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annotate graphembed.xml @ 0:388a17402cca draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
author iuc
date Tue, 10 Dec 2019 16:40:04 +0000
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388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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1 <tool id="graphembed" name="GraphEmbed" version="@VERSION@.0" >
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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2 <description>Compute and plot a 2D embedding of a data matrix given supervised class information</description>
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3 <macros>
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4 <token name="@VERSION@">2.4</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">graph_embed</requirement>
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8 </requirements>
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9 <version_command><![CDATA[
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10 graphembed --version | cut -d'v' -f 2
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11 ]]></version_command>
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12 <command detect_errors='exit_code'><![CDATA[
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13 graphembed
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14 -i '$i'
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15 -t '$t'
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16 -c '$class_confidence'
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17 -k '$k'
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18 -d '$d'
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19 -z '$z'
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20 -l '$l'
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21 #if str($advanced.option) == 'yes'
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22 '$advanced.correlation_transformation'
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23 '$advanced.feature_selection'
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24 '$advanced.normalization'
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25 --cmap_name '$advanced.cmap_name'
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26 --min_threshold '$advanced.min_threshold'
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27 --max_threshold '$advanced.max_threshold'
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28 --random_state '$advanced.random_state'
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29 #end if
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30 --do_not_add_timestamp
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31 --figure_size 15
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32 -o ./
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33
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34 ]]>
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35 </command>
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36
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37 <inputs>
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38 <param argument="-i" type="data" format="tabular" label="Input Matrix"
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39 help="An feature-observation matrix, with features as rows and observations as columns (e.g. Genes vs Cells)" />
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40 <param argument="-t" type="data" format="tabular" label="Observation Classes"
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41 help="A two-column file with observations in the first column, and an integer representing their assigned class in the second column (e.g. 'YFPCD24X3w_20 2')" />
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42 <param argument="--class_confidence" type="float" value="1.0"
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43 label="Confidence bias for clustering" />
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44 <param argument="-k" type="integer" value="5" min="0"
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45 label="Number of links towards closest neighbour with the same class" />
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46 <param argument="-d" type="integer" value="1" min="0"
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47 label="Number of links towards denser neighbours with a different class" />
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48 <param argument="-z" type="integer" value="10" min="0"
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49 label="Number of nearest neighbours to limit the horizon of where to
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50 search for denser neighbours of a different class" />
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51 <param argument="-l" type="integer" value="0"
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52 label="Number of mutual nearest neighbours that define outlier instances." />
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53 <conditional name="advanced" >
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54 <param name="option" type="select" label="Use Advanced Parameters?">
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55 <option value="yes" >Yes</option>
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56 <option value="no" selected="true" >No</option>
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57 </param>
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58 <when value="no" ></when>
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59 <when value="yes" >
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60 <param argument="--correlation_transformation" type="boolean" optional="true"
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61 falsevalue="" truevalue="--correlation_transformation"
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62 label="Convert data matrix to corr coeff matrix" />
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63 <param argument="--normalization" type="boolean" optional="true"
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64 falsevalue="" truevalue="--normalization"
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65 label="Convert data matrix to normalized matrix" />
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66 <param argument="--feature_selection" type="boolean" optional="true"
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67 falsevalue="" truevalue="--feature_selection"
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68 label="Select most discriminative features" />
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69 <param argument="--cmap_name" type="select"
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70 label="Color map" >
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71 <option value="cubehelix" />
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72 <option value="terrain" />
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73 <option value="nipy_spectral" />
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74 <option value="gist_stern" />
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75 <option value="gist_ncar" selected="true" />
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76 </param>
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77 <param argument="--min_threshold" type="integer" value="5"
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78 label="Min num instances per class" />
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79 <param argument="--max_threshold" type="integer" value="400"
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80 label="Max num instances per class" />
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81 <param argument="--random_state" type="integer" value="1"
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82 label="Random seed" />
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83 </when>
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84 </conditional>
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85 <param name="showlog" type="boolean" checked="true" label="Output Log file" />
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86 </inputs>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
87
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
parents:
diff changeset
88 <outputs>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
parents:
diff changeset
89 <data name="out_coords" format="tabular" from_work_dir="2D_coords.txt"
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
parents:
diff changeset
90 label="${tool.name} on ${on_string}: 2D coords" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
parents:
diff changeset
91 <data name="out_target" format="tabular" from_work_dir="classes.txt"
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
parents:
diff changeset
92 label="${tool.name} on ${on_string}: Classes" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
parents:
diff changeset
93 <data name="out_clean" format="pdf" from_work_dir="img_1_clean.pdf"
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
