Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/MapToExon_RefSeqMat.xml @ 1:78770028dcf1 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:59:33 -0400
parents cdd489d98766
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
78770028dcf1 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
matces
parents: 0
diff changeset
1 <tool id="Annotation_RefSeq" name="GIN" version="1.3.0">
0
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
2 <description>Gene Intervals Notator</description>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
3 <command interpreter="perl">MapToExon_RefSeqMat_new.pl $input1 $input2 $promoter $3prime $priority $output</command>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
4 <inputs>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
5 <param format="tabular" name="input1" type="data" label="GFF file"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
6 <param format="tabular" name="input2" type="data" label="Annotation table"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
7 <param name="promoter" type="integer" size="10" value="-2000" label="Promoter definition (bp)"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
8 <param name="3prime" type="integer" size="10" value="2000" label="3prime extension (bp)"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
9 <param name="priority" type="select" label="Annotation priority">
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
10 <option value="prom">promoter</option>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
11 <option value="gene">gene</option>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
12 </param>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
13
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
14 </inputs>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
15 <outputs>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
16 <data format="tabular" name="output"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
17 </outputs>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
18
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
19 <help>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
20 .. class:: infomark
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
21
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
22 **What it does**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
23
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
24 GIN annotates peak queries (GFF files) with user defined transcript-annotation-tables (e.g. RefSeq, UCSC genes, Ensembl Genes etc).
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
25 It calculates the relative position of the peack with respect to the associated features (e.g. promoter, exon, intron, intergenic)
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
26
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
27 PLEASE, for more detailed information refer to the CARPET user Manual:
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
28 click to download_ it.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
29
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
30 .. _download: /static/example_file/CARPET_userManual.zip
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
31
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
32 --------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
33
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
34 .. class:: warningmark
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
35
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
36 **Annotation Table**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
37
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
38 Annotation table is directly downloadable from **"Get Data"** section (**"UCSC Main table browser"** link).
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
39 Pay attention to choose the right output format (**"all field from selected table"**) and check **"send output to Galaxy"**.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
40
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
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...
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
42
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
43 **All annotation tables must have headers.**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
44
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
45 Click here_ to download an Annotation Table file example.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
46
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
47 .. _here: /static/example_file/UCSC_hs_refGene_chr19.zip
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
48
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
49 --------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
50
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
51 .. class:: warningmark
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
52
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
53 **Custom annotation table**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
54
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
55 .. class:: infomark
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
56
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
57
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
58 **About format**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
59
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
60 Annotation table format must be the same downlodable from UCSC. In the specific case of this tool the following fields must be present:
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
61
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
62 1. **chrom** - The name of the chromosome (e.g. chr1, chrY_random).
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
63 2. **chromStart** - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
64 3. **chromEnd** - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
65 4. **name** - The name of the BED line.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
66 5. **strand** - Defines the strand - either + or - .
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
67 6. **blockCount** - The number of blocks (exons) in the BED line.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
68 7. **blockSizes** - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
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.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
70
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
71
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
72 The table **must** have headers
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
73
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
74
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
75 --------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
76
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
77 **Options**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
78
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
79 - **Promoter definition:** extent of TSS (Trascription Starting Site) upstream sequence in base pairs.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
80 - **Annotaion priority:**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
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
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
82 - if **gene**: GIN tries to locate a peak in an exon as first choice.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
83
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
84 --------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
85
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
86 **How does it work?**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
87
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
88 **- Floowchart**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
89
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
90 .. image:: static/images/CARPET/floowchart.png
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
91
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
92
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
93 **- Output**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
94
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
95 .. image:: static/images/CARPET/output_ann.png
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
96
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
97
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
98 </help>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
99 </tool>