Mercurial > repos > iuc > snapatac2_plotting

annotate 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
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children efd9d236bfd2
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4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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1 <tool id="snapatac2_plotting" name="SnapATAC2 Plotting" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <requirements>
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6 <expand macro="requirements"/>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @PREP_ADATA@
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10 @CMD@
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="script_file"><![CDATA[
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14 @CMD_imports@
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15 @CMD_read_inputs@
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16
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17 #if $method.method == 'pl.frag_size_distr'
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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18 #if $method.log_scale
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19 fig = sa.pl.frag_size_distr(adata, show=False)
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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20 fig.update_yaxes(type="log")
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21 sa.pl.render_plot(fig, @CMD_params_render_plot@)
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22 #else
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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23 sa.pl.frag_size_distr(adata, @CMD_params_render_plot@)
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24 #end if
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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25 #else if $method.method == 'pl.tsse'
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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26 sa.pl.tsse(
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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27 adata,
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28 min_fragment = $method.min_fragment,
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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29 @CMD_params_render_plot@
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30 )
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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31 #else if $method.method == 'pl.umap'
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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32 sa.pl.umap(
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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33 adata,
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34 color = '$method.color',
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35 use_rep = '$method.use_rep',
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36 #if $method.marker_size
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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37 marker_size = $method.marker_size,
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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38 #end if
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39 marker_opacity = $method.marker_opacity,
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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40 #if $method.sample_size
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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41 sample_size = $method.sample_size,
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42 #end if
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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43 @CMD_params_render_plot@
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44 )
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45 #else if $method.method == 'pl.regions'
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46 sa.pl.regions(
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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47 adata,
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48 groupby = '$method.groupby',
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49 peaks = '$method.peaks',
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50 @CMD_params_render_plot@
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51 )
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52 #else if $method.method == 'pl.spectral_eigenvalues'
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53 sa.pl.spectral_eigenvalues(
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54 adata,
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55 @CMD_params_render_plot@
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56 )
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57 #end if
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58 ]]></configfile>
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59 </configfiles>
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60 <inputs>
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61 <conditional name="method">
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62 <param name="method" type="select" label="Method used for plotting">
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63 <option value="pl.frag_size_distr">Plot fragment size distribution, using 'pl.frag_size_distr'</option>
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64 <option value="pl.tsse">Plot the TSS enrichment vs. number of fragments density figure, using 'pl.tsse'</option>
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65 <option value="pl.umap">Plot the UMAP embedding, using 'pl.umap'</option>
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66 <option value="pl.spectral_eigenvalues">Plot the eigenvalues of spectral embedding, using 'pl.spectral_eigenvalues'</option>
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67 </param>
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68 <when value="pl.frag_size_distr">
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69 <expand macro="inputs_anndata"/>
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70 <param name="log_scale" type="boolean" checked="False" label="Change the y-axis (fragment counts) to log scale"/>
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71 <expand macro="params_render_plot"/>
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72 </when>
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73 <when value="pl.tsse">
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74 <expand macro="inputs_anndata"/>
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75 <param argument="min_fragment" type="integer" value="500" label="Minimum number of unique fragments"/>
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76 <expand macro="params_render_plot"/>
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77 </when>
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78 <when value="pl.umap">
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79 <expand macro="inputs_anndata"/>
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80 <param argument="color" type="text" value="" optional="true" label="Color"/>
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81 <param argument="use_rep" type="text" value="X_umap" label="Use the indicated representation in .obsm"/>
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82 <param argument="marker_size" type="float" value="" optional="true" label="Size of the dots"/>
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83 <param argument="marker_opacity" type="float" value="1" label="Opactiy of the dots"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
84 <param argument="sample_size" type="integer" value="" optional="true" label="Number of cells to use"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
85 <expand macro="params_render_plot"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
86 </when>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
87 <when value="pl.spectral_eigenvalues">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
88 <expand macro="inputs_anndata"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
89 <expand macro="params_render_plot"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
90 </when>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
91 </conditional>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
92 <expand macro="inputs_common_advanced"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
93 </inputs>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
94 <outputs>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
95 <data name="out_png" format="png" from_work_dir="plot.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
96 <filter>method['out_file'] == 'png'</filter>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
97 </data>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
98 <data name="out_pdf" format="pdf" from_work_dir="plot.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
99 <filter>method['out_file'] == 'pdf'</filter>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
100 </data>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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101 <data name="out_svg" format="svg" from_work_dir="plot.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
102 <filter>method['out_file'] == 'svg'</filter>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
103 </data>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
104 <data name="hidden_output" format="txt" label="Log file" hidden="true">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
105 <filter>advanced_common['show_log']</filter>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
106 </data>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
107 </outputs>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
108 <tests>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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109 <test expect_num_outputs="2">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
110 <!-- pl.frag_size_distr -->
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
111 <conditional name="method">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
112 <param name="method" value="pl.frag_size_distr"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
113 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
114 <param name="log_scale" value="True"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
115 <param name="out_file" value="pdf"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
