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comparison build/tools/Sbml2Tab/Sbml2Tab.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
comparison
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10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.0"> 2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.1">
3 <description>Create a tabulated file listing reaction attributes from a SBML file</description> 3 <description>Create a tabulated file listing reaction attributes from a SBML file</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:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i):
11 -irr "$i" 11 -irr "$i"
12 #end if 12 #end if
13 #if str($r): 13 #if str($r):
32 <outputs> 32 <outputs>
33 <data format="tsv" name="out"/> 33 <data format="tsv" name="out"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
37
37 <param name="in" value="toy_model.xml"/> 38 <param name="in" value="toy_model.xml"/>
39
38 <output ftype="tsv" name="out"> 40 <output ftype="tsv" name="out">
41
39 <assert_contents> 42 <assert_contents>
43
40 <has_n_lines n="8"/> 44 <has_n_lines n="8"/>
45
41 <has_n_columns n="9"/> 46 <has_n_columns n="9"/>
47
42 <has_text text="2.0 E[c] --&gt; D[c]"/> 48 <has_text text="2.0 E[c] --&gt; D[c]"/>
49
43 <has_text text="A[c] &lt;==&gt; B[c]"/> 50 <has_text text="A[c] &lt;==&gt; B[c]"/>
51
44 </assert_contents> 52 </assert_contents>
53
45 </output> 54 </output>
55
46 </test> 56 </test>
47 <test> 57 <test>
58
48 <param name="in" value="toy_model.xml"/> 59 <param name="in" value="toy_model.xml"/>
60
49 <param name="i" value="-&gt;"/> 61 <param name="i" value="-&gt;"/>
62
50 <param name="r" value="="/> 63 <param name="r" value="="/>
64
51 <output ftype="tsv" name="out"> 65 <output ftype="tsv" name="out">
66
52 <assert_contents> 67 <assert_contents>
68
53 <has_n_lines n="8"/> 69 <has_n_lines n="8"/>
70
54 <has_n_columns n="9"/> 71 <has_n_columns n="9"/>
72
55 <has_text text="2.0 E[c] -&gt; D[c]"/> 73 <has_text text="2.0 E[c] -&gt; D[c]"/>
74
56 <has_text text="A[c] = B[c]"/> 75 <has_text text="A[c] = B[c]"/>
76
57 </assert_contents> 77 </assert_contents>
78
58 </output> 79 </output>
80
59 </test> 81 </test>
60 </tests> 82 </tests>
61 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> 83 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help>
62 <citations/> 84 <citations/>
63 </tool> 85 </tool>