Mercurial > repos > iuc > snapatac2_plotting

annotate plotting.xml @ 4:0e60b8370245 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 16:40:09 +0000
parents 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@">
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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 <expand macro="xrefs"/>
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6 <requirements>
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7 <expand macro="requirements"/>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @CMD_PREP_ADATA@
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11 @CMD@
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12 ]]></command>
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13 <configfiles>
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14 <configfile name="script_file"><![CDATA[
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15 @CONF_IMPORTS@
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16 @CONF_READ_INPUTS@
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18 #if $method.method == 'pl.frag_size_distr'
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19 #if $method.log_scale
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20 fig = snap.pl.frag_size_distr(adata, show=False)
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21 fig.update_yaxes(type="log")
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22 snap.pl.render_plot(fig, @CONF_PARAMS_RENDER_PLOT@)
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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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23 #else
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24 snap.pl.frag_size_distr(adata, @CONF_PARAMS_RENDER_PLOT@)
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25 #end if
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26
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27 #else if $method.method == 'pl.tsse'
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28 snap.pl.tsse(
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29 adata,
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30 min_fragment = $method.min_fragment,
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31 @CONF_PARAMS_RENDER_PLOT@
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32 )
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33 #else if $method.method == 'pl.umap'
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34 snap.pl.umap(
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35 adata,
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36 color = '$method.color',
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37 use_rep = '$method.use_rep',
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38 #if $method.marker_size
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39 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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40 #end if
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41 marker_opacity = $method.marker_opacity,
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42 #if $method.sample_size
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43 sample_size = $method.sample_size,
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44 #end if
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45 @CONF_PARAMS_RENDER_PLOT@
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46 )
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47
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48 #else if $method.method == 'pl.spectral_eigenvalues'
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49 snap.pl.spectral_eigenvalues(
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50 adata,
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51 @CONF_PARAMS_RENDER_PLOT@
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52 )
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53 #end if
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54 ]]></configfile>
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55 </configfiles>
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56 <inputs>
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57 <conditional name="method">
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58 <param name="method" type="select" label="Method used for plotting">
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59 <option value="pl.frag_size_distr">Plot fragment size distribution, using 'pl.frag_size_distr'</option>
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60 <option value="pl.tsse">Plot the TSS enrichment vs. number of fragments density figure, using 'pl.tsse'</option>
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61 <option value="pl.umap">Plot the UMAP embedding, using 'pl.umap'</option>
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62 <option value="pl.spectral_eigenvalues">Plot the eigenvalues of spectral embedding, using 'pl.spectral_eigenvalues'</option>
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63 </param>
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64 <when value="pl.frag_size_distr">
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65 <expand macro="param_inputs_anndata"/>
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66 <param argument="use_rep" type="text" value="frag_size_distr" label="Use the indicated representation in .obsm"/>
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67 <param name="log_scale" type="boolean" checked="False" label="Change the y-axis (fragment counts) to log scale"/>
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68 <expand macro="param_render_plot"/>
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69 </when>
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70 <when value="pl.tsse">
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71 <expand macro="param_inputs_anndata"/>
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72 <param argument="min_fragment" type="integer" value="500" label="Minimum number of unique fragments"/>
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73 <expand macro="param_render_plot"/>
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74 </when>
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75 <when value="pl.umap">
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76 <expand macro="param_inputs_anndata"/>
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77 <param argument="color" type="text" value="" optional="true" label="Color" help="Color to use for the points. retrieved from .obs"/>
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78 <param argument="use_rep" type="text" value="X_umap" label="Use the indicated representation in .obsm"/>
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79 <param argument="marker_size" type="float" value="" optional="true" label="Size of the dots"/>
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80 <param argument="marker_opacity" type="float" value="1" label="Opacity of the dots"/>
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81 <param argument="sample_size" type="integer" value="" optional="true" label="Number of cells to use"/>
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82 <expand macro="param_render_plot"/>
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83 </when>
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84 <when value="pl.spectral_eigenvalues">
4
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85 <expand macro="param_inputs_anndata"/>
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86 <expand macro="param_render_plot"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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87 </when>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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88 </conditional>
4
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89 <expand macro="param_common_advanced"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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90 </inputs>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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91 <outputs>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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92 <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
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93 <filter>method['out_file'] == 'png'</filter>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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94 </data>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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95 <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
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96 <filter>method['out_file'] == 'pdf'</filter>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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97 </data>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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98 <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
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99 <filter>method['out_file'] == 'svg'</filter>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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100 </data>
4
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101 <data name="out_html" format="html" from_work_dir="plot.html" label="HTML plot from ${tool.name} (${method.method}) on ${on_string}">
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102 <filter>method['out_file'] == 'html'</filter>
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103 </data>
0
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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
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105 <filter>advanced_common['show_log']</filter>
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106 </data>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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107 </outputs>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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108 <tests>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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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
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110 <!-- 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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111 <conditional name="method">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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112 <param name="method" value="pl.frag_size_distr"/>
4
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113 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.import_data.pbmc_500_chr21.h5ad"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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114 <param name="log_scale" value="True"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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115 <param name="out_file" value="pdf"/>
4
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116 <expand macro="test_param_render_plot"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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117 </conditional>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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118 <section name="advanced_common">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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119 <param name="show_log" value="true"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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120 </section>
4
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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"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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122 <output name="hidden_output">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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123 <assert_contents>
