Mercurial > repos > iuc > snapatac2_plotting

comparison plotting.xml @ 1:fecf9664c885 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
author iuc
date Thu, 23 May 2024 15:19:43 +0000
parents 0cfd2d2f7351
children 05bd4db20227
comparison
equal deleted inserted replaced
0:0cfd2d2f7351 1:fecf9664c885
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @PREP_ADATA@ 9 @PREP_ADATA@
10 @CMD@ 10 @CMD@
11 ]]></command> 11 ]]></command>
12 <configfiles> 12 <configfiles>
13 <configfile name="script_file"><![CDATA[ 13 <configfile name="script_file"><![CDATA[
14 @CMD_imports@ 14 @CMD_imports@
15 @CMD_read_inputs@ 15 @CMD_read_inputs@
16 16
17 #if $method.method == 'pl.frag_size_distr' 17 #if $method.method == 'pl.frag_size_distr'
18 #if $method.log_scale 18 #if $method.log_scale
19 fig = sa.pl.frag_size_distr(adata, show=False) 19 fig = sa.pl.frag_size_distr(adata, show=False)
20 fig.update_yaxes(type="log") 20 fig.update_yaxes(type="log")
21 sa.pl.render_plot(fig, @CMD_params_render_plot@) 21 sa.pl.render_plot(fig, @CMD_params_render_plot@)
22 #else 22 #else
23 sa.pl.frag_size_distr(adata, @CMD_params_render_plot@) 23 sa.pl.frag_size_distr(adata, @CMD_params_render_plot@)
24 #end if 24 #end if
25 #else if $method.method == 'pl.tsse' 25 #else if $method.method == 'pl.tsse'
26 sa.pl.tsse( 26 sa.pl.tsse(
27 adata, 27 adata,
28 min_fragment = $method.min_fragment, 28 min_fragment = $method.min_fragment,
29 @CMD_params_render_plot@ 29 @CMD_params_render_plot@
30 ) 30 )
31 #else if $method.method == 'pl.umap' 31 #else if $method.method == 'pl.umap'
32 sa.pl.umap( 32 sa.pl.umap(
33 adata, 33 adata,
34 color = '$method.color', 34 color = '$method.color',
35 use_rep = '$method.use_rep', 35 use_rep = '$method.use_rep',
36 marker_size = $method.marker_size, 36 #if $method.marker_size
37 marker_opacity = $method.marker_opacity, 37 marker_size = $method.marker_size,
38 sample_size = $method.sample_size, 38 #end if
39 @CMD_params_render_plot@ 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@
40 ) 44 )
41 #else if $method.method == 'pl.regions' 45 #else if $method.method == 'pl.regions'
42 sa.pl.regions( 46 sa.pl.regions(
43 adata, 47 adata,
44 groupby = '$method.groupby', 48 groupby = '$method.groupby',
45 peaks = '$method.peaks', 49 peaks = '$method.peaks',
46 @CMD_params_render_plot@ 50 @CMD_params_render_plot@
47 ) 51 )
48 #else if $method.method == 'pl.spectral_eigenvalues' 52 #else if $method.method == 'pl.spectral_eigenvalues'
49 sa.pl.spectral_eigenvalues( 53 sa.pl.spectral_eigenvalues(
50 adata, 54 adata,
51 @CMD_params_render_plot@ 55 @CMD_params_render_plot@
52 ) 56 )
53 #end if 57 #end if
54 ]]></configfile> 58 ]]></configfile>
55 </configfiles> 59 </configfiles>
56 <inputs> 60 <inputs>
57 <conditional name="method"> 61 <conditional name="method">
58 <param name="method" type="select" label="Method used for plotting"> 62 <param name="method" type="select" label="Method used for plotting">
59 <option value="pl.frag_size_distr">Plot fragment size distribution, using 'pl.frag_size_distr'</option> 63 <option value="pl.frag_size_distr">Plot fragment size distribution, using 'pl.frag_size_distr'</option>
104 <tests> 108 <tests>
105 <test expect_num_outputs="2"> 109 <test expect_num_outputs="2">
106 <!-- pl.frag_size_distr --> 110 <!-- pl.frag_size_distr -->
107 <conditional name="method"> 111 <conditional name="method">
108 <param name="method" value="pl.frag_size_distr"/> 112 <param name="method" value="pl.frag_size_distr"/>
109 <param name="adata" location="https://zenodo.org/records/11199963/files/pp.import_data.pbmc_500_chr21.h5ad"/> 113 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
110 <param name="log_scale" value="True"/> 114 <param name="log_scale" value="True"/>
111 <param name="out_file" value="pdf"/> 115 <param name="out_file" value="pdf"/>
112 <expand macro="render_plot_test"/> 116 <expand macro="render_plot_test"/>
113 </conditional> 117 </conditional>
114 <section name="advanced_common"> 118 <section name="advanced_common">
115 <param name="show_log" value="true"/> 119 <param name="show_log" value="true"/>
116 </section> 120 </section>
117 <output name="out_pdf" location="https://zenodo.org/records/11199963/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/11260316/files/pl.frag_size_distr.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
118 <output name="hidden_output"> 122 <output name="hidden_output">
119 <assert_contents> 123 <assert_contents>
120 <has_text_matching expression="sa.pl.frag_size_distr"/> 124 <has_text_matching expression="sa.pl.frag_size_distr"/>
121 <has_text_matching expression="fig.update_yaxes"/> 125 <has_text_matching expression="fig.update_yaxes"/>
122 <expand macro="render_plot_matching_text"/> 126 <expand macro="render_plot_matching_text"/>
