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comparison tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.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
equal deleted inserted replaced
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_SeedsAndTargets" name="SeedsAndTargets" version="2.0.0"> 2 <tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="2.0.1">
3 <description>Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology</description> 3 <description>Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology</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 networkAnalysis.SeedsAndTargets -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath"
11 #if str($inputSide) != 'None': 11 #if str($inputSide) != 'None':
12 -sc "$inputSide" 12 -sc "$inputSide"
13 #end if 13 #end if
42 <outputs> 42 <outputs>
43 <data format="tsv" name="outputPath"/> 43 <data format="tsv" name="outputPath"/>
44 </outputs> 44 </outputs>
45 <tests> 45 <tests>
46 <test> 46 <test>
47
47 <param name="inputPath" value="XF_network.sbml"/> 48 <param name="inputPath" value="XF_network.sbml"/>
49
48 <param name="source" value="true"/> 50 <param name="source" value="true"/>
51
49 <output ftype="tsv" name="outputPath"> 52 <output ftype="tsv" name="outputPath">
53
50 <assert_contents> 54 <assert_contents>
55
51 <has_n_columns n="1"/> 56 <has_n_columns n="1"/>
57
52 <has_n_lines n="109"/> 58 <has_n_lines n="109"/>
59
53 <has_line_matching expression="M_\S+_\w" n="109"/> 60 <has_line_matching expression="M_\S+_\w" n="109"/>
61
54 </assert_contents> 62 </assert_contents>
63
55 </output> 64 </output>
65
56 </test> 66 </test>
57 <test> 67 <test>
68
58 <param name="inputPath" value="XF_network.sbml"/> 69 <param name="inputPath" value="XF_network.sbml"/>
70
59 <param name="sink" value="true"/> 71 <param name="sink" value="true"/>
72
60 <param name="useInternal" value="true"/> 73 <param name="useInternal" value="true"/>
74
61 <param name="comp" value="e"/> 75 <param name="comp" value="e"/>
76
62 <output ftype="tsv" name="outputPath"> 77 <output ftype="tsv" name="outputPath">
78
63 <assert_contents> 79 <assert_contents>
80
64 <has_n_columns n="1"/> 81 <has_n_columns n="1"/>
82
65 <has_n_lines n="5"/> 83 <has_n_lines n="5"/>
84
66 <has_line_matching expression="^M_\S+_\w" n="5"/> 85 <has_line_matching expression="^M_\S+_\w" n="5"/>
86
67 </assert_contents> 87 </assert_contents>
88
68 </output> 89 </output>
90
69 </test> 91 </test>
70 <test> 92 <test>
93
71 <param name="inputPath" value="XF_network.sbml"/> 94 <param name="inputPath" value="XF_network.sbml"/>
95
72 <param name="sink" value="true"/> 96 <param name="sink" value="true"/>
97
73 <param name="useBorensteinAlg" value="true"/> 98 <param name="useBorensteinAlg" value="true"/>
99
74 <param name="comp" value="e"/> 100 <param name="comp" value="e"/>
101
75 <output ftype="tsv" name="outputPath"> 102 <output ftype="tsv" name="outputPath">
103
76 <assert_contents> 104 <assert_contents>
105
77 <has_n_columns n="1"/> 106 <has_n_columns n="1"/>
107
78 <has_n_lines n="26"/> 108 <has_n_lines n="26"/>
109
79 <has_line_matching expression="^M_\S+_\w" n="26"/> 110 <has_line_matching expression="^M_\S+_\w" n="26"/>
111
80 </assert_contents> 112 </assert_contents>
113
81 </output> 114 </output>
115
82 </test> 116 </test>
83 </tests> 117 </tests>
84 <help><![CDATA[Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology 118 <help><![CDATA[Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology
85 Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms. 119 Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms.
86 This application can use seed definition and SCC-based detection algorithm by Borenstein et al. or, alternatively, degree-based sink and source detection with compartment adjustment. 120 This application can use seed definition and SCC-based detection algorithm by Borenstein et al. or, alternatively, degree-based sink and source detection with compartment adjustment.