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comparison build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.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_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="develop"> 2 <tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="2.0.0">
3 <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description> 3 <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</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.Sbml2CarbonSkeletonNet -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CarbonSkeletonNet -i "$inputPath"
11 -g "$inputAAM" 11 -g "$inputAAM"
12 $keepSingleCarbon 12 $keepSingleCarbon
13 $mergeComp 13 $mergeComp
44 <outputs> 44 <outputs>
45 <data format="txt" name="output"/> 45 <data format="txt" name="output"/>
46 </outputs> 46 </outputs>
47 <tests> 47 <tests>
48 <test> 48 <test>
49
50
51
52 <param name="inputPath" value="Human-GEM_pathways.xml"/> 49 <param name="inputPath" value="Human-GEM_pathways.xml"/>
53
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56 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 50 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
57
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60 <param name="format" value="gml"/> 51 <param name="format" value="gml"/>
61
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64 <output name="output"> 52 <output name="output">
65
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68 <assert_contents> 53 <assert_contents>
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72 <has_n_lines n="2602"/> 54 <has_n_lines n="2602"/>
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76 </assert_contents> 55 </assert_contents>
77
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80 </output> 56 </output>
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84 </test> 57 </test>
85 <test> 58 <test>
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89 <param name="inputPath" value="Human-GEM_pathways.xml"/> 59 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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93 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 60 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
94
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97 <param name="keepSingleCarbon" value="true"/> 61 <param name="keepSingleCarbon" value="true"/>
98
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101 <param name="format" value="gml"/> 62 <param name="format" value="gml"/>
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105 <output name="output"> 63 <output name="output">
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109 <assert_contents> 64 <assert_contents>
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113 <has_n_lines n="2629"/> 65 <has_n_lines n="2629"/>
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117 </assert_contents> 66 </assert_contents>
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121 </output> 67 </output>
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125 </test> 68 </test>
126 <test> 69 <test>
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130 <param name="inputPath" value="Human-GEM_pathways.xml"/> 70 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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134 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 71 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
135
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138 <param name="mergeComp" value="true"/> 72 <param name="mergeComp" value="true"/>
139
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142 <param name="format" value="gml"/> 73 <param name="format" value="gml"/>
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146 <output name="output"> 74 <output name="output">
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150 <assert_contents> 75 <assert_contents>
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154 <has_n_lines n="2406"/> 76 <has_n_lines n="2406"/>
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158 </assert_contents> 77 </assert_contents>
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162 </output> 78 </output>
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166 </test> 79 </test>
167 <test> 80 <test>
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171 <param name="inputPath" value="Human-GEM_pathways.xml"/> 81 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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175 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 82 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
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179 <param name="mergeEdges" value="true"/> 83 <param name="mergeEdges" value="true"/>
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183 <param name="format" value="gml"/> 84 <param name="format" value="gml"/>
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187 <output name="output"> 85 <output name="output">
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191 <assert_contents> 86 <assert_contents>
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195 <has_n_lines n="2071"/> 87 <has_n_lines n="2071"/>
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199 </assert_contents> 88 </assert_contents>
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203 </output> 89 </output>
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207 </test> 90 </test>
208 <test> 91 <test>
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212 <param name="inputPath" value="Human-GEM_pathways.xml"/> 92 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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216 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 93 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
217
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220 <param name="removeIsolated" value="true"/> 94 <param name="removeIsolated" value="true"/>
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224 <param name="format" value="gml"/> 95 <param name="format" value="gml"/>
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228 <output name="output"> 96 <output name="output">
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232 <assert_contents> 97 <assert_contents>
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236 <has_n_lines n="2490"/> 98 <has_n_lines n="2490"/>
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240 </assert_contents> 99 </assert_contents>
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244 </output> 100 </output>
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248 </test> 101 </test>
249 <test> 102 <test>
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253 <param name="inputPath" value="Human-GEM_pathways.xml"/> 103 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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257 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 104 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
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261 <param name="undirected" value="true"/> 105 <param name="undirected" value="true"/>
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265 <param name="format" value="gml"/> 106 <param name="format" value="gml"/>
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269 <output name="output"> 107 <output name="output">
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273 <assert_contents> 108 <assert_contents>
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277 <has_n_lines n="3214"/> 109 <has_n_lines n="3214"/>
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281 </assert_contents> 110 </assert_contents>
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285 </output> 111 </output>
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289 </test> 112 </test>
290 <test> 113 <test>
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294 <param name="inputPath" value="Human-GEM_pathways.xml"/> 114 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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298 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 115 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
299
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302 <param name="format" value="matrix"/> 116 <param name="format" value="matrix"/>
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306 <output name="output"> 117 <output name="output">
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310 <assert_contents> 118 <assert_contents>
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314 <has_n_lines n="112"/> 119 <has_n_lines n="112"/>
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318 </assert_contents> 120 </assert_contents>
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322 </output> 121 </output>
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326 </test> 122 </test>
327 <test> 123 <test>
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331 <param name="inputPath" value="Human-GEM_pathways.xml"/> 124 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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335 <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/> 125 <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/>
336
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339 <param name="fromIndexes" value="true"/> 126 <param name="fromIndexes" value="true"/>
340
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343 <param name="format" value="gml"/> 127 <param name="format" value="gml"/>
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347 <output name="output"> 128 <output name="output">
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351 <assert_contents> 129 <assert_contents>
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355 <has_n_lines n="2611"/> 130 <has_n_lines n="2611"/>
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359 </assert_contents> 131 </assert_contents>
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363 </output> 132 </output>
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367 </test> 133 </test>
368 </tests> 134 </tests>
369 <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produces a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) performs atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help> 135 <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produces a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) performs atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help>
370 <citations/> 136 <citations/>
371 </tool> 137 </tool>