" value="X_mofa" label="Name of the obsm basis to use" help="can also be a basis inside any modality, e.g. 'rna:X_pca'">
90 <expand macro="sanitize_query" />
91 </param>
92 <expand macro="params_embedding"/>
93 </when>
94 <when value="pl.histogram">
95 <expand macro="param_keys"/>
96 <param argument="groupby" type="text" optional="true" label="Column name(s) of .obs slot of the AnnData object according to which the plot is split">
97 <expand macro="sanitize_query" />
98 </param>
99 </when>
100 <when value="pl.mofa">
101 <expand macro="params_embedding"/>
102 </when>
103 <when value="pl.mofa_loadings">
104 <param argument="factors" type="text" optional="true" label="Comma separated list of factors" help="For example, '1,2,3' means [1, 2, 3], first, second, third factors">
105 <expand macro="sanitize_query" />
106 </param>
107 <param argument="include_lowest" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to show the variables with both highest and lowest loadings"/>
108 <param argument="n_points" type="integer" optional="true" label="Number of variables to plot for each factor"/>
109 </when>
110 <when value="pl.umap">
111 <expand macro="params_embedding"/>
112 </when>
113 </conditional>
114 <param name="plot_ext" type="select" label="Type of output plot">
115 <option value="png" selected="true">PNG</option>
116 <option value="svg">SVG</option>
117 <option value="pdf">PDF</option>
118 </param>
119 <expand macro="inputs_common_advanced" />
120 </inputs>
121 <outputs>
122 <data name="out_png" format="png" from_work_dir="plot.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
123 <filter>plot_ext == 'png'</filter>
124 </data>
125 <data name="out_pdf" format="pdf" from_work_dir="plot.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
126 <filter>plot_ext == 'pdf'</filter>
127 </data>
128 <data name="out_svg" format="svg" from_work_dir="plot.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
129 <filter>plot_ext == 'svg'</filter>
130 </data>
131 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
132 <filter>advanced_common['show_log']</filter>
133 </data>
134 </outputs>
135 <tests>
136 <test expect_num_outputs="2">
137 <!-- test1: pl.embedding -->
138 <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.mofa.h5mu"/>
139 <param name="method" value="pl.embedding"/>
140 <param name="basis" value="X_mofa"/>
141 <param name="color" value="rna:leiden,atac:leiden"/>
142 <param name="use_raw" value="False"/>
143 <param name="plot_ext" value="pdf"/>
144 <section name="advanced_common">
145 <param name="show_log" value="true" />
146 </section>
147 <output name="hidden_output">
148 <assert_contents>
149 <has_text_matching expression="mu.pl.embedding"/>
150 <has_text_matching expression="basis='X_mofa'"/>
151 <has_text_matching expression="color=\['rna:leiden', 'atac:leiden'\]"/>
152 <has_text_matching expression="use_raw=False"/>
153 </assert_contents>
154 </output>
155 <output name="out_pdf" ftype="pdf" location="https://zenodo.org/records/12570984/files/pl.embedding.pdf" compare="sim_size" delta_frac="0.1"/>
156 </test>
157 <test expect_num_outputs="2">
158 <!-- test2 pl.histogram -->
159 <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.mofa.h5mu"/>
160 <param name="method" value="pl.histogram"/>
161 <conditional name="key_variables">
162 <param name="type" value="custom"/>
163 <param name="keys" value="rna:n_genes_by_counts,rna:total_counts"/>
164 </conditional>
165 <param name="plot_ext" value="png"/>
166 <section name="advanced_common">
167 <param name="show_log" value="true" />
168 </section>
169 <output name="hidden_output">
170 <assert_contents>
171 <has_text_matching expression="mu.pl.histogram"/>
172 <has_text_matching expression="keys=\['rna:n_genes_by_counts', 'rna:total_counts'\]"/>
173 </assert_contents>
174 </output>
175 <output name="out_png" ftype="png" location="https://zenodo.org/records/12570984/files/pl.histogram.png" compare="image_diff"/>
176 </test>
177 <test expect_num_outputs="2">
