Mercurial > repos > recetox > matchms_networking

annotate matchms_networking.xml @ 6:9982b85ff4e7 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:28:13 +0000
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children d8e937f335b8
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1 <tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy2" profile="21.09">
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2 <description>create similarity network graph from matchms similarity scores</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>help.xml</import>
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7 </macros>
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8 <expand macro="creator"/>
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9 <edam_operations>
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10 <edam_operation>operation_3927</edam_operation>
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11 <edam_operation>operation_3925</edam_operation>
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12 </edam_operations>
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13 <expand macro="bio.tools"/>
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15 <requirements>
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16 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
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17 </requirements>
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19 <command detect_errors="aggressive"><![CDATA[
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20 sh ${matchms_networking_cli}
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21 ]]></command>
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23 <environment_variables>
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24 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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25 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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26 </environment_variables>
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28 <configfiles>
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29 <configfile name="matchms_networking_cli">
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30 python3 ${__tool_directory__}/matchms_networking_wrapper.py \
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31 --score_name '${score_layer_name}_score' \
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32 --graph_format '$graph_format' \
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33 --identifier '$identifier_key' \
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34 --top_n '$top_n' \
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35 --max_links '$max_links' \
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36 --score_cutoff '$score_cutoff' \
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37 --link_method '$link_method' \
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38 #if $keep_unconnected_nodes
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39 --keep_unconnected_nodes \
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40 #end if
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41 '$scores' \
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42 '$similarity_network_file'
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43 </configfile>
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44 </configfiles>
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46 <inputs>
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47 <param label="Similarity scores" name="scores" type="data" format="json"
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48 help="matchms similarity-scores file."/>
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49 <param label="Score Layer" name="score_layer_name" type="select" help="Metric of the score layer to create a network from.">
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50 <expand macro="similarity_metrics"/>
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51 </param>
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52 <param label="Identifier key" name="identifier_key" type="text" value="compound_name"
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53 help="Unique metadata identifier of each spectrum from which scores are computed."/>
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54 <param label="Network-graph format" name="graph_format" type="select"
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55 help="Output format of the similarity network.">
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56 <option value="graphml">graphml</option>
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57 <option value="cyjs">cyjs</option>
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58 <option value="gexf">gexf</option>
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59 <option value="gml">gml</option>
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60 <option value="json">json</option>
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61 </param>
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62 <param label="Number of top edges to keep" name="top_n" type="integer" value="20"
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63 help="The number of highest-score edges to keep between a pair of nodes. Depending on 'Link method' parameter the top N edges will be selected either from disjoined
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64 sets of individual specta or joined subset of scores between the given pair of spectra. This value has to be higher than the 'Maximum number of links'."/>
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65 <param label="Maximum number of links per node" name="max_links" type="integer" value="10"
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66 help="Maximum number of links to add per node."/>
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67 <param label="Score cutoff" name="score_cutoff" type="float" value="0.7" min="0.0" max="1.0"
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68 help="Minimum similarity score value to link two spectra."/>
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69 <param label="Link method" name="link_method" type="select" display="radio"
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70 help="Method for computing top N edges for each node.
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71 If selected 'Single', top N nodes will be selected from disjoined sets of highest scores for nodes of a given pair (i.e., if a given edge belongs to top N scores of at least one node, it is kept).
