Mercurial > repos > matces > carpet_toolsuite
comparison carpet-src-1/tools/CARPET/MapToExon_RefSeqMat.xml @ 0:cdd489d98766
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | matces |
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date | Tue, 07 Jun 2011 16:50:41 -0400 |
parents | |
children | 78770028dcf1 |
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1 <tool id="Annotation_RefSeq" name="GIN" version="1.2.0"> | |
2 <description>Gene Intervals Notator</description> | |
3 <command interpreter="perl">MapToExon_RefSeqMat_new.pl $input1 $input2 $promoter $3prime $priority $output</command> | |
4 <inputs> | |
5 <param format="tabular" name="input1" type="data" label="GFF file"/> | |
6 <param format="tabular" name="input2" type="data" label="Annotation table"/> | |
7 <param name="promoter" type="integer" size="10" value="-2000" label="Promoter definition (bp)"/> | |
8 <param name="3prime" type="integer" size="10" value="2000" label="3prime extension (bp)"/> | |
9 <param name="priority" type="select" label="Annotation priority"> | |
10 <option value="prom">promoter</option> | |
11 <option value="gene">gene</option> | |
12 </param> | |
13 | |
14 </inputs> | |
15 <outputs> | |
16 <data format="tabular" name="output"/> | |
17 </outputs> | |
18 | |
19 <help> | |
20 .. class:: infomark | |
21 | |
22 **What it does** | |
23 | |
24 GIN annotates peak queries (GFF files) with user defined transcript-annotation-tables (e.g. RefSeq, UCSC genes, Ensembl Genes etc). | |
25 It calculates the relative position of the peack with respect to the associated features (e.g. promoter, exon, intron, intergenic) | |
26 | |
27 PLEASE, for more detailed information refer to the CARPET user Manual: | |
28 click to download_ it. | |
29 | |
30 .. _download: /static/example_file/CARPET_userManual.zip | |
31 | |
32 -------- | |
33 | |
34 .. class:: warningmark | |
35 | |
36 **Annotation Table** | |
37 | |
38 Annotation table is directly downloadable from **"Get Data"** section (**"UCSC Main table browser"** link). | |
39 Pay attention to choose the right output format (**"all field from selected table"**) and check **"send output to Galaxy"**. | |
40 | |
41 It is possible to download many different annotation tables coming from different organisms and database such as RefSeq, UCSC gene, FlyBase, EST, etc etc... | |
42 | |
43 **All annotation tables must have headers.** | |
44 | |
45 Click here_ to download an Annotation Table file example. | |
46 | |
47 .. _here: /static/example_file/UCSC_hs_refGene_chr19.zip | |
48 | |
49 -------- | |
50 | |
51 .. class:: warningmark | |
52 | |
53 **Custom annotation table** | |
54 | |
55 .. class:: infomark | |
56 | |
57 | |
58 **About format** | |
59 | |
60 Annotation table format must be the same downlodable from UCSC. In the specific case of this tool the following fields must be present: | |
61 | |
62 1. **chrom** - The name of the chromosome (e.g. chr1, chrY_random). | |
63 2. **chromStart** - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) | |
64 3. **chromEnd** - The ending position in the chromosome, plus 1 (i.e., a half-open interval). | |
65 4. **name** - The name of the BED line. | |
66 5. **strand** - Defines the strand - either + or - . | |
67 6. **blockCount** - The number of blocks (exons) in the BED line. | |
68 7. **blockSizes** - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. | |
69 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. | |
70 | |
71 | |
72 The table **must** have headers | |
73 | |
74 | |
75 -------- | |
76 | |
77 **Options** | |
78 | |
79 - **Promoter definition:** extent of TSS (Trascription Starting Site) upstream sequence in base pairs. | |
80 - **Annotaion priority:** | |
81 - if **promoter**: GIN tries to locate a peak in a promoter locus as first choice. If more than one promoter is found, the peak is associated to the closer transcriptional unit | |
82 - if **gene**: GIN tries to locate a peak in an exon as first choice. | |
83 | |
84 -------- | |
85 | |
86 **How does it work?** | |
87 | |
88 **- Floowchart** | |
89 | |
90 .. image:: static/images/CARPET/floowchart.png | |
91 | |
92 | |
93 **- Output** | |
94 | |
95 .. image:: static/images/CARPET/output_ann.png | |
96 | |
97 | |
98 </help> | |
99 </tool> |