Mercurial > repos > metexplore > met4j

comparison build/tools/LoadPoint/LoadPoint.xml @ 10:6a112eaf8f38 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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_LoadPoint" name="LoadPoint" version="develop"> 2 <tool id="met4j_LoadPoint" name="LoadPoint" version="2.0.0">
3 <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</description> 3 <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</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 networkAnalysis.LoadPoint -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath"
11 #if str($sideCompoundFile) != 'None': 11 #if str($sideCompoundFile) != 'None':
12 -s "$sideCompoundFile" 12 -s "$sideCompoundFile"
13 #end if 13 #end if
28 <outputs> 28 <outputs>
29 <data format="tsv" name="outputPath"/> 29 <data format="tsv" name="outputPath"/>
30 </outputs> 30 </outputs>
31 <tests> 31 <tests>
32 <test> 32 <test>
33
34
35
36
37
38
39
40
41
42
43
44 <param name="inputPath" value="toy_model.xml"/> 33 <param name="inputPath" value="toy_model.xml"/>
45
46
47
48
49
50
51
52
53
54
55
56 <output ftype="tsv" name="outputPath"> 34 <output ftype="tsv" name="outputPath">
57
58
59
60
61
62
63
64
65
66
67
68 <assert_contents> 35 <assert_contents>
69
70
71
72
73
74
75
76
77
78
79
80 <has_n_columns n="3"/> 36 <has_n_columns n="3"/>
81
82
83
84
85
86
87
88
89
90
91
92 <has_n_lines n="8"/> 37 <has_n_lines n="8"/>
93
94
95
96
97
98
99
100
101
102
103
104 </assert_contents> 38 </assert_contents>
105
106
107
108
109
110
111
112
113
114
115
116 </output> 39 </output>
117
118
119
120
121
122
123
124
125
126
127
128 </test> 40 </test>
129 </tests> 41 </tests>
130 <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. 42 <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.
131 From Rahman et al. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinf. (2006): 43 From Rahman et al. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinf. (2006):
132 For a given metabolic network, the load L on metabolite m can be defined as : 44 For a given metabolic network, the load L on metabolite m can be defined as :