94 label="${tool.name} on ${on_string}: Embed." />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
95 <data name="out_links" format="pdf" from_work_dir="img_2_links.pdf"
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
96 label="${tool.name} on ${on_string}: Embed + 1st shift" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
parents:
diff changeset
97 <data name="out_hull" format="pdf" from_work_dir="img_4_hull.pdf"
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
parents:
diff changeset
98 label="${tool.name} on ${on_string}: Embed + hulls + edges" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
99 <data name="out_hulllink" format="pdf" from_work_dir="img_5_hull_link.pdf"
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
100 label="${tool.name} on ${on_string}: Embed + hulls + 1st shift" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
101 <data name="out_log" format="txt" from_work_dir="log"
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
102 label="${tool.name} on ${on_string}: Log" >
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
103 <filter>showlog</filter>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
104 </data>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
105 </outputs>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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106
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
107 <tests>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
108 <test expect_num_outputs="7" >
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
109 <param name="i" value="prot_expression.mini.tsv" ftype="tabular" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
110 <param name="t" value="target.tsv" ftype="tabular" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
111 <output name="out_coords" >
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
112 <assert_contents>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
113 <has_text text="-3.8328 2.0278" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
114 <has_text text="7.0832 -4.1420" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
115 </assert_contents>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
116 </output>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
117 <output name="out_target" >
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
118 <assert_contents>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
119 <has_text text="14" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
120 <has_text text="8" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
121 </assert_contents>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
122 </output>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
123 </test>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
124 <test expect_num_outputs="6" >
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
125 <param name="i" value="prot_expression.mini.tsv" ftype="tabular" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
126 <param name="t" value="target.tsv" ftype="tabular" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
127 <param name="class_confidence" value="1.5" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
128 <param name="k" value="5" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
129 <param name="z" value="10" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
130 <param name="l" value="0" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
131 <param name="random_state" value="2" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
132 <conditional name="advanced" >
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
133 <param name="option" value="yes" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
134 <param name="correlation_transformation" value="true" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
135 <param name="feature_selection" value="true" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
136 <param name="normalization" value="true" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
137 </conditional>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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138 <param name="showlog" value="false" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
139 <output name="out_target" >
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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140 <assert_contents>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
141 <has_text text="14" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
142 <has_text text="16" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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143 </assert_contents>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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144 </output>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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145 <output name="out_coords" >
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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146 <assert_contents>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
147 <has_text text="25.9260 0.0171" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
148 <has_text text="-6.4521 -24.8940" />
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
149 </assert_contents>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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150 </output>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
151 </test>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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152 </tests>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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153 <help>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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154 ============
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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155 GraphEmbed
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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156 ============
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
157 *Compute a 2D embedding of a data matrix given supervised class information.*
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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158
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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159 Input: A discrete label for each instance is expected.
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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160
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
161 A graph is built where nodes are instances and there exist two types of edges:
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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162
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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163 * 'knn' edges
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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164 An edge to the k-th nearest instance that has the same label.
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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165 * 'k_shift' edges
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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166 An edge to the k-th nearest instance that is denser and has a different label
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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167
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
iuc
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diff changeset
168 Density is defined as the sum of the pairwise cosine similarity between an instance and all the other instances. The desired edge length is the euclidean distance between the instances. If the endpoints of an edge have the same label then the desired distance is divided by 1 + class_confidence. A k-shift edge is deleted if at least one of the endpoints is an outlier. Outlier nodes are defined as those instances that have no mutual k neighbors.
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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169
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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diff changeset
170 Finally the embedding is computed as the 2D coordinates of the corresponding graph embedding using the force layout algorithm from Tomihisa Kamada, and Satoru Kawai. "An algorithm for drawing general undirected graphs.", Information processing letters 31, no. 1 (1989): 7-15. </help>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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171 <citations>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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172 <citation type="doi">10.5281/zenodo.825832</citation>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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173 </citations>
388a17402cca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ commit fa8fcfdd990ab21b053c3a209018a21c89f6a82b"
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174 </tool>