Mercurial > repos > iuc > snapatac2_plotting

comparison plotting.xml @ 6:1ac4a5f05f33 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
author iuc
date Tue, 25 Nov 2025 16:41:12 +0000
parents 05bd4db20227
children
comparison
equal deleted inserted replaced
5:05bd4db20227 6:1ac4a5f05f33
5 <expand macro="xrefs"/> 5 <expand macro="xrefs"/>
6 <requirements> 6 <requirements>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @PREP_ADATA@ 10 @CMD_PREP_ADATA@
11 @CMD@ 11 @CMD@
12 ]]></command> 12 ]]></command>
13 <configfiles> 13 <configfiles>
14 <configfile name="script_file"><![CDATA[ 14 <configfile name="script_file"><![CDATA[
15 @CMD_imports@ 15 @CONF_IMPORTS@
16 @CMD_read_inputs@ 16 @CONF_READ_INPUTS@
17 17
18 #if $method.method == 'pl.frag_size_distr' 18 #if $method.method == 'pl.frag_size_distr'
19 #if $method.log_scale 19 #if $method.log_scale
20 fig = sa.pl.frag_size_distr(adata, show=False) 20 fig = snap.pl.frag_size_distr(adata, show=False)
21 fig.update_yaxes(type="log") 21 fig.update_yaxes(type="log")
22 sa.pl.render_plot(fig, @CMD_params_render_plot@) 22 snap.pl.render_plot(fig, @CONF_PARAMS_RENDER_PLOT@)
23 #else 23 #else
24 sa.pl.frag_size_distr(adata, @CMD_params_render_plot@) 24 snap.pl.frag_size_distr(adata, @CONF_PARAMS_RENDER_PLOT@)
25 #end if 25 #end if
26
26 #else if $method.method == 'pl.tsse' 27 #else if $method.method == 'pl.tsse'
27 sa.pl.tsse( 28 snap.pl.tsse(
28 adata, 29 adata,
29 min_fragment = $method.min_fragment, 30 min_fragment = $method.min_fragment,
30 @CMD_params_render_plot@ 31 @CONF_PARAMS_RENDER_PLOT@
31 ) 32 )
32 #else if $method.method == 'pl.umap' 33 #else if $method.method == 'pl.umap'
33 sa.pl.umap( 34 snap.pl.umap(
34 adata, 35 adata,
35 color = '$method.color', 36 color = '$method.color',
36 use_rep = '$method.use_rep', 37 use_rep = '$method.use_rep',
37 #if $method.marker_size 38 #if $method.marker_size
38 marker_size = $method.marker_size, 39 marker_size = $method.marker_size,
39 #end if 40 #end if
40 marker_opacity = $method.marker_opacity, 41 marker_opacity = $method.marker_opacity,
41 #if $method.sample_size 42 #if $method.sample_size
42 sample_size = $method.sample_size, 43 sample_size = $method.sample_size,
43 #end if 44 #end if
44 @CMD_params_render_plot@ 45 @CONF_PARAMS_RENDER_PLOT@
45 ) 46 )
46 #else if $method.method == 'pl.regions' 47
47 sa.pl.regions( 48 #else if $method.method == 'pl.spectral_eigenvalues'
49 snap.pl.spectral_eigenvalues(
48 adata, 50 adata,
49 groupby = '$method.groupby', 51 @CONF_PARAMS_RENDER_PLOT@
50 peaks = '$method.peaks',
51 @CMD_params_render_plot@
52 )
53 #else if $method.method == 'pl.spectral_eigenvalues'
54 sa.pl.spectral_eigenvalues(
55 adata,
56 @CMD_params_render_plot@
57 ) 52 )
58 #end if 53 #end if
59 ]]></configfile> 54 ]]></configfile>
60 </configfiles> 55 </configfiles>
61 <inputs> 56 <inputs>
65 <option value="pl.tsse">Plot the TSS enrichment vs. number of fragments density figure, using 'pl.tsse'</option> 60 <option value="pl.tsse">Plot the TSS enrichment vs. number of fragments density figure, using 'pl.tsse'</option>
66 <option value="pl.umap">Plot the UMAP embedding, using 'pl.umap'</option> 61 <option value="pl.umap">Plot the UMAP embedding, using 'pl.umap'</option>
67 <option value="pl.spectral_eigenvalues">Plot the eigenvalues of spectral embedding, using 'pl.spectral_eigenvalues'</option> 62 <option value="pl.spectral_eigenvalues">Plot the eigenvalues of spectral embedding, using 'pl.spectral_eigenvalues'</option>
68 </param> 63 </param>
69 <when value="pl.frag_size_distr"> 64 <when value="pl.frag_size_distr">
70 <expand macro="inputs_anndata"/> 65 <expand macro="param_inputs_anndata"/>
66 <param argument="use_rep" type="text" value="frag_size_distr" label="Use the indicated representation in .obsm"/>
71 <param name="log_scale" type="boolean" checked="False" label="Change the y-axis (fragment counts) to log scale"/> 67 <param name="log_scale" type="boolean" checked="False" label="Change the y-axis (fragment counts) to log scale"/>
72 <expand macro="params_render_plot"/> 68 <expand macro="param_render_plot"/>
73 </when> 69 </when>
74 <when value="pl.tsse"> 70 <when value="pl.tsse">
75 <expand macro="inputs_anndata"/> 71 <expand macro="param_inputs_anndata"/>
