Mercurial > repos > iuc > pcdl_plot_contour

annotate pcdl_plot_contour.xml @ 0:dc77ad27cd20 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 18:59:37 +0000
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dc77ad27cd20 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_contour" name="pcdl_plot_contour" version="3.0.1+galaxy0" profile="21.05">
dc77ad27cd20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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2 <macros>
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3 <import>pcdl_macros.xml</import>
dc77ad27cd20 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>
dc77ad27cd20 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
dc77ad27cd20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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10 mkdir output_pc &&
dc77ad27cd20 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:
dc77ad27cd20 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))
dc77ad27cd20 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 &&
dc77ad27cd20 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
dc77ad27cd20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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16 pcdl_plot_contour 'output_pc' '$focus_subs'
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17 --verbose $verbose
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18 --z_slice $z_slice
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19 --extrema '$extrema'
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20 --alpha $alpha
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21 --fill $fill
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22 --cmap '$cmap'
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23 --title '$title'
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24 --grid $grid
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25 --xlim '$xlim'
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26 --ylim '$ylim'
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27 --xyequal $xyequal
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28 --figsizepx $figsizepx_x $figsizepx_y
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29 --directory 'jakku'
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30 --ext $ext
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31 --figbgcolor '$figbgcolor'
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32 ]]></command>
dc77ad27cd20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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33 <inputs>
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34 <section name="essential" title="essential:" expanded="true">
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35 <expand macro="path"/>
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36 <expand macro="focus_subs"/>
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37 <expand macro="z_slice"/>
dc77ad27cd20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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38 <expand macro="extrema"/>
dc77ad27cd20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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39 <expand macro="alpha"/>
dc77ad27cd20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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40 <expand macro="fill"/>
dc77ad27cd20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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41 <expand macro="cmap"/>
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42 <expand macro="title"/>
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43 <expand macro="grid"/>
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44 <expand macro="xlim"/>
dc77ad27cd20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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45 <expand macro="ylim"/>
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46 <expand macro="xyequal"/>
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47 <expand macro="figsizepx_x"/>
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48 <expand macro="figsizepx_y"/>
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49 <expand macro="ext"/>
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50 <expand macro="figbgcolor"/>
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51 </section>
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52 <section name="advanced" title="advanced:" expanded="false">
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53 <expand macro="verbose"/>
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54 </section>
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55 </inputs>
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56 <outputs>
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57 <collection name="contour_plot" type="list">
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58 <discover_datasets pattern="(?P&lt;designation&gt;output.+)\.jpeg" format="jpg" directory="jakku" visible="false"/>
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59 </collection>
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60 </outputs>
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61 <tests>
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62 <test expect_num_outputs="1">
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63 <section name="essential">
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64 <param name="path">
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65 <expand macro="output"/>
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66 </param>
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67 <param name="focus_subs" value="oxygen"/>
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68 </section>
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69 <section name="advanced">
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70 <param name="verbose" value="false"/>
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71 </section>
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72 <output_collection name="contour_plot" count="2">
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73 <element name="output00000000_oxygen">
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74 <assert_contents>
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75 <has_text text="JFIF"/>
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76 </assert_contents>
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77 </element>
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78 <element name="output00000001_oxygen">
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79 <assert_contents>
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80 <has_text text="JFIF"/>
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81 </assert_contents>
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82 </element>
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83 </output_collection>
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84 </test>
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85 </tests>
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86 <help><![CDATA[
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87 Function generates matplotlib contour (or contourf) plots, inclusive color bar, for the substrate specified.
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88
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89 Homepage: https://github.com/elmbeech/physicelldataloader
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90 ]]></help>
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91 <citations>
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92 <expand macro="citation"/>
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93 </citations>
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94 </tool>