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comparison tools/attributes/SetIds/SetIds.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_SetIds" name="SetIds" version="develop"> 2 <tool id="met4j_SetIds" name="SetIds" version="2.0.0">
3 <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</description> 3 <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</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 attributes.SetIds#if str($colname) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetIds#if str($colname) != 'nan':
11 -cnew "$colname" 11 -cnew "$colname"
12 #end if 12 #end if
13 #if str($colid): 13 #if str($colid):
60 <outputs> 60 <outputs>
61 <data format="sbml" name="out"/> 61 <data format="sbml" name="out"/>
62 </outputs> 62 </outputs>
63 <tests> 63 <tests>
64 <test> 64 <test>
65
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71 <param name="sbml" value="toy_model.xml"/> 65 <param name="sbml" value="toy_model.xml"/>
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78 <param name="tab" value="idMetabolites.tsv"/> 66 <param name="tab" value="idMetabolites.tsv"/>
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85 <param name="o" value="METABOLITE"/> 67 <param name="o" value="METABOLITE"/>
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92 <output ftype="sbml" name="out"> 68 <output ftype="sbml" name="out">
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99 <assert_contents> 69 <assert_contents>
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106 <is_valid_xml/> 70 <is_valid_xml/>
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113 <has_line_matching expression=".*id=.metaboliteA.*" n="1"/> 71 <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>
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120 <has_line_matching expression=".*id=.metaboliteB.*" n="1"/> 72 <has_line_matching expression=".*id=.metaboliteB.*" n="1"/>
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127 </assert_contents> 73 </assert_contents>
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134 </output> 74 </output>
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141 </test> 75 </test>
142 <test> 76 <test>
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149 <param name="sbml" value="toy_model.xml"/> 77 <param name="sbml" value="toy_model.xml"/>
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156 <param name="tab" value="idReactions.tsv"/> 78 <param name="tab" value="idReactions.tsv"/>
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163 <output ftype="sbml" name="out"> 79 <output ftype="sbml" name="out">
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170 <assert_contents> 80 <assert_contents>
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177 <is_valid_xml/> 81 <is_valid_xml/>
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184 <has_line_matching expression=".*id=.reaction1.*" n="1"/> 82 <has_line_matching expression=".*id=.reaction1.*" n="1"/>
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191 <has_line_matching expression=".*id=.reaction2.*" n="1"/> 83 <has_line_matching expression=".*id=.reaction2.*" n="1"/>
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198 </assert_contents> 84 </assert_contents>
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205 </output> 85 </output>
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212 </test> 86 </test>
213 <test> 87 <test>
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220 <param name="sbml" value="XF_network.sbml"/> 88 <param name="sbml" value="XF_network.sbml"/>
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227 <param name="tab" value="idPathways.tsv"/> 89 <param name="tab" value="idPathways.tsv"/>
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234 <param name="o" value="PATHWAY"/> 90 <param name="o" value="PATHWAY"/>
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241 <output ftype="sbml" name="out"> 91 <output ftype="sbml" name="out">
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248 <assert_contents> 92 <assert_contents>
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255 <is_valid_xml/> 93 <is_valid_xml/>
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262 <has_line_matching expression=".*groups:id=.CEB.*" n="1"/> 94 <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>
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269 <has_line_matching expression=".*groups:id=.NSP.*" n="1"/> 95 <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>
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276 </assert_contents> 96 </assert_contents>
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283 </output> 97 </output>
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290 </test> 98 </test>
291 <test> 99 <test>
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298 <param name="sbml" value="XF_network.sbml"/> 100 <param name="sbml" value="XF_network.sbml"/>
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305 <param name="tab" value="idGenes.tsv"/> 101 <param name="tab" value="idGenes.tsv"/>
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312 <param name="o" value="GENE"/> 102 <param name="o" value="GENE"/>
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319 <output ftype="sbml" name="out"> 103 <output ftype="sbml" name="out">
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326 <assert_contents> 104 <assert_contents>
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333 <is_valid_xml/> 105 <is_valid_xml/>
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340 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> 106 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
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347 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> 107 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
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354 </assert_contents> 108 </assert_contents>
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361 </output> 109 </output>
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368 </test> 110 </test>
369 <test> 111 <test>
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376 <param name="sbml" value="XF_network.sbml"/> 112 <param name="sbml" value="XF_network.sbml"/>
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383 <param name="tab" value="idCompartments.tsv"/> 113 <param name="tab" value="idCompartments.tsv"/>
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390 <param name="o" value="COMPARTMENT"/> 114 <param name="o" value="COMPARTMENT"/>
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397 <output ftype="sbml" name="out"> 115 <output ftype="sbml" name="out">
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404 <assert_contents> 116 <assert_contents>
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411 <is_valid_xml/> 117 <is_valid_xml/>
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418 <has_line_matching expression=".*id=.cytosol.*" n="1"/> 118 <has_line_matching expression=".*id=.cytosol.*" n="1"/>
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425 <has_line_matching expression=".*id=.extra.*" n="1"/> 119 <has_line_matching expression=".*id=.extra.*" n="1"/>
426
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432 </assert_contents> 120 </assert_contents>
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439 </output> 121 </output>
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446 </test> 122 </test>
447 </tests> 123 </tests>
448 <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids 124 <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids
449 The ids must correspond between the tabulated file and the SBML file. 125 The ids must correspond between the tabulated file and the SBML file.
450 If prefix or suffix is different in the SBML file, use the -p or the -s options. 126 If prefix or suffix is different in the SBML file, use the -p or the -s options.