116 <expand macro="render_plot_test"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
117 </conditional>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
118 <section name="advanced_common">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
119 <param name="show_log" value="true"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
120 </section>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
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"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
122 <output name="hidden_output">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
123 <assert_contents>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
124 <has_text_matching expression="sa.pl.frag_size_distr"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
125 <has_text_matching expression="fig.update_yaxes"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
126 <expand macro="render_plot_matching_text"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
127 </assert_contents>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
128 </output>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
129 </test>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
130 <test expect_num_outputs="2">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
131 <!-- pl.tsse -->
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
132 <conditional name="method">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
133 <param name="method" value="pl.tsse"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
134 <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
135 <param name="min_fragment" value="500"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
136 <param name="out_file" value="png"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
137 <expand macro="render_plot_test"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
138 </conditional>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
139 <section name="advanced_common">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
140 <param name="show_log" value="true"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
141 </section>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
142 <output name="hidden_output">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
143 <assert_contents>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
144 <has_text_matching expression="sa.pl.tsse"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
145 <has_text_matching expression="min_fragment = 500"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
146 <expand macro="render_plot_matching_text"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
147 </assert_contents>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
148 </output>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
149 <output name="out_png" location="https://zenodo.org/records/11260316/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
150 </test>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
151 <test expect_num_outputs="2">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
152 <!-- pl.umap -->
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
153 <conditional name="method">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
154 <param name="method" value="pl.umap"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
155 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
156 <param name="color" value="leiden"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
157 <param name="use_rep" value="X_umap"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
158 <param name="marker_size" value="1"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
159 <param name="marker_opacity" value="0.8"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
160 <param name="sample_size" value="100"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
161 <expand macro="render_plot_test"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
162 <param name="out_file" value="svg"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
163 </conditional>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
164 <section name="advanced_common">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
165 <param name="show_log" value="true"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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166 </section>
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167 <output name="hidden_output">
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168 <assert_contents>
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169 <has_text_matching expression="sa.pl.umap"/>
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170 <has_text_matching expression="color = 'leiden'"/>
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171 <has_text_matching expression="use_rep = 'X_umap'"/>
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172 <has_text_matching expression="marker_size = 1"/>
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173 <has_text_matching expression="marker_opacity = 0.8"/>
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174 <has_text_matching expression="sample_size = 100"/>
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175 <expand macro="render_plot_matching_text"/>
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176 </assert_contents>
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177 </output>
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178 <output name="out_svg" location="https://zenodo.org/records/11260316/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/>
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179 </test>
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180 <test expect_num_outputs="2">
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181 <!-- pl.spectral_eigenvalues -->
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182 <conditional name="method">
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183 <param name="method" value="pl.spectral_eigenvalues"/>
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184 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
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185 <expand macro="render_plot_test"/>
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186 <param name="out_file" value="pdf"/>
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187 </conditional>
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188 <section name="advanced_common">
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189 <param name="show_log" value="true"/>
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190 </section>
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191 <output name="hidden_output">
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192 <assert_contents>
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193 <has_text_matching expression="sa.pl.spectral_eigenvalues"/>
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194 <expand macro="render_plot_matching_text"/>
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195 </assert_contents>
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196 </output>
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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"/>
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198 </test>
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199 </tests>
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200 <help><![CDATA[
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201 Plot fragment size distribution, using `pl.frag_size_distr`
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202 ===========================================================
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203
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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204 Plot fragment size distribution.
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205
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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206 `metrics.frag_size_distr` must be ran first in order to use this function.
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207
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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208 Plot the TSS enrichment vs. number of fragments density figure, using `pl.tsse`
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209 ===============================================================================
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210
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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211 Plot the TSS enrichment vs. number of fragments density figure.
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212
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213 More details on the `SnapATAC2 documentation
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214 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.tsse.html>`__
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215
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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216 Plot the UMAP embedding, using `pl.umap`
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217 ========================================
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218
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219 Plot the UMAP embedding.
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220
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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221 More details on the `SnapATAC2 documentation
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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222 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__
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223
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224 Plot the eigenvalues of spectral embedding, using `pl.spectral_eigenvalues`
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225 ===========================================================================
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226
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227 Plot the eigenvalues of spectral embedding.
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228
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229 More details on the `SnapATAC2 documentation
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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230 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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231 ]]></help>
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232 <expand macro="citations"/>
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233 </tool>