Mercurial > repos > iuc > pcdl_plot_scatter

annotate pcdl_plot_scatter.xml @ 0:bc08e5879459 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
author iuc
date Mon, 04 Aug 2025 18:59:56 +0000
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bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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1 <tool id="pcdl_plot_scatter" name="pcdl_plot_scatter" version="3.0.1+galaxy0" profile="21.05">
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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2 <macros>
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iuc
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3 <import>pcdl_macros.xml</import>
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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4 </macros>
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5 <requirements>
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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6 <expand macro="requirement"/>
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7 </requirements>
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8 <command><![CDATA[
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9 #import re
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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10 mkdir output_pc &&
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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11 #for $file in $path:
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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12 #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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13 ln -s '$file' output_pc/$filename &&
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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14 #end for
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15
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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16 pcdl_plot_scatter 'output_pc' '$focus_cell'
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17 --custom_data_type $custom_data_type
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18 --microenv $microenv
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19 --physiboss $physiboss
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20 --settingxml 'none'
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21 --verbose $verbose
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22 --z_slice $z_slice
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23 --z_axis '$z_axis'
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24 --alpha $alpha
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25 --cmap '$cmap'
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26 --title '$title'
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27 --grid $grid
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28 --legend_loc '$legend_loc'
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29 --xlim '$xlim'
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30 --ylim '$ylim'
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31 --xyequal $xyequal
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32 --s $s
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33 --figsizepx $figsizepx_x $figsizepx_y
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34 --directory 'jakku'
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35 --ext $ext
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36 --figbgcolor '$figbgcolor'
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37 ]]></command>
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38 <inputs>
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39 <section name="essential" title="essential:" expanded="true">
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40 <expand macro="path"/>
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41 <expand macro="focus_cell"/>
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42 <expand macro="custom_data_type"/>
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43 <expand macro="z_slice"/>
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44 <expand macro="z_axis"/>
bc08e5879459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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45 <expand macro="alpha"/>
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46 <expand macro="cmap"/>
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47 <expand macro="title"/>
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48 <expand macro="grid"/>
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49 <expand macro="legend_loc"/>
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50 <expand macro="xlim"/>
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51 <expand macro="ylim"/>
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52 <expand macro="xyequal"/>
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53 <expand macro="s"/>
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54 <expand macro="figsizepx_x"/>
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55 <expand macro="figsizepx_y"/>
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56 <expand macro="ext"/>
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57 <expand macro="figbgcolor"/>
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58 </section>
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59 <section name="advanced" title="advanced:" expanded="false">
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60 <expand macro="microenv"/>
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61 <expand macro="physiboss"/>
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62 <expand macro="verbose"/>
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63 </section>
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64 </inputs>
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65 <outputs>
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66 <collection name="scatter_plot" type="list">
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67 <discover_datasets pattern="(?P&lt;designation&gt;output.+)\.jpeg" format="jpg" directory="jakku" visible="false"/>
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68 </collection>
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69 </outputs>
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70 <tests>
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71 <test expect_num_outputs="1">
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72 <section name="essential">
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73 <param name="path">
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74 <expand macro="output"/>
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75 </param>
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76 </section>
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77 <section name="advanced">
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78 <param name="verbose" value="false"/>
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79 </section>
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80 <output_collection name="scatter_plot" count="2">
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81 <element name="output00000000_cell_type">
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82 <assert_contents>
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83 <has_text text="JFIF"/>
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84 </assert_contents>
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85 </element>
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86 <element name="output00000001_cell_type">
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87 <assert_contents>
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88 <has_text text="JFIF"/>
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89 </assert_contents>
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90 </element>
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91 </output_collection>
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92 </test>
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93 </tests>
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94 <help><![CDATA[
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95 Function generates pandas scatter plots.
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96
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97 Homepage: https://github.com/elmbeech/physicelldataloader
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98 ]]></help>
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99 <citations>
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100 <expand macro="citation"/>
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101 </citations>
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102 </tool>