76 <param argument="min_fragment" type="integer" value="500" label="Minimum number of unique fragments"/> 72 <param argument="min_fragment" type="integer" value="500" label="Minimum number of unique fragments"/>
77 <expand macro="params_render_plot"/> 73 <expand macro="param_render_plot"/>
78 </when> 74 </when>
79 <when value="pl.umap"> 75 <when value="pl.umap">
80 <expand macro="inputs_anndata"/> 76 <expand macro="param_inputs_anndata"/>
81 <param argument="color" type="text" value="" optional="true" label="Color"/> 77 <param argument="color" type="text" value="" optional="true" label="Color" help="Color to use for the points. retrieved from .obs"/>
82 <param argument="use_rep" type="text" value="X_umap" label="Use the indicated representation in .obsm"/> 78 <param argument="use_rep" type="text" value="X_umap" label="Use the indicated representation in .obsm"/>
83 <param argument="marker_size" type="float" value="" optional="true" label="Size of the dots"/> 79 <param argument="marker_size" type="float" value="" optional="true" label="Size of the dots"/>
84 <param argument="marker_opacity" type="float" value="1" label="Opactiy of the dots"/> 80 <param argument="marker_opacity" type="float" value="1" label="Opacity of the dots"/>
85 <param argument="sample_size" type="integer" value="" optional="true" label="Number of cells to use"/> 81 <param argument="sample_size" type="integer" value="" optional="true" label="Number of cells to use"/>
86 <expand macro="params_render_plot"/> 82 <expand macro="param_render_plot"/>
87 </when> 83 </when>
88 <when value="pl.spectral_eigenvalues"> 84 <when value="pl.spectral_eigenvalues">
89 <expand macro="inputs_anndata"/> 85 <expand macro="param_inputs_anndata"/>
90 <expand macro="params_render_plot"/> 86 <expand macro="param_render_plot"/>
91 </when> 87 </when>
92 </conditional> 88 </conditional>
93 <expand macro="inputs_common_advanced"/> 89 <expand macro="param_common_advanced"/>
94 </inputs> 90 </inputs>
95 <outputs> 91 <outputs>
96 <data name="out_png" format="png" from_work_dir="plot.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}"> 92 <data name="out_png" format="png" from_work_dir="plot.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
97 <filter>method['out_file'] == 'png'</filter> 93 <filter>method['out_file'] == 'png'</filter>
98 </data> 94 </data>
100 <filter>method['out_file'] == 'pdf'</filter> 96 <filter>method['out_file'] == 'pdf'</filter>
101 </data> 97 </data>
102 <data name="out_svg" format="svg" from_work_dir="plot.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}"> 98 <data name="out_svg" format="svg" from_work_dir="plot.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
103 <filter>method['out_file'] == 'svg'</filter> 99 <filter>method['out_file'] == 'svg'</filter>
104 </data> 100 </data>
101 <data name="out_html" format="html" from_work_dir="plot.html" label="HTML plot from ${tool.name} (${method.method}) on ${on_string}">
102 <filter>method['out_file'] == 'html'</filter>
103 </data>
105 <data name="hidden_output" format="txt" label="Log file" hidden="true"> 104 <data name="hidden_output" format="txt" label="Log file" hidden="true">
106 <filter>advanced_common['show_log']</filter> 105 <filter>advanced_common['show_log']</filter>
107 </data> 106 </data>
108 </outputs> 107 </outputs>
109 <tests> 108 <tests>
110 <test expect_num_outputs="2"> 109 <test expect_num_outputs="2">
111 <!-- pl.frag_size_distr --> 110 <!-- pl.frag_size_distr -->
112 <conditional name="method"> 111 <conditional name="method">
113 <param name="method" value="pl.frag_size_distr"/> 112 <param name="method" value="pl.frag_size_distr"/>
114 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/> 113 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.import_data.pbmc_500_chr21.h5ad"/>
115 <param name="log_scale" value="True"/> 114 <param name="log_scale" value="True"/>
116 <param name="out_file" value="pdf"/> 115 <param name="out_file" value="pdf"/>
117 <expand macro="render_plot_test"/> 116 <expand macro="test_param_render_plot"/>
118 </conditional> 117 </conditional>
119 <section name="advanced_common"> 118 <section name="advanced_common">
120 <param name="show_log" value="true"/> 119 <param name="show_log" value="true"/>
121 </section> 120 </section>
