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comparison get_data/kegg_glycan/linkKEGG.xml @ 0:89592faa2875 draft

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author chrisb
date Wed, 23 Mar 2016 14:35:56 -0400
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1 <tool id="glytools_kegg_link" name="GAP Cross-reference with KEGG databases " version="0.3.1">
2 <description> searches KEGG for related database entries</description>
3 <requirements>
4 <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
5 </requirements>
6 <command interpreter="python"><![CDATA[linkKEGG.py -t $targetdb -s $source -o $output ]]></command>
7 <inputs>
8 <param name="targetdb" type="select" label="Target Database">
9 <option value="glycan" selected="true"> target KEGG glycan database</option>
10 <option value="pathway" selected="false"> target KEGG pathway database</option>
11 <option value="brite" selected="false"> target KEGG brite database</option>
12 <option value="module" selected="false"> target KEGG module database</option>
13 <option value="ko" selected="false"> target KEGG ko database</option>
14 <option value="genome" selected="false"> target KEGG genome database</option>
15 <option value="compound" selected="false"> target KEGG compound database</option>
16 <option value="reaction" selected="false"> target KEGG reaction database</option>
17 <option value="rpair" selected="false"> target KEGG rpair database</option>
18 <option value="rclass" selected="false"> target KEGG rclass database</option>
19 <option value="enzyme" selected="false"> target KEGG enzyme database</option>
20 <option value="disease" selected="false"> target KEGG disease database</option>
21 <option value="drug" selected="false"> target KEGG drug database</option>
22 <option value="dgroup" selected="false"> target KEGG dgroup database</option>
23 <option value="environ" selected="false"> target KEGG environ database</option>
24 </param>
25 <param name="source" type="text" value="ec:2.4.1.11" optional="false" label="Source database or entry" help="Source database or db entry to use to search target db. Example dbsource is genome. Example db entry is map00010"/>
26 </inputs>
27 <outputs>
28 <data format="txt" name="output" label="linked entries from KEGG database search"/>
29 </outputs>
30 <citations>
31 <!-- -->
32 <citation type="doi">10.1002/0471250953.bi0112s38</citation>
33 </citations>
34 <tests>
35 <test>
36 <param name="targetdb" value="glycan" />
37 <param name="source" value="ec:2.4.1.11"" />
38 <output name="output" file="link_test1.txt" />
39 </test>
40 </tests>
41 <help> <![CDATA[
42 .. class:: infomark
43
44 **What this tool does**
45
46 This tool find connections between entries or db's found at KEGG. For instance which enzymes work on UDP-Glucose, or which reactions is UDP-Glucose involved in,
47 or which glycans are acted by an enzyme that acts on UDP-Glucose (ec:2.4.1.11).
48
49 ----
50
51 .. class:: infomark
52
53 **Example 1**
54
55 target and source sequence::
56
57 enzyme
58 gl:G10608
59
60 output sequence::
61
62 gl:G10608 ec:2.4.1.11
63 gl:G10608 ec:2.4.1.12
64 gl:G10608 ec:2.4.1.13
65 gl:G10608 ec:2.4.1.14
66 gl:G10608 ec:2.4.1.15
67 gl:G10608 ec:2.4.1.183
68 gl:G10608 ec:2.4.1.188
69 gl:G10608 ec:2.4.1.34
70 gl:G10608 ec:2.4.1.53
71 gl:G10608 ec:2.4.1.80
72
73 .. class:: infomark
74
75 **Example 2**
76
77 target and source sequence::
78
79 reaction
80 gl:G10608
81
82 output sequence::
83
84 gl:G10608 rn:R06020
85 gl:G10608 rn:R06023
86 gl:G10608 rn:R06036
87 gl:G10608 rn:R06043
88 gl:G10608 rn:R06045
89 gl:G10608 rn:R06051
90 gl:G10608 rn:R06062
91 gl:G10608 rn:R06073
92 gl:G10608 rn:R06181
93 gl:G10608 rn:R06226
94 gl:G10608 rn:R06275
95 gl:G10608 rn:R09315
96 gl:G10608 rn:R09316
97
98 .. class:: infomark
99
100 **Example 3**
101
102 target and source sequence::
103
104 glycan
105 ec:2.4.1.11
106
107 output sequence::
108
109 ec:2.4.1.11 gl:G10495
110 ec:2.4.1.11 gl:G10608
111 ec:2.4.1.11 gl:G10619
112
113 ]]>
114
115 </help>
116
117 </tool>