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comparison tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
parents 35c9abcd8934
children
comparison
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5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.2.1"> 2 <tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="MET4J_VERSION_TEST">
3 <description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> 3 <description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</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:1.2.1</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($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 <param name="sbml" value="toy_model.xml"/> 53 <param name="sbml" value="toy_model.xml"/>
54 <param name="tab" value="charges.tsv"/> 54 <param name="tab" value="charges.tsv"/>
55 <output ftype="sbml" name="out"> 55 <output ftype="sbml" name="out">
56 <assert_contents> 56 <assert_contents>
57 <is_valid_xml/> 57 <is_valid_xml/>
58 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> 58 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
59 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 59 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
60 </assert_contents> 60 </assert_contents>
61 </output> 61 </output>
62 </test> 62 </test>
63 <test> 63 <test>
64 <param name="sbml" value="toy_model.xml"/> 64 <param name="sbml" value="toy_model.xml"/>
65 <param name="tab" value="chargesWithComment.tsv"/> 65 <param name="tab" value="chargesWithComment.tsv"/>
66 <output ftype="sbml" name="out"> 66 <output ftype="sbml" name="out">
67 <assert_contents> 67 <assert_contents>
68 <is_valid_xml/> 68 <is_valid_xml/>
69 <has_line_matching expression=".*fbc:charge=.2.*" n="0"/> 69 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
70 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 70 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
71 </assert_contents> 71 </assert_contents>
72 </output> 72 </output>
73 </test> 73 </test>
74 <test> 74 <test>
75 <param name="sbml" value="toy_model.xml"/> 75 <param name="sbml" value="toy_model.xml"/>
76 <param name="tab" value="charges.tsv"/> 76 <param name="tab" value="charges.tsv"/>
77 <param name="nSkip" value="1"/> 77 <param name="nSkip" value="1"/>
78 <output ftype="sbml" name="out"> 78 <output ftype="sbml" name="out">
79 <assert_contents> 79 <assert_contents>
80 <is_valid_xml/> 80 <is_valid_xml/>
81 <has_line_matching expression=".*fbc:charge=.2.*" n="0"/> 81 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
82 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 82 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
83 </assert_contents> 83 </assert_contents>
84 </output> 84 </output>
85 </test> 85 </test>
86 <test> 86 <test>
87 <param name="sbml" value="toy_model.xml"/> 87 <param name="sbml" value="toy_model.xml"/>
88 <param name="tab" value="charges.tsv"/> 88 <param name="tab" value="charges.tsv"/>
89 <param name="ci" value="2"/> 89 <param name="ci" value="2"/>
90 <param name="cc" value="3"/> 90 <param name="cc" value="3"/>
91 <output ftype="sbml" name="out"> 91 <output ftype="sbml" name="out">
92 <assert_contents> 92 <assert_contents>
93 <is_valid_xml/> 93 <is_valid_xml/>
94 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> 94 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
95 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 95 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
96 </assert_contents> 96 </assert_contents>
97 </output> 97 </output>
98 </test> 98 </test>
99 <test> 99 <test>
100 <param name="sbml" value="XF_network.sbml"/> 100 <param name="sbml" value="XF_network.sbml"/>
101 <param name="tab" value="chargesXF.tsv"/> 101 <param name="tab" value="chargesXF.tsv"/>
102 <param name="p" value="true"/> 102 <param name="p" value="true"/>
103 <param name="s" value="true"/> 103 <param name="s" value="true"/>
104 <output ftype="sbml" name="out"> 104 <output ftype="sbml" name="out">
105 <assert_contents> 105 <assert_contents>
106 <is_valid_xml/> 106 <is_valid_xml/>
107 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/> 107 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>
108 </assert_contents> 108 </assert_contents>
109 </output> 109 </output>
110 </test> 110 </test>
111 </tests> 111 </tests>
112 <help><![CDATA[Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas 112 <help><![CDATA[Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas
113 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.
114 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.
115 The charge will be written in the SBML file in two locations:+ 115 The charge will be written in the SBML file in two locations:+