Mercurial > repos > recetox > matchms_networking

comparison matchms_networking.xml @ 11:3289420aaaca draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
author recetox
date Wed, 22 Nov 2023 14:44:02 +0000
parents bd6a398a05e9
children
comparison
equal deleted inserted replaced
10:5a24a419aafe 11:3289420aaaca
76 <param label="Keep unconnected nodes" name="keep_unconnected_nodes" type="boolean" checked="true" 76 <param label="Keep unconnected nodes" name="keep_unconnected_nodes" type="boolean" checked="true"
77 help="If set to No all unconnected nodes will be removed."/> 77 help="If set to No all unconnected nodes will be removed."/>
78 </inputs> 78 </inputs>
79 79
80 <outputs> 80 <outputs>
81 <data label="Similarity network of ${scores.name}" name="similarity_network_file" format="graphml"> 81 <data label="Similarity network of ${scores.name}" name="similarity_network_file" format="xml">
82 <change_format> 82 <change_format>
83 <when input="graph_format" value="graphml" format="graphml"/> 83 <when input="graph_format" value="graphml" format="xml"/>
84 <when input="graph_format" value="cyjs" format="cyjs"/> 84 <when input="graph_format" value="cyjs" format="json"/>
85 <when input="graph_format" value="gexf" format="gexf"/> 85 <when input="graph_format" value="gexf" format="xml"/>
86 <when input="graph_format" value="gml" format="gml"/> 86 <when input="graph_format" value="gml" format="xml"/>
87 <when input="graph_format" value="json" format="json"/> 87 <when input="graph_format" value="json" format="json"/>
88 </change_format> 88 </change_format>
89 </data> 89 </data>
90 </outputs> 90 </outputs>
91 91
92 <tests> 92 <tests>
93 <test> 93 <test>
94 <param name="scores" value="scores.json" ftype="json"/> 94 <param name="scores" value="scores.json" ftype="json"/>
95 <param name="graph_format" value="graphml"/> 95 <param name="graph_format" value="graphml"/>
96 <param name="identifier_key" value="compound_name"/> 96 <param name="identifier_key" value="compound_name"/>
97 <output name="similarity_network_file" ftype="graphml"> 97 <output name="similarity_network_file" ftype="xml">
98 <assert_contents> 98 <assert_contents>
99 <is_valid_xml /> 99 <is_valid_xml />
100 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="51"/> 100 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="51"/>
101 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="4"/> 101 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="4"/>
102 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="4"/> 102 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="4"/>
105 </test> 105 </test>
106 <test> 106 <test>
107 <param name="scores" value="scores.json" ftype="json"/> 107 <param name="scores" value="scores.json" ftype="json"/>
108 <param name="graph_format" value="cyjs"/> 108 <param name="graph_format" value="cyjs"/>
109 <param name="identifier_key" value="compound_name"/> 109 <param name="identifier_key" value="compound_name"/>
110 <output name="similarity_network_file" ftype="cyjs"> 110 <output name="similarity_network_file" ftype="json">
111 <assert_contents> 111 <assert_contents>
112 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="51"/> 112 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="51"/>
113 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="4"/> 113 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="4"/>
114 </assert_contents> 114 </assert_contents>
115 </output> 115 </output>
116 </test> 116 </test>
117 <test> 117 <test>
118 <param name="scores" value="scores.json" ftype="json"/> 118 <param name="scores" value="scores.json" ftype="json"/>
119 <param name="graph_format" value="gexf"/> 119 <param name="graph_format" value="gexf"/>
120 <param name="identifier_key" value="compound_name"/> 120 <param name="identifier_key" value="compound_name"/>
121 <output name="similarity_network_file" ftype="gexf"> 121 <output name="similarity_network_file" ftype="xml">
122 <assert_contents> 122 <assert_contents>
123 <is_valid_xml /> 123 <is_valid_xml />
124 <has_line_matching expression='.*node id="C[0-9]*" label="C[0-9]*" \/.' n="51"/> 124 <has_line_matching expression='.*node id="C[0-9]*" label="C[0-9]*" \/.' n="51"/>
125 <has_line_matching expression='\s*.edge source="C[0-9]*" target="C[0-9]*" id="[0-9]*" weight="0.[0-9]*" \/.' n="4"/> 125 <has_line_matching expression='\s*.edge source="C[0-9]*" target="C[0-9]*" id="[0-9]*" weight="0.[0-9]*" \/.' n="4"/>
126 </assert_contents> 126 </assert_contents>
128 </test> 128 </test>
129 <test> 129 <test>
130 <param name="scores" value="scores.json" ftype="json"/> 130 <param name="scores" value="scores.json" ftype="json"/>
131 <param name="graph_format" value="gml"/> 131 <param name="graph_format" value="gml"/>
