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comparison carpet-src-1/tools/CARPET/annotation_expr.xml @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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1 <tool id="Annotation_Expr" name="ENO" version="1.0.0">
2 <description>Expression NOtator</description>
3 <command interpreter="perl">annotation_expr_intron.pl $input1 $input2 $output</command>
4 <inputs>
5 <param format="tabular" name="input1" type="data" label="Expression file"/>
6 <param format="tabular" name="input2" type="data" label="Annotation table"/>
7 </inputs>
8 <outputs>
9 <data format="tabular" name="output"/>
10 </outputs>
11 <help>
12 .. class:: infomark
13
14 **What it does**
15
16 ENO assigns each exon of a transcript the relative matching probes of the array. If a probe matches with more than one transcript, it is associated to every transcript.
17
18 PLEASE, for more detailed information refer to the CARPET user Manual:
19 click to download_ it.
20
21 .. _download: /static/example_file/CARPET_userManual.zip
22
23 --------
24
25 .. class:: warningmark
26
27 **Annotation Table**
28
29 Annotation table was directly downloadable from **"Get Data"** section (**"UCSC Main table browser"** link).
30 Pay attention to choose the right output format (**"all field from selected table"**) and check **"send output to Galaxy"**.
31
32 It is possible to download many different annotation tables coming from different organisms and database such as RefSeq, UCSC gene, FlyBase, EST, etc etc...
33
34 **All annotation tables must have headers.**
35
36
37 --------
38
39 .. class:: warningmark
40
41 **Custom annotation table**
42
43 .. class:: infomark
44
45
46 **About format**
47
48 Annotation table format must be the same downlodable from UCSC. In the specific case of this tool the following fields must be present:
49
50 1. **chrom** - The name of the chromosome (e.g. chr1, chrY_random).
51 2. **chromStart** - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
52 3. **chromEnd** - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
53 4. **name** - The name of the BED line.
54 5. **strand** - Defines the strand - either + or - .
55 6. **blockCount** - The number of blocks (exons) in the BED line.
56 7. **blockSizes** - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
57 8. **blockStarts** - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
58
59
60 The table **must** have headers
61
62
63 ---------
64
65 .. class:: infomark
66
67 **How does it work?**
68
69 .. image:: static/images/CARPET/Eno.png
70
71
72
73 </help>
74 </tool>