Mercurial > repos > miller-lab > genome_diversity

annotate map_ensembl_transcripts.xml @ 28:184d14e4270d

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to Miller Lab devshed revision 4ede22dd5500
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 17 Jul 2013 12:46:46 -0400
parents d6b961721037
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
1 <tool id="gd_new_oscar" name="Get Pathways" version="1.0.0">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
2 <description>: Look up KEGG pathways for given Ensembl transcripts</description>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
3
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
4 <command interpreter="python">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
5 rtrnKEGGpthwfENSEMBLTc.py
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
6 "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.oscar.loc"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
7 "--species=${input.metadata.dbkey}"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
8 "--input=${input}"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
9 "--posENSEMBLclmn=${ensembl_col}"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
10 "--output=${output}"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
11 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
12
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
13 <inputs>
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
14 <param name="input" type="data" format="tabular" label="Dataset" >
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
15 <validator type="unspecified_build" message="This dataset does not have a database/build and cannot be used with this tool" />
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
16 </param>
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
17 <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript ID" />
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
18 </inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
19
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
20 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
21 <data name="output" format="tabular" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
22 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
23
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
24 <!--
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
25 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
26 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
27 <param name="input" value="test_in/ensembl.tabular" ftype="tabular">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
28 <metadata name="dbkey" value="canFam2" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
29 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
30 <param name="ensembl_col" value="1" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
31
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
32 <output name="output" file="test_out/map_ensembl_transcripts/map_ensembl_transcripts.tabular" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
33 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
34 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
35 -->
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
36
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
37 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
38
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
39 **Dataset formats**
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
40
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
41 The input and output datasets are in tabular_ format.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
42 The input dataset must have a column with an ENSEMBL transcript ID and have
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
43 the database/build set. Even though positions are not needed the correct
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
44 database/build must be given to look up the pathways.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
45 The output dataset will have added columns for the pathway.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
46 (`Dataset missing?`_)
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
47
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
48 .. _tabular: ./static/formatHelp.html#tab
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
49 .. _Dataset missing?: ./static/formatHelp.html
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
50
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
51 -----
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
52
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
53 **What it does**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
54
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
55 Adds the fields "KEGG gene ID" and "KEGG pathways" to an input table of ENSEMBL
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
56 transcript IDs. A "U" in the KEGG gene ID field indicates that the
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
57 tool cannot link the ENSEMBL transcript ID to a KEGG gene ID.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
58 An "N" in the pathway field means the KEGG pathway is unknown.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
59
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
60 -----
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
61
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
62 **Example**
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
63
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
64 - input::
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
65
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
66 ENSCAFT00000000001
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
67 ENSCAFT00000000144
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
68 ENSCAFT00000000160
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
69 ENSCAFT00000000215
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
70 etc.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
71
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
72 - output::
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
73
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
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
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
75 ENSCAFT00000000144 483960 N
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
76 ENSCAFT00000000160 610160 N
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
77 ENSCAFT00000000215 U N
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
78 etc.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
79
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
80 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
81 </tool>