132 <param name="identifier_key" value="compound_name"/> 132 <param name="identifier_key" value="compound_name"/>
133 <output name="similarity_network_file" ftype="gml"> 133 <output name="similarity_network_file" ftype="xml">
134 <assert_contents> 134 <assert_contents>
135 <has_line_matching expression='\s*node \[\n\s*id [0-9]*\n\s*label "C[0-9]*"\n\s*\]' n="51"/> 135 <has_line_matching expression='\s*node \[\n\s*id [0-9]*\n\s*label "C[0-9]*"\n\s*\]' n="51"/>
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"/> 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"/>
137 </assert_contents> 137 </assert_contents>
138 </output> 138 </output>
151 <test> 151 <test>
152 <param name="scores" value="scores.json" ftype="json"/> 152 <param name="scores" value="scores.json" ftype="json"/>
153 <param name="graph_format" value="graphml"/> 153 <param name="graph_format" value="graphml"/>
154 <param name="identifier_key" value="compound_name"/> 154 <param name="identifier_key" value="compound_name"/>
155 <param name="keep_unconnected_nodes" value="false"/> 155 <param name="keep_unconnected_nodes" value="false"/>
156 <output name="similarity_network_file" ftype="graphml"> 156 <output name="similarity_network_file" ftype="xml">
157 <assert_contents> 157 <assert_contents>
158 <is_valid_xml /> 158 <is_valid_xml />
159 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="8"/> 159 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="8"/>
160 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="4"/> 160 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="4"/>
161 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="4"/> 161 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="4"/>
166 <param name="scores" value="scores.json" ftype="json"/> 166 <param name="scores" value="scores.json" ftype="json"/>
167 <param name="graph_format" value="graphml"/> 167 <param name="graph_format" value="graphml"/>
168 <param name="identifier_key" value="compound_name"/> 168 <param name="identifier_key" value="compound_name"/>
169 <param name="score_cutoff" value="0.4"/> 169 <param name="score_cutoff" value="0.4"/>
170 <param name="keep_unconnected_nodes" value="false"/> 170 <param name="keep_unconnected_nodes" value="false"/>
171 <output name="similarity_network_file" ftype="graphml"> 171 <output name="similarity_network_file" ftype="xml">
172 <assert_contents> 172 <assert_contents>
173 <is_valid_xml /> 173 <is_valid_xml />
174 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="20"/> 174 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="20"/>
175 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="13"/> 175 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="13"/>
176 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="13"/> 176 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="13"/>
182 <param name="graph_format" value="cyjs"/> 182 <param name="graph_format" value="cyjs"/>
183 <param name="identifier_key" value="compound_name"/> 183 <param name="identifier_key" value="compound_name"/>
184 <param name="score_cutoff" value="0.8"/> 184 <param name="score_cutoff" value="0.8"/>
185 <param name="link_method" value="mutual"/> 185 <param name="link_method" value="mutual"/>
186 <param name="keep_unconnected_nodes" value="false"/> 186 <param name="keep_unconnected_nodes" value="false"/>
187 <output name="similarity_network_file" ftype="cyjs"> 187 <output name="similarity_network_file" ftype="json">
188 <assert_contents> 188 <assert_contents>
189 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="6"/> 189 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="6"/>
190 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="3"/> 190 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="3"/>
191 </assert_contents> 191 </assert_contents>
192 </output> 192 </output>
195 <param name="scores" value="networking/test9.json" ftype="json"/> 195 <param name="scores" value="networking/test9.json" ftype="json"/>
196 <param name="graph_format" value="graphml"/> 196 <param name="graph_format" value="graphml"/>
197 <param name="identifier_key" value="compound_name"/> 197 <param name="identifier_key" value="compound_name"/>
198 <param name="score_cutoff" value="0.4"/> 198 <param name="score_cutoff" value="0.4"/>
199 <param name="keep_unconnected_nodes" value="false"/> 199 <param name="keep_unconnected_nodes" value="false"/>
200 <output name="similarity_network_file" ftype="graphml"> 200 <output name="similarity_network_file" ftype="xml">
201 <assert_contents> 201 <assert_contents>
202 <is_valid_xml /> 202 <is_valid_xml />
203 </assert_contents> 203 </assert_contents>
204 </output> 204 </output>
205 </test> 205 </test>