Mercurial > repos > iuc > snapatac2_plotting

comparison plotting.xml @ 0:4a1c0fe5be8f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
author iuc
date Fri, 05 Jul 2024 11:05:33 +0000
parents
children efd9d236bfd2
comparison
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-1:000000000000 0:4a1c0fe5be8f
1 <tool id="snapatac2_plotting" name="SnapATAC2 Plotting" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <requirements>
6 <expand macro="requirements"/>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 @PREP_ADATA@
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.frag_size_distr'
18 #if $method.log_scale
19 fig = sa.pl.frag_size_distr(adata, show=False)
20 fig.update_yaxes(type="log")
21 sa.pl.render_plot(fig, @CMD_params_render_plot@)
22 #else
23 sa.pl.frag_size_distr(adata, @CMD_params_render_plot@)
24 #end if
25 #else if $method.method == 'pl.tsse'
26 sa.pl.tsse(
27 adata,
28 min_fragment = $method.min_fragment,
29 @CMD_params_render_plot@
30 )
31 #else if $method.method == 'pl.umap'
32 sa.pl.umap(
33 adata,
34 color = '$method.color',
35 use_rep = '$method.use_rep',
36 #if $method.marker_size
37 marker_size = $method.marker_size,
38 #end if
39 marker_opacity = $method.marker_opacity,
40 #if $method.sample_size
41 sample_size = $method.sample_size,
42 #end if
43 @CMD_params_render_plot@
44 )
45 #else if $method.method == 'pl.regions'
46 sa.pl.regions(
47 adata,
48 groupby = '$method.groupby',
49 peaks = '$method.peaks',
50 @CMD_params_render_plot@
51 )
52 #else if $method.method == 'pl.spectral_eigenvalues'
53 sa.pl.spectral_eigenvalues(
54 adata,
55 @CMD_params_render_plot@
56 )
57 #end if
58 ]]></configfile>
59 </configfiles>
60 <inputs>
61 <conditional name="method">
62 <param name="method" type="select" label="Method used for plotting">
63 <option value="pl.frag_size_distr">Plot fragment size distribution, using 'pl.frag_size_distr'</option>
64 <option value="pl.tsse">Plot the TSS enrichment vs. number of fragments density figure, using 'pl.tsse'</option>
65 <option value="pl.umap">Plot the UMAP embedding, using 'pl.umap'</option>
66 <option value="pl.spectral_eigenvalues">Plot the eigenvalues of spectral embedding, using 'pl.spectral_eigenvalues'</option>
67 </param>
68 <when value="pl.frag_size_distr">
69 <expand macro="inputs_anndata"/>
70 <param name="log_scale" type="boolean" checked="False" label="Change the y-axis (fragment counts) to log scale"/>
71 <expand macro="params_render_plot"/>
72 </when>
73 <when value="pl.tsse">
74 <expand macro="inputs_anndata"/>
75 <param argument="min_fragment" type="integer" value="500" label="Minimum number of unique fragments"/>
76 <expand macro="params_render_plot"/>
77 </when>
78 <when value="pl.umap">
79 <expand macro="inputs_anndata"/>
80 <param argument="color" type="text" value="" optional="true" label="Color"/>
81 <param argument="use_rep" type="text" value="X_umap" label="Use the indicated representation in .obsm"/>
82 <param argument="marker_size" type="float" value="" optional="true" label="Size of the dots"/>
83 <param argument="marker_opacity" type="float" value="1" label="Opactiy of the dots"/>
84 <param argument="sample_size" type="integer" value="" optional="true" label="Number of cells to use"/>
85 <expand macro="params_render_plot"/>
86 </when>
87 <when value="pl.spectral_eigenvalues">
88 <expand macro="inputs_anndata"/>
89 <expand macro="params_render_plot"/>
90 </when>
91 </conditional>
92 <expand macro="inputs_common_advanced"/>
93 </inputs>
94 <outputs>
95 <data name="out_png" format="png" from_work_dir="plot.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
96 <filter>method['out_file'] == 'png'</filter>
97 </data>
98 <data name="out_pdf" format="pdf" from_work_dir="plot.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
99 <filter>method['out_file'] == 'pdf'</filter>
100 </data>
101 <data name="out_svg" format="svg" from_work_dir="plot.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
102 <filter>method['out_file'] == 'svg'</filter>
103 </data>
104 <data name="hidden_output" format="txt" label="Log file" hidden="true">
105 <filter>advanced_common['show_log']</filter>
106 </data>
107 </outputs>
108 <tests>
109 <test expect_num_outputs="2">
110 <!-- pl.frag_size_distr -->
111 <conditional name="method">
112 <param name="method" value="pl.frag_size_distr"/>
113 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
114 <param name="log_scale" value="True"/>
115 <param name="out_file" value="pdf"/>
116 <expand macro="render_plot_test"/>
