Mercurial > repos > iuc > pcdl_make_graph_gml

annotate pcdl_make_graph_gml.xml @ 0:6d0f91e057f3 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 19:01:20 +0000
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6d0f91e057f3 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_make_graph_gml" name="pcdl_make_graph_gml" version="3.0.1+galaxy0" profile="21.05">
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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2 <macros>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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3 <import>pcdl_macros.xml</import>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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4 </macros>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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5 <requirements>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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6 <expand macro="requirement"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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7 </requirements>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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8 <command><![CDATA[
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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9 #import re
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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10 mkdir output_pc &&
6d0f91e057f3 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:
6d0f91e057f3 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))
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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13 ln -s '$file' output_pc/$filename &&
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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14 #end for
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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15
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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16 pcdl_make_graph_gml 'output_pc' $graph_type
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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17 --custom_data_type $custom_data_type
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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18 --microenv $microenv
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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19 --physiboss $physiboss
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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20 --settingxml 'none'
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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21 --verbose $verbose
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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22 --edge_attribute $edge_attribute
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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23 --node_attribute $node_attribute
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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24 ]]></command>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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25 <inputs>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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26 <section name="essential" title="essential:" expanded="true">
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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27 <expand macro="path"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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28 <expand macro="graph_type"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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29 <expand macro="custom_data_type"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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30 <expand macro="edge_attribute"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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31 <expand macro="node_attribute"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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32 </section>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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33 <section name="advanced" title="advanced:" expanded="false">
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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34 <expand macro="microenv"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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35 <expand macro="physiboss"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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36 <expand macro="verbose"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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37 </section>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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38 </inputs>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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39 <outputs>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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40 <collection name="graph_gml" type="list">
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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41 <discover_datasets pattern="(?P&lt;designation&gt;.+\.gml)" format="txt" directory="output_pc" visible="false"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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42 </collection>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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43 </outputs>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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44 <tests>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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45 <test expect_num_outputs="1">
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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46 <section name="essential">
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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47 <param name="path">
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48 <expand macro="output"/>
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49 </param>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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50 <param name="graph_type" value="attached"/>
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51 </section>
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52 <section name="advanced">
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53 <param name="verbose" value="false"/>
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54 </section>
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55 <output_collection name="graph_gml" count="2">
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56 <element name="output00000000_attached.gml">
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57 <assert_contents>
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58 <has_text text="graph ["/>
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59 <has_text text="node ["/>
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60 <has_text text="]"/>
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61 </assert_contents>
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62 </element>
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63 <element name="output00000001_attached.gml">
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64 <assert_contents>
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65 <has_text text="graph ["/>
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66 <has_text text="node ["/>
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67 <has_text text="]"/>
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68 </assert_contents>
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69 </element>
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70 </output_collection>
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71 </test>
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72 <test expect_num_outputs="1">
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73 <section name="essential">
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74 <param name="path">
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75 <expand macro="output"/>
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76 </param>
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77 <param name="graph_type" value="neighbor"/>
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78 </section>
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79 <section name="advanced">
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80 <param name="verbose" value="false"/>
6d0f91e057f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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81 </section>
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82 <output_collection name="graph_gml" count="2">
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83 <element name="output00000000_neighbor.gml">
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84 <assert_contents>
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85 <has_text text="graph ["/>
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86 <has_text text="node ["/>
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87 <has_text text="]"/>
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88 </assert_contents>
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89 </element>
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90 <element name="output00000001_neighbor.gml">
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91 <assert_contents>
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92 <has_text text="graph ["/>
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93 <has_text text="node ["/>
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94 <has_text text="]"/>
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95 </assert_contents>
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96 </element>
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97 </output_collection>
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98 </test>
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99 <test expect_num_outputs="1">
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100 <section name="essential">
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101 <param name="path">
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102 <expand macro="output"/>
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103 </param>
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104 <param name="graph_type" value="spring"/>
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105 </section>
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106 <section name="advanced">
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107 <param name="verbose" value="false"/>
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108 </section>
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109 <output_collection name="graph_gml" count="2">
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110 <element name="output00000000_spring.gml">
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111 <assert_contents>
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112 <has_text text="graph ["/>
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113 <has_text text="node ["/>
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114 <has_text text="]"/>
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115 </assert_contents>
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116 </element>
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117 <element name="output00000001_spring.gml">
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118 <assert_contents>
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119 <has_text text="graph ["/>
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120 <has_text text="node ["/>
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121 <has_text text="]"/>
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122 </assert_contents>
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123 </element>
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124 </output_collection>
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125 </test>
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126 </tests>
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127 <help><![CDATA[
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128 Function to generate graph files in the gml graph modelling language standard format. Gml was the outcome of an initiative that started at the international symposium on graph drawing 1995 in Passau and ended at Graph Drawing 1996 in Berkeley. The networkx python library (https://networkx.org/) and igraph C and python libraries (https://igraph.org/) for graph analysis are gml compatible and can as such read and write this file format.
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129
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130 Homepage: https://github.com/elmbeech/physicelldataloader
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131 ]]></help>
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132 <citations>
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133 <expand macro="citation"/>
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134 </citations>
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135 </tool>