125 </test> 129 </test>
126 <test expect_num_outputs="2"> 130 <test expect_num_outputs="2">
127 <!-- pl.tsse --> 131 <!-- pl.tsse -->
128 <conditional name="method"> 132 <conditional name="method">
129 <param name="method" value="pl.tsse"/> 133 <param name="method" value="pl.tsse"/>
130 <param name="adata" location="https://zenodo.org/records/11199963/files/metrics.tsse.pbmc_500_chr21.h5ad"/> 134 <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
131 <param name="min_fragment" value="500"/> 135 <param name="min_fragment" value="500"/>
132 <param name="out_file" value="png"/> 136 <param name="out_file" value="png"/>
133 <expand macro="render_plot_test"/> 137 <expand macro="render_plot_test"/>
134 </conditional> 138 </conditional>
135 <section name="advanced_common"> 139 <section name="advanced_common">
140 <has_text_matching expression="sa.pl.tsse"/> 144 <has_text_matching expression="sa.pl.tsse"/>
141 <has_text_matching expression="min_fragment = 500"/> 145 <has_text_matching expression="min_fragment = 500"/>
142 <expand macro="render_plot_matching_text"/> 146 <expand macro="render_plot_matching_text"/>
143 </assert_contents> 147 </assert_contents>
144 </output> 148 </output>
145 <output name="out_png" location="https://zenodo.org/records/11199963/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/> 149 <output name="out_png" location="https://zenodo.org/records/11260316/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
146 </test> 150 </test>
147 <test expect_num_outputs="2"> 151 <test expect_num_outputs="2">
148 <!-- pl.umap --> 152 <!-- pl.umap -->
149 <conditional name="method"> 153 <conditional name="method">
150 <param name="method" value="pl.umap"/> 154 <param name="method" value="pl.umap"/>
151 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11199963/files/tl.leiden.pbmc_500_chr21.h5ad"/> 155 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
152 <param name="color" value="leiden"/> 156 <param name="color" value="leiden"/>
153 <param name="use_rep" value="X_umap"/> 157 <param name="use_rep" value="X_umap"/>
154 <param name="marker_size" value="1"/> 158 <param name="marker_size" value="1"/>
155 <param name="marker_opacity" value="0.8"/> 159 <param name="marker_opacity" value="0.8"/>
156 <param name="sample_size" value="100"/> 160 <param name="sample_size" value="100"/>
169 <has_text_matching expression="marker_opacity = 0.8"/> 173 <has_text_matching expression="marker_opacity = 0.8"/>
170 <has_text_matching expression="sample_size = 100"/> 174 <has_text_matching expression="sample_size = 100"/>
171 <expand macro="render_plot_matching_text"/> 175 <expand macro="render_plot_matching_text"/>
172 </assert_contents> 176 </assert_contents>
173 </output> 177 </output>
174 <output name="out_svg" location="https://zenodo.org/records/11199963/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/> 178 <output name="out_svg" location="https://zenodo.org/records/11260316/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/>
175 </test> 179 </test>
176 <test expect_num_outputs="2"> 180 <test expect_num_outputs="2">
177 <!-- pl.spectral_eigenvalues --> 181 <!-- pl.spectral_eigenvalues -->
178 <conditional name="method"> 182 <conditional name="method">
179 <param name="method" value="pl.spectral_eigenvalues"/> 183 <param name="method" value="pl.spectral_eigenvalues"/>
180 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/> 184 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
181 <expand macro="render_plot_test"/> 185 <expand macro="render_plot_test"/>
182 <param name="out_file" value="pdf"/> 186 <param name="out_file" value="pdf"/>
183 </conditional> 187 </conditional>
184 <section name="advanced_common"> 188 <section name="advanced_common">
185 <param name="show_log" value="true"/> 189 <param name="show_log" value="true"/>
188 <assert_contents> 192 <assert_contents>
189 <has_text_matching expression="sa.pl.spectral_eigenvalues"/> 193 <has_text_matching expression="sa.pl.spectral_eigenvalues"/>
190 <expand macro="render_plot_matching_text"/> 194 <expand macro="render_plot_matching_text"/>
191 </assert_contents> 195 </assert_contents>
192 </output> 196 </output>
193 <output name="out_pdf" location="https://zenodo.org/records/11199963/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> 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"/>
194 </test> 198 </test>
195 </tests> 199 </tests>
196 <help><![CDATA[ 200 <help><![CDATA[
197 Plot fragment size distribution, using `pl.frag_size_distr` 201 Plot fragment size distribution, using `pl.frag_size_distr`
198 =========================================================== 202 ===========================================================