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72 If selected 'Mutual', top N nodes will be selected from a joined subset of a given spectra pair (i.e., if and only if a given edge belongs to top N scores of both nodes, it is kept).">
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73 <option value="single" selected="true">Single</option>
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74 <option value="mutual">Mutual</option>
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75 </param>
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76 <param label="Keep unconnected nodes" name="keep_unconnected_nodes" type="boolean" checked="true"
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77 help="If set to No all unconnected nodes will be removed."/>
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78 </inputs>
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80 <outputs>
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81 <data label="Similarity network of ${scores.name}" name="similarity_network_file" format="graphml">
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82 <change_format>
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83 <when input="graph_format" value="graphml" format="graphml"/>
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84 <when input="graph_format" value="cyjs" format="cyjs"/>
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85 <when input="graph_format" value="gexf" format="gexf"/>
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86 <when input="graph_format" value="gml" format="gml"/>
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87 <when input="graph_format" value="json" format="json"/>
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88 </change_format>
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89 </data>
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90 </outputs>
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91
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92 <tests>
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93 <test>
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94 <param name="scores" value="scores.json" ftype="json"/>
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95 <param name="graph_format" value="graphml"/>
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96 <param name="identifier_key" value="compound_name"/>
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97 <output name="similarity_network_file" ftype="graphml">
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98 <assert_contents>
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99 <is_valid_xml />
5
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100 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="51"/>
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101 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="4"/>
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102 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="4"/>
0
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103 </assert_contents>
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104 </output>
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105 </test>
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106 <test>
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107 <param name="scores" value="scores.json" ftype="json"/>
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108 <param name="graph_format" value="cyjs"/>
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109 <param name="identifier_key" value="compound_name"/>
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110 <output name="similarity_network_file" ftype="cyjs">
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111 <assert_contents>
5
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112 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="51"/>
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113 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="4"/>
0
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114 </assert_contents>
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115 </output>
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116 </test>
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117 <test>
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118 <param name="scores" value="scores.json" ftype="json"/>
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119 <param name="graph_format" value="gexf"/>
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120 <param name="identifier_key" value="compound_name"/>
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121 <output name="similarity_network_file" ftype="gexf">
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122 <assert_contents>
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123 <is_valid_xml />
5
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124 <has_line_matching expression='.*node id="C[0-9]*" label="C[0-9]*" \/.' n="51"/>
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125 <has_line_matching expression='\s*.edge source="C[0-9]*" target="C[0-9]*" id="[0-9]*" weight="0.[0-9]*" \/.' n="4"/>
0
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126 </assert_contents>
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127 </output>
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128 </test>
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129 <test>
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130 <param name="scores" value="scores.json" ftype="json"/>
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131 <param name="graph_format" value="gml"/>
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132 <param name="identifier_key" value="compound_name"/>
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133 <output name="similarity_network_file" ftype="gml">
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134 <assert_contents>
5
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135 <has_line_matching expression='\s*node \[\n\s*id [0-9]*\n\s*label "C[0-9]*"\n\s*\]' n="51"/>
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136 <has_line_matching expression='\s*edge \[\n\s*source [0-9]*\n\s*target [0-9]*\n\s*weight 0\.[0-9]*\n\s*\]' n="4"/>
0
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137 </assert_contents>
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138 </output>
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139 </test>
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140 <test>
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141 <param name="scores" value="scores.json" ftype="json"/>
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142 <param name="graph_format" value="json"/>
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143 <param name="identifier_key" value="compound_name"/>
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144 <output name="similarity_network_file" ftype="json">
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145 <assert_contents>
5
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146 <has_text_matching expression='{"id": "C[0-9]*"}' n="51"/>
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147 <has_text_matching expression='{"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}' n="4"/>
0
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148 </assert_contents>
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149 </output>
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150 </test>
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151 <test>
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152 <param name="scores" value="scores.json" ftype="json"/>
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153 <param name="graph_format" value="graphml"/>
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154 <param name="identifier_key" value="compound_name"/>
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155 <param name="keep_unconnected_nodes" value="false"/>
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156 <output name="similarity_network_file" ftype="graphml">
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157 <assert_contents>
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158 <is_valid_xml />
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159 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="8"/>
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160 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="4"/>
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161 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="4"/>
0
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162 </assert_contents>
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163 </output>
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164 </test>
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165 <test>
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166 <param name="scores" value="scores.json" ftype="json"/>
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167 <param name="graph_format" value="graphml"/>
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168 <param name="identifier_key" value="compound_name"/>
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169 <param name="score_cutoff" value="0.4"/>
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170 <param name="keep_unconnected_nodes" value="false"/>
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171 <output name="similarity_network_file" ftype="graphml">
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172 <assert_contents>
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173 <is_valid_xml />
5
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174 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="20"/>
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175 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="13"/>
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176 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="13"/>
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177 </assert_contents>
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178 </output>
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179 </test>
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180 <test>
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181 <param name="scores" value="scores.json" ftype="json"/>
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182 <param name="graph_format" value="cyjs"/>
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183 <param name="identifier_key" value="compound_name"/>
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184 <param name="score_cutoff" value="0.8"/>
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185 <param name="link_method" value="mutual"/>
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186 <param name="keep_unconnected_nodes" value="false"/>
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187 <output name="similarity_network_file" ftype="cyjs">
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188 <assert_contents>
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189 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="6"/>
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190 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="3"/>
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191 </assert_contents>
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192 </output>
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193 </test>
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194 </tests>
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195
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196 <help>
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197 @HELP_matchms_networking@
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198 @HELP_matchms@
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199 </help>
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200
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201 <expand macro="citations"/>
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202
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203 </tool>