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comparison tools/convert/Sbml2Graph/Sbml2Graph.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
comparison
equal deleted inserted replaced
9:0976a6257300 10:6a112eaf8f38
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="develop"> 2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="2.0.0">
3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</description> 3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
11 $bipartite 11 $bipartite
12 $compound 12 $compound
13 $reaction 13 $reaction
32 <outputs> 32 <outputs>
33 <data format="txt" name="output"/> 33 <data format="txt" name="output"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
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40 <param name="inputPath" value="toy_model.xml"/> 37 <param name="inputPath" value="toy_model.xml"/>
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44 <param name="format" value="gml"/> 38 <param name="format" value="gml"/>
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48 <output name="output"> 39 <output name="output">
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52 <assert_contents> 40 <assert_contents>
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56 <has_line_matching expression=".*node.*" n="8"/> 41 <has_line_matching expression=".*node.*" n="8"/>
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60 <has_line_matching expression=".*edge.*" n="9"/> 42 <has_line_matching expression=".*edge.*" n="9"/>
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64 </assert_contents> 43 </assert_contents>
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68 </output> 44 </output>
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72 </test> 45 </test>
73 <test> 46 <test>
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77 <param name="inputPath" value="toy_model.xml"/> 47 <param name="inputPath" value="toy_model.xml"/>
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81 <param name="bipartite" value="true"/> 48 <param name="bipartite" value="true"/>
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85 <param name="compound" value="false"/> 49 <param name="compound" value="false"/>
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89 <param name="format" value="gml"/> 50 <param name="format" value="gml"/>
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93 <output name="output"> 51 <output name="output">
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97 <assert_contents> 52 <assert_contents>
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101 <has_line_matching expression=".*node.*" n="15"/> 53 <has_line_matching expression=".*node.*" n="15"/>
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105 <has_line_matching expression=".*edge.*" n="17"/> 54 <has_line_matching expression=".*edge.*" n="17"/>
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109 </assert_contents> 55 </assert_contents>
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113 </output> 56 </output>
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117 </test> 57 </test>
118 <test> 58 <test>
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122 <param name="inputPath" value="toy_model.xml"/> 59 <param name="inputPath" value="toy_model.xml"/>
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126 <param name="reaction" value="true"/> 60 <param name="reaction" value="true"/>
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130 <param name="compound" value="false"/> 61 <param name="compound" value="false"/>
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134 <param name="format" value="gml"/> 62 <param name="format" value="gml"/>
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138 <output name="output"> 63 <output name="output">
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142 <assert_contents> 64 <assert_contents>
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147 <has_line_matching expression=".*node.*" n="7"/> 65 <has_line_matching expression=".*node.*" n="7"/>
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151 <has_line_matching expression=".*edge.*" n="8"/> 66 <has_line_matching expression=".*edge.*" n="8"/>
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156 </assert_contents> 67 </assert_contents>
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161 </output> 68 </output>
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165 </test> 69 </test>
166 </tests> 70 </tests>
167 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format. 71 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
168 The graph can be either a compound graph, a reaction graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> 72 The graph can be either a compound graph, a reaction graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help>
169 <citations> 73 <citations>