|
2
|
1 <tool id="peptidegenomiccoordinate" name="Peptide Genomic Coordinate" version="0.1.2">
|
|
1
|
2 <description>Get genomic location/coordinate of peptides using mzsqlite DB and genomic mapping sqlite DB</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="2.7.9">python</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command detect_errors="aggressive"><![CDATA[
|
|
|
7 python '$__tool_directory__/peptideGenomicCoordinate.py' '$peptideinput' '$mzsqlite' '$mapping' '$peptide_bed'
|
|
|
8 ]]></command>
|
|
3
|
9
|
|
1
|
10 <inputs>
|
|
|
11 <param type="data" name="peptideinput" format="tabular" label="Peptide List (without any header line)"/>
|
|
|
12 <param type="data" name="mzsqlite" format="sqlite" label="mz to sqlite (mzsqlite) file"/>
|
|
|
13 <param type="data" name="mapping" format="sqlite" label="genomic mapping sqlite file"/>
|
|
|
14 </inputs>
|
|
3
|
15
|
|
1
|
16 <outputs>
|
|
|
17 <data format="bed" name="peptide_bed" label="${tool.name} on ${on_string}">
|
|
|
18 <actions>
|
|
|
19 <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
|
|
|
20 </actions>
|
|
|
21 </data>
|
|
|
22 </outputs>
|
|
3
|
23
|
|
1
|
24 <tests>
|
|
|
25 <test>
|
|
|
26 <param name="peptide_input" value="peptides.tabular"/>
|
|
|
27 <param name="sqlite" value="test_mz_to_sqlite.sqlite"/>
|
|
|
28 <param name="sqlite" value="test_genomic_mapping_sqlite.sqlite"/>
|
|
|
29 <output name="peptide_bed" file="peptides_BED.bed"/>
|
|
|
30 </test>
|
|
|
31 </tests>
|
|
|
32 <help><![CDATA[
|
|
|
33 **PeptideGenomicCoordinate**
|
|
|
34
|
|
|
35 Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files.
|
|
|
36 This program loads two sqlite databases (mzsqlite and genomic mapping sqlite files) and calculates the genomic coordinates of the peptides provided as input. This outputs bed file for peptides.
|
|
|
37
|
|
|
38 Input: Peptide list file, mzsqlite sqlite DB file, and genomic mapping sqlite DB file
|
|
|
39 Output: Tabular BED file with all the columns
|
|
|
40
|
|
|
41 mzsqlite file from: https://toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.0
|
|
|
42 genome mapping sqlite file from: https://toolshed.g2.bx.psu.edu/view/galaxyp/translate_bed/038ecf54cbec
|
|
|
43
|
|
|
44
|
|
|
45 P.S. : Requires sqlite
|
|
|
46
|
|
|
47 ]]></help>
|
|
|
48 <citations>
|
|
|
49 <citation type="bibtex">
|
|
|
50 @misc{peptidegenomiccoodinate,
|
|
|
51 author={Kumar, Praveen},
|
|
|
52 year={2018},
|
|
|
53 title={PeptideGenomicCoordinate}
|
|
|
54 }
|
|
|
55 </citation>
|
|
|
56 </citations>
|
|
|
57 </tool>
|