117 </conditional>
118 <section name="advanced_common">
119 <param name="show_log" value="true"/>
120 </section>
121 <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.frag_size_distr.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
122 <output name="hidden_output">
123 <assert_contents>
124 <has_text_matching expression="sa.pl.frag_size_distr"/>
125 <has_text_matching expression="fig.update_yaxes"/>
126 <expand macro="render_plot_matching_text"/>
127 </assert_contents>
128 </output>
129 </test>
130 <test expect_num_outputs="2">
131 <!-- pl.tsse -->
132 <conditional name="method">
133 <param name="method" value="pl.tsse"/>
134 <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
135 <param name="min_fragment" value="500"/>
136 <param name="out_file" value="png"/>
137 <expand macro="render_plot_test"/>
138 </conditional>
139 <section name="advanced_common">
140 <param name="show_log" value="true"/>
141 </section>
142 <output name="hidden_output">
143 <assert_contents>
144 <has_text_matching expression="sa.pl.tsse"/>
145 <has_text_matching expression="min_fragment = 500"/>
146 <expand macro="render_plot_matching_text"/>
147 </assert_contents>
148 </output>
149 <output name="out_png" location="https://zenodo.org/records/11260316/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
150 </test>
151 <test expect_num_outputs="2">
152 <!-- pl.umap -->
153 <conditional name="method">
154 <param name="method" value="pl.umap"/>
155 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
156 <param name="color" value="leiden"/>
157 <param name="use_rep" value="X_umap"/>
158 <param name="marker_size" value="1"/>
159 <param name="marker_opacity" value="0.8"/>
160 <param name="sample_size" value="100"/>
161 <expand macro="render_plot_test"/>
162 <param name="out_file" value="svg"/>
163 </conditional>
164 <section name="advanced_common">
165 <param name="show_log" value="true"/>
166 </section>
167 <output name="hidden_output">
168 <assert_contents>
169 <has_text_matching expression="sa.pl.umap"/>
170 <has_text_matching expression="color = 'leiden'"/>
171 <has_text_matching expression="use_rep = 'X_umap'"/>
172 <has_text_matching expression="marker_size = 1"/>
173 <has_text_matching expression="marker_opacity = 0.8"/>
174 <has_text_matching expression="sample_size = 100"/>
175 <expand macro="render_plot_matching_text"/>
176 </assert_contents>
177 </output>
178 <output name="out_svg" location="https://zenodo.org/records/11260316/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/>
179 </test>
180 <test expect_num_outputs="2">
181 <!-- pl.spectral_eigenvalues -->
182 <conditional name="method">
183 <param name="method" value="pl.spectral_eigenvalues"/>
184 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
185 <expand macro="render_plot_test"/>
186 <param name="out_file" value="pdf"/>
187 </conditional>
188 <section name="advanced_common">
189 <param name="show_log" value="true"/>
190 </section>
191 <output name="hidden_output">
192 <assert_contents>
193 <has_text_matching expression="sa.pl.spectral_eigenvalues"/>
194 <expand macro="render_plot_matching_text"/>
195 </assert_contents>
196 </output>
197 <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
198 </test>
199 </tests>
200 <help><![CDATA[
201 Plot fragment size distribution, using `pl.frag_size_distr`
202 ===========================================================
203
204 Plot fragment size distribution.
205
206 `metrics.frag_size_distr` must be ran first in order to use this function.
207
208 Plot the TSS enrichment vs. number of fragments density figure, using `pl.tsse`
209 ===============================================================================
210
211 Plot the TSS enrichment vs. number of fragments density figure.
212
213 More details on the `SnapATAC2 documentation
214 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.tsse.html>`__
215
216 Plot the UMAP embedding, using `pl.umap`
217 ========================================
218
219 Plot the UMAP embedding.
220
221 More details on the `SnapATAC2 documentation
222 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__
223
224 Plot the eigenvalues of spectral embedding, using `pl.spectral_eigenvalues`
225 ===========================================================================
226
227 Plot the eigenvalues of spectral embedding.
228
229 More details on the `SnapATAC2 documentation
230 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__
231 ]]></help>
232 <expand macro="citations"/>
233 </tool>