Mercurial > repos > matces > carpet_toolsuite
annotate 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 |
---|---|
date | Tue, 07 Jun 2011 16:50:41 -0400 |
parents | |
children | 78770028dcf1 |
rev | line source |
---|---|
0
cdd489d98766
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff
changeset
|
1 <tool id="Annotation_RefSeq" name="GIN" version="1.2.0"> |
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> |