122 <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"/> 121 <output name="out_pdf" location="https://zenodo.org/records/17512085/files/pl.frag_size_distr.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
123 <output name="hidden_output"> 122 <output name="hidden_output">
124 <assert_contents> 123 <assert_contents>
125 <has_text_matching expression="sa.pl.frag_size_distr"/> 124 <has_text_matching expression="snap.pl.frag_size_distr"/>
126 <has_text_matching expression="fig.update_yaxes"/> 125 <has_text_matching expression="fig.update_yaxes"/>
127 <expand macro="render_plot_matching_text"/> 126 <expand macro="test_render_plot_matching_text"/>
128 </assert_contents> 127 </assert_contents>
129 </output> 128 </output>
130 </test> 129 </test>
131 <test expect_num_outputs="2"> 130 <test expect_num_outputs="2">
132 <!-- pl.tsse --> 131 <!-- pl.tsse -->
133 <conditional name="method"> 132 <conditional name="method">
134 <param name="method" value="pl.tsse"/> 133 <param name="method" value="pl.tsse"/>
135 <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/> 134 <param name="adata" location="https://zenodo.org/records/17512085/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
136 <param name="min_fragment" value="500"/> 135 <param name="min_fragment" value="500"/>
137 <param name="out_file" value="png"/> 136 <param name="out_file" value="png"/>
138 <expand macro="render_plot_test"/> 137 <expand macro="test_param_render_plot"/>
139 </conditional> 138 </conditional>
140 <section name="advanced_common"> 139 <section name="advanced_common">
141 <param name="show_log" value="true"/> 140 <param name="show_log" value="true"/>
142 </section> 141 </section>
143 <output name="hidden_output"> 142 <output name="hidden_output">
144 <assert_contents> 143 <assert_contents>
145 <has_text_matching expression="sa.pl.tsse"/> 144 <has_text_matching expression="snap.pl.tsse"/>
146 <has_text_matching expression="min_fragment = 500"/> 145 <has_text_matching expression="min_fragment = 500"/>
147 <expand macro="render_plot_matching_text"/> 146 <expand macro="test_render_plot_matching_text"/>
148 </assert_contents> 147 </assert_contents>
149 </output> 148 </output>
150 <output name="out_png" location="https://zenodo.org/records/11260316/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/> 149 <output name="out_png">
150 <assert_contents>
151 <has_image_center_of_mass center_of_mass="325,223" eps="30"/>
152 <has_image_channels channels="4"/>
153 <has_image_height height="450"/>
154 <has_image_width width="650"/>
155 </assert_contents>
156 </output>
151 </test> 157 </test>
152 <test expect_num_outputs="2"> 158 <test expect_num_outputs="2">
153 <!-- pl.umap --> 159 <!-- pl.umap -->
154 <conditional name="method"> 160 <conditional name="method">
155 <param name="method" value="pl.umap"/> 161 <param name="method" value="pl.umap"/>
156 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/> 162 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
157 <param name="color" value="leiden"/> 163 <param name="color" value="leiden"/>
158 <param name="use_rep" value="X_umap"/> 164 <param name="use_rep" value="X_umap"/>
159 <param name="marker_size" value="1"/> 165 <param name="marker_size" value="1"/>
160 <param name="marker_opacity" value="0.8"/> 166 <param name="marker_opacity" value="0.8"/>
161 <param name="sample_size" value="100"/> 167 <param name="sample_size" value="100"/>
162 <expand macro="render_plot_test"/> 168 <expand macro="test_param_render_plot"/>
163 <param name="out_file" value="svg"/> 169 <param name="out_file" value="svg"/>
164 </conditional> 170 </conditional>
165 <section name="advanced_common"> 171 <section name="advanced_common">
166 <param name="show_log" value="true"/> 172 <param name="show_log" value="true"/>
167 </section> 173 </section>
168 <output name="hidden_output"> 174 <output name="hidden_output">
169 <assert_contents> 175 <assert_contents>
170 <has_text_matching expression="sa.pl.umap"/> 176 <has_text_matching expression="snap.pl.umap"/>
171 <has_text_matching expression="color = 'leiden'"/> 177 <has_text_matching expression="color = 'leiden'"/>
172 <has_text_matching expression="use_rep = 'X_umap'"/> 178 <has_text_matching expression="use_rep = 'X_umap'"/>
173 <has_text_matching expression="marker_size = 1"/> 179 <has_text_matching expression="marker_size = 1"/>