4
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124 <has_text_matching expression="snap.pl.frag_size_distr"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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125 <has_text_matching expression="fig.update_yaxes"/>
4
0e60b8370245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
126 <expand macro="test_render_plot_matching_text"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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127 </assert_contents>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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128 </output>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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129 </test>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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130 <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
131 <!-- pl.tsse -->
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
132 <conditional name="method">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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133 <param name="method" value="pl.tsse"/>
4
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134 <param name="adata" location="https://zenodo.org/records/17512085/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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135 <param name="min_fragment" value="500"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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136 <param name="out_file" value="png"/>
4
0e60b8370245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
137 <expand macro="test_param_render_plot"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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138 </conditional>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
139 <section name="advanced_common">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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140 <param name="show_log" value="true"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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141 </section>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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142 <output name="hidden_output">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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143 <assert_contents>
4
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144 <has_text_matching expression="snap.pl.tsse"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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145 <has_text_matching expression="min_fragment = 500"/>
4
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diff changeset
146 <expand macro="test_render_plot_matching_text"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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147 </assert_contents>
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148 </output>
4
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diff changeset
149 <output name="out_png">
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150 <assert_contents>
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diff changeset
151 <has_image_center_of_mass center_of_mass="325,223" eps="30"/>
0e60b8370245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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152 <has_image_channels channels="4"/>
0e60b8370245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
153 <has_image_height height="450"/>
0e60b8370245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
154 <has_image_width width="650"/>
0e60b8370245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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155 </assert_contents>
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156 </output>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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157 </test>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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158 <test expect_num_outputs="2">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
159 <!-- pl.umap -->
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parents:
diff changeset
160 <conditional name="method">
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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161 <param name="method" value="pl.umap"/>
4
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diff changeset
162 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
0
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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163 <param name="color" value="leiden"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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164 <param name="use_rep" value="X_umap"/>
4a1c0fe5be8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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165 <param name="marker_size" value="1"/>
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166 <param name="marker_opacity" value="0.8"/>
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167 <param name="sample_size" value="100"/>
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168 <expand macro="test_param_render_plot"/>
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169 <param name="out_file" value="svg"/>
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170 </conditional>
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171 <section name="advanced_common">
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172 <param name="show_log" value="true"/>
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173 </section>
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174 <output name="hidden_output">
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175 <assert_contents>
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176 <has_text_matching expression="snap.pl.umap"/>
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177 <has_text_matching expression="color = 'leiden'"/>
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178 <has_text_matching expression="use_rep = 'X_umap'"/>
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179 <has_text_matching expression="marker_size = 1"/>
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180 <has_text_matching expression="marker_opacity = 0.8"/>
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181 <has_text_matching expression="sample_size = 100"/>
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182 <expand macro="test_render_plot_matching_text"/>
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183 </assert_contents>
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184 </output>
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185 <output name="out_svg" location="https://zenodo.org/records/17512085/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/>
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186 </test>
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187 <test expect_num_outputs="2">
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188 <!-- pl.spectral_eigenvalues -->
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189 <conditional name="method">
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190 <param name="method" value="pl.spectral_eigenvalues"/>
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191 <param name="adata" ftype="h5ad" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/>
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192 <expand macro="test_param_render_plot"/>
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193 <param name="out_file" value="pdf"/>
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194 </conditional>
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195 <section name="advanced_common">
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196 <param name="show_log" value="true"/>
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197 </section>
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198 <output name="hidden_output">
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199 <assert_contents>
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200 <has_text_matching expression="snap.pl.spectral_eigenvalues"/>
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201 <expand macro="test_render_plot_matching_text"/>
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202 </assert_contents>
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203 </output>
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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"/>
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205 </test>
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206 </tests>
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207 <help><![CDATA[
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208 Plot fragment size distribution, using `pl.frag_size_distr`
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209 ===========================================================
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210
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211 Plot fragment size distribution.
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212
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213 `metrics.frag_size_distr` must be ran first in order to use this function.
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214
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215 Plot the TSS enrichment vs. number of fragments density figure, using `pl.tsse`
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216 ===============================================================================
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217
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218 Plot the TSS enrichment vs. number of fragments density figure.
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219
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220 More details on the `SnapATAC2 documentation
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221 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.tsse.html>`__
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222
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223 Plot the UMAP embedding, using `pl.umap`
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224 ========================================
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225
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226 Plot the UMAP embedding.
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227
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228 More details on the `SnapATAC2 documentation
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229 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__
0
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230
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231 Plot the eigenvalues of spectral embedding, using `pl.spectral_eigenvalues`
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232 ===========================================================================
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233
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234 Plot the eigenvalues of spectral embedding.
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235
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236 More details on the `SnapATAC2 documentation
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237 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__
0
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238 ]]></help>
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239 <expand macro="citations"/>
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240 </tool>