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comparison map_ensembl_transcripts.xml @ 21:d6b961721037

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Miller Lab Devshed version 4c04e35b18f6
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 05 Nov 2012 12:44:17 -0500
parents 8ae67e9fb6ff
children
comparison
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20:8a4b8efbc82c 21:d6b961721037
9 "--posENSEMBLclmn=${ensembl_col}" 9 "--posENSEMBLclmn=${ensembl_col}"
10 "--output=${output}" 10 "--output=${output}"
11 </command> 11 </command>
12 12
13 <inputs> 13 <inputs>
14 <param name="input" type="data" format="tabular" label="Table" /> 14 <param name="input" type="data" format="tabular" label="Dataset" >
15 <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript code" /> 15 <validator type="unspecified_build" message="This dataset does not have a database/build and cannot be used with this tool" />
16 </param>
17 <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript ID" />
16 </inputs> 18 </inputs>
17 19
18 <outputs> 20 <outputs>
19 <data name="output" format="tabular" /> 21 <data name="output" format="tabular" />
20 </outputs> 22 </outputs>
32 </tests> 34 </tests>
33 --> 35 -->
34 36
35 <help> 37 <help>
36 38
39 **Dataset formats**
40
41 The input and output datasets are in tabular_ format.
42 The input dataset must have a column with an ENSEMBL transcript ID and have
43 the database/build set. Even though positions are not needed the correct
44 database/build must be given to look up the pathways.
45 The output dataset will have added columns for the pathway.
46 (`Dataset missing?`_)
47
48 .. _tabular: ./static/formatHelp.html#tab
49 .. _Dataset missing?: ./static/formatHelp.html
50
51 -----
52
37 **What it does** 53 **What it does**
38 54
39 Adds the fields KEGG gene codes and KEGG pathways to an input table of ENSEMBL transcript codes. 55 Adds the fields "KEGG gene ID" and "KEGG pathways" to an input table of ENSEMBL
56 transcript IDs. A "U" in the KEGG gene ID field indicates that the
57 tool cannot link the ENSEMBL transcript ID to a KEGG gene ID.
58 An "N" in the pathway field means the KEGG pathway is unknown.
40 59
60 -----
61
62 **Example**
63
64 - input::
65
66 ENSCAFT00000000001
67 ENSCAFT00000000144
68 ENSCAFT00000000160
69 ENSCAFT00000000215
70 etc.
71
72 - output::
73
74 ENSCAFT00000000001 476153 cfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
75 ENSCAFT00000000144 483960 N
76 ENSCAFT00000000160 610160 N
77 ENSCAFT00000000215 U N
78 etc.
79
41 </help> 80 </help>
42 </tool> 81 </tool>