Mercurial > repos > metexplore > met4j

annotate build/tools/Sbml2Graph/Sbml2Graph.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 1274e2a62479
children 6a112eaf8f38
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="develop">
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3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
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11 $bipartite
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12 $compound
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13 $reaction
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14 #if str($format):
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15 -f "$format"
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16 #end if
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17 -o "$output"
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18 ]]></command>
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19 <inputs>
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20 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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21 <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/>
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22 <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/>
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23 <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/>
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24 <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id &#9; edge type &#9; target id). Other options include GML, JsonGraph, and tabulated node list (label &#9; node id &#9; node type)." name="format" optional="true" type="select" value="tab">
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25 <option value="gml">gml</option>
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26 <option selected="true" value="tab">tab</option>
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27 <option value="nodeList">nodeList</option>
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28 <option value="json">json</option>
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29 <option value="matrix">matrix</option>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data format="txt" name="output"/>
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34 </outputs>
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35 <tests>
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36 <test>
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40 <param name="inputPath" value="toy_model.xml"/>
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44 <param name="format" value="gml"/>
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48 <output name="output">
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52 <assert_contents>
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56 <has_line_matching expression=".*node.*" n="8"/>
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60 <has_line_matching expression=".*edge.*" n="9"/>
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64 </assert_contents>
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68 </output>
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72 </test>
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73 <test>
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77 <param name="inputPath" value="toy_model.xml"/>
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81 <param name="bipartite" value="true"/>
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85 <param name="compound" value="false"/>
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89 <param name="format" value="gml"/>
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93 <output name="output">
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97 <assert_contents>
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101 <has_line_matching expression=".*node.*" n="15"/>
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105 <has_line_matching expression=".*edge.*" n="17"/>
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108
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109 </assert_contents>
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112
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113 </output>
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116
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117 </test>
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118 <test>
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121
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122 <param name="inputPath" value="toy_model.xml"/>
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125
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126 <param name="reaction" value="true"/>
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129
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130 <param name="compound" value="false"/>
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134 <param name="format" value="gml"/>
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138 <output name="output">
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141
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142 <assert_contents>
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147 <has_line_matching expression=".*node.*" n="7"/>
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151 <has_line_matching expression=".*edge.*" n="8"/>
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155
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156 </assert_contents>
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160
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161 </output>
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164
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165 </test>
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166 </tests>
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167 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
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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>
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169 <citations>
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170 <citation type="doi">10.1109/tcbb.2008.79</citation>
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171 </citations>
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172 </tool>