174 <has_text_matching expression="marker_opacity = 0.8"/> 180 <has_text_matching expression="marker_opacity = 0.8"/>
175 <has_text_matching expression="sample_size = 100"/> 181 <has_text_matching expression="sample_size = 100"/>
176 <expand macro="render_plot_matching_text"/> 182 <expand macro="test_render_plot_matching_text"/>
177 </assert_contents> 183 </assert_contents>
178 </output> 184 </output>
179 <output name="out_svg" location="https://zenodo.org/records/11260316/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/> 185 <output name="out_svg" location="https://zenodo.org/records/17512085/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/>
180 </test> 186 </test>
181 <test expect_num_outputs="2"> 187 <test expect_num_outputs="2">
182 <!-- pl.spectral_eigenvalues --> 188 <!-- pl.spectral_eigenvalues -->
183 <conditional name="method"> 189 <conditional name="method">
184 <param name="method" value="pl.spectral_eigenvalues"/> 190 <param name="method" value="pl.spectral_eigenvalues"/>
185 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/> 191 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/>
186 <expand macro="render_plot_test"/> 192 <expand macro="test_param_render_plot"/>
187 <param name="out_file" value="pdf"/> 193 <param name="out_file" value="pdf"/>
188 </conditional> 194 </conditional>
189 <section name="advanced_common"> 195 <section name="advanced_common">
190 <param name="show_log" value="true"/> 196 <param name="show_log" value="true"/>
191 </section> 197 </section>
192 <output name="hidden_output"> 198 <output name="hidden_output">
193 <assert_contents> 199 <assert_contents>
194 <has_text_matching expression="sa.pl.spectral_eigenvalues"/> 200 <has_text_matching expression="snap.pl.spectral_eigenvalues"/>
195 <expand macro="render_plot_matching_text"/> 201 <expand macro="test_render_plot_matching_text"/>
196 </assert_contents> 202 </assert_contents>
197 </output> 203 </output>
198 <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> 204 <output name="out_pdf" location="https://zenodo.org/records/17512085/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
199 </test> 205 </test>
200 </tests> 206 </tests>
201 <help><![CDATA[ 207 <help><![CDATA[
202 Plot fragment size distribution, using `pl.frag_size_distr` 208 Plot fragment size distribution, using `pl.frag_size_distr`
203 =========================================================== 209 ===========================================================
210 =============================================================================== 216 ===============================================================================
211 217
212 Plot the TSS enrichment vs. number of fragments density figure. 218 Plot the TSS enrichment vs. number of fragments density figure.
213 219
214 More details on the `SnapATAC2 documentation 220 More details on the `SnapATAC2 documentation
215 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.tsse.html>`__ 221 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.tsse.html>`__
216 222
217 Plot the UMAP embedding, using `pl.umap` 223 Plot the UMAP embedding, using `pl.umap`
218 ======================================== 224 ========================================
219 225
220 Plot the UMAP embedding. 226 Plot the UMAP embedding.
221 227
222 More details on the `SnapATAC2 documentation 228 More details on the `SnapATAC2 documentation
223 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__ 229 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__
224 230
225 Plot the eigenvalues of spectral embedding, using `pl.spectral_eigenvalues` 231 Plot the eigenvalues of spectral embedding, using `pl.spectral_eigenvalues`
226 =========================================================================== 232 ===========================================================================
227 233
228 Plot the eigenvalues of spectral embedding. 234 Plot the eigenvalues of spectral embedding.
229 235
230 More details on the `SnapATAC2 documentation 236 More details on the `SnapATAC2 documentation
231 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__ 237 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__
232 ]]></help> 238 ]]></help>
233 <expand macro="citations"/> 239 <expand macro="citations"/>
234 </tool> 240 </tool>