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comparison build/tools/SetCharges/SetCharges.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_SetCharges" name="SetCharges" version="develop"> 2 <tool id="met4j_SetCharges" name="SetCharges" version="2.0.0">
3 <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</description> 3 <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</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.SetCharges#if str($colcharge) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetCharges#if str($colcharge) != 'nan':
11 -cc "$colcharge" 11 -cc "$colcharge"
12 #end if 12 #end if
13 #if str($colid) != 'nan': 13 #if str($colid) != 'nan':
48 <outputs> 48 <outputs>
49 <data format="sbml" name="out"/> 49 <data format="sbml" name="out"/>
50 </outputs> 50 </outputs>
51 <tests> 51 <tests>
52 <test> 52 <test>
53
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59 <param name="sbml" value="toy_model.xml"/> 53 <param name="sbml" value="toy_model.xml"/>
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66 <param name="tab" value="charges.tsv"/> 54 <param name="tab" value="charges.tsv"/>
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73 <output ftype="sbml" name="out"> 55 <output ftype="sbml" name="out">
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80 <assert_contents> 56 <assert_contents>
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87 <is_valid_xml/> 57 <is_valid_xml/>
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94 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> 58 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
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101 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 59 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
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108 </assert_contents> 60 </assert_contents>
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115 </output> 61 </output>
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122 </test> 62 </test>
123 <test> 63 <test>
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130 <param name="sbml" value="toy_model.xml"/> 64 <param name="sbml" value="toy_model.xml"/>
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137 <param name="tab" value="chargesWithComment.tsv"/> 65 <param name="tab" value="chargesWithComment.tsv"/>
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144 <output ftype="sbml" name="out"> 66 <output ftype="sbml" name="out">
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151 <assert_contents> 67 <assert_contents>
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158 <is_valid_xml/> 68 <is_valid_xml/>
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165 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> 69 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
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172 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 70 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
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179 </assert_contents> 71 </assert_contents>
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186 </output> 72 </output>
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193 </test> 73 </test>
194 <test> 74 <test>
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201 <param name="sbml" value="toy_model.xml"/> 75 <param name="sbml" value="toy_model.xml"/>
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208 <param name="tab" value="charges.tsv"/> 76 <param name="tab" value="charges.tsv"/>
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215 <param name="nSkip" value="1"/> 77 <param name="nSkip" value="1"/>
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222 <output ftype="sbml" name="out"> 78 <output ftype="sbml" name="out">
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229 <assert_contents> 79 <assert_contents>
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236 <is_valid_xml/> 80 <is_valid_xml/>
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243 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> 81 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
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250 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 82 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
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257 </assert_contents> 83 </assert_contents>
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264 </output> 84 </output>
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271 </test> 85 </test>
272 <test> 86 <test>
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279 <param name="sbml" value="toy_model.xml"/> 87 <param name="sbml" value="toy_model.xml"/>
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286 <param name="tab" value="charges.tsv"/> 88 <param name="tab" value="charges.tsv"/>
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293 <param name="ci" value="2"/> 89 <param name="ci" value="2"/>
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300 <param name="cc" value="3"/> 90 <param name="cc" value="3"/>
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307 <output ftype="sbml" name="out"> 91 <output ftype="sbml" name="out">
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314 <assert_contents> 92 <assert_contents>
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321 <is_valid_xml/> 93 <is_valid_xml/>
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328 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> 94 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
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335 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 95 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
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342 </assert_contents> 96 </assert_contents>
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349 </output> 97 </output>
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356 </test> 98 </test>
357 <test> 99 <test>
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364 <param name="sbml" value="XF_network.sbml"/> 100 <param name="sbml" value="XF_network.sbml"/>
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371 <param name="tab" value="chargesXF.tsv"/> 101 <param name="tab" value="chargesXF.tsv"/>
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378 <param name="p" value="true"/> 102 <param name="p" value="true"/>
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385 <param name="s" value="true"/> 103 <param name="s" value="true"/>
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392 <output ftype="sbml" name="out"> 104 <output ftype="sbml" name="out">
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399 <assert_contents> 105 <assert_contents>
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406 <is_valid_xml/> 106 <is_valid_xml/>
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413 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/> 107 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>
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420 </assert_contents> 108 </assert_contents>
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427 </output> 109 </output>
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434 </test> 110 </test>
435 </tests> 111 </tests>
436 <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges 112 <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges
437 The charge must be a number. The ids must correspond between the tabulated file and the SBML file. 113 The charge must be a number. The ids must correspond between the tabulated file and the SBML file.
438 If prefix or suffix is different in the SBML file, use the -p or the -s options. 114 If prefix or suffix is different in the SBML file, use the -p or the -s options.