178 <!-- test3: pl.mofa -->
179 <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.mofa.h5mu"/>
180 <param name="method" value="pl.mofa"/>
181 <param name="use_raw" value="False"/>
182 <param name="plot_ext" value="svg"/>
183 <section name="advanced_common">
184 <param name="show_log" value="true" />
185 </section>
186 <output name="hidden_output">
187 <assert_contents>
188 <has_text_matching expression="mu.pl.mofa"/>
189 <has_text_matching expression="use_raw=False"/>
190 </assert_contents>
191 </output>
192 <output name="out_svg" ftype="svg" location="https://zenodo.org/records/12570984/files/pl.mofa.svg" compare="sim_size" delta_frac="0.1"/>
193 </test>
194 <test expect_num_outputs="2">
195 <!-- test4: pl.mofa_loadings -->
196 <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.mofa.h5mu"/>
197 <param name="method" value="pl.mofa_loadings"/>
198 <param name="factors" value="1,2,3"/>
199 <param name="include_lowest" value="True"/>
200 <section name="advanced_common">
201 <param name="show_log" value="true" />
202 </section>
203 <output name="hidden_output">
204 <assert_contents>
205 <has_text_matching expression="mu.pl.mofa_loadings"/>
206 <has_text_matching expression="factors='1,2,3'"/>
207 <has_text_matching expression="include_lowest=True"/>
208 </assert_contents>
209 </output>
210 <output name="out_png" ftype="png" location="https://zenodo.org/records/12570984/files/pl.mofa_loadings.png" compare="image_diff"/>
211 </test>
212 <test expect_num_outputs="2">
213 <!-- test5: pl.umap -->
214 <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.umap.h5mu"/>
215 <param name="method" value="pl.umap"/>
216 <param name="use_raw" value="False"/>
217 <section name="advanced_common">
218 <param name="show_log" value="true" />
219 </section>
220 <output name="hidden_output">
221 <assert_contents>
222 <has_text_matching expression="mu.pl.umap"/>
223 <has_text_matching expression="use_raw=False"/>
224 </assert_contents>
225 </output>
226 <output name="out_png" ftype="png" location="https://zenodo.org/records/12570984/files/pl.umap.png" compare="image_diff"/>
227 </test>
228 </tests>
229 <help><![CDATA[
230 Scatter: Scatter plot along observations (.obs column) ('muon.pl.embedding')
231 ============================================================================
232
233 Produce a scatter plot in the define basis (.obs), which can also be a basis inside any modality.
234
235 More details on the `muon documentation
236 <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.embedding.html#muon.pl.embedding>`__
237
238 Scatter: Scatter plot in MOFA factor coordinates ('muon.pl.mofa')
239 =================================================================
240
241 Scatter plot in MOFA factors coordinates.
242
243 More details on the `muon documentation
244 <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.mofa.html#muon.pl.mofa>`__
245
246 Scatter: UMAP scatter plot ('muon.pl.umap')
247 ===========================================
248
249 UMAP Scatter plot.
250
251 More details on the `muon documentation
252 <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.umap.html#muon.pl.umap>`__
253
254 Histogram: Plot Histogram of Fragment lengths within specified region ('muon.pl.histogram')
255 ===========================================================================================
256
257 Plot Histogram of Fragment lengths within specified region.
258
259 More details on the `muon documentation
260 <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.histogram.html#muon.pl.histogram>`__
261
262 Ranking: Rank genes according to contributions to MOFA factors ('muon.pl.mofa_loadings')
263 ========================================================================================
264
265 Rank genes according to contributions to MOFA factors.
266
267 More details on the `muon documentation
268 <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.mofa_loadings.html#muon.pl.mofa_loadings>`__
269 ]]></help>
270 <expand macro="citations"/>
271 </tool>