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comparison bed_to_protein_map.xml @ 0:024ed7b0ad93 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62-dirty
author galaxyp
date Thu, 04 Jan 2018 16:29:38 -0500
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1 <tool id="bed_to_protein_map" name="bed to protein map" version="0.1.0">
2 <description>genomic location of proteins for MVP</description>
3 <requirements>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8 <command><![CDATA[
9 python '$__tool_directory__/bed_to_protein_map.py' '$input' '$output'
10 ]]></command>
11 <inputs>
12 <param name="input" type="data" format="bed" label="A BED file with 12 columns, thickStart and thickEnd define protein coding region"/>
13 </inputs>
14 <outputs>
15 <data name="output" format="tabular">
16 <actions>
17 <action name="column_names" type="metadata" default="name,chrom,start,end,strand,cds_start,cds_end"/>
18 </actions>
19 </data>
20 </outputs>
21 <tests>
22 <test>
23 <param name="input" ftype="bed" value="input.bed"/>
24 <output name="output" file="output.tabular"/>
25 </test>
26 </tests>
27 <help><![CDATA[
28 Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP).
29
30 Example input BED dataset::
31
32 X 276352 291629 ENST00000430923 20 + 284187 291629 80,80,80 5 42,148,137,129,131 0,7814,12380,14295,15146
33 X 304749 318819 ENST00000326153 20 - 305073 318787 80,80,80 10 448,153,149,209,159,68,131,71,138,381 0,2610,2982,6669,8016,9400,10140,10479,12164,13689
34
35
36 Output::
37
38 name chrom start end strand cds_start cds_end
39 ENST00000430923 X 284187 284314 + 0 127
40 ENST00000430923 X 288732 288869 + 127 264
41 ENST00000430923 X 290647 290776 + 264 393
42 ENST00000430923 X 291498 291629 + 393 524
43 ENST00000326153 X 318438 318787 - 0 349
44 ENST00000326153 X 316913 317051 - 349 487
45 ENST00000326153 X 315228 315299 - 487 558
46 ENST00000326153 X 314889 315020 - 558 689
47 ENST00000326153 X 314149 314217 - 689 757
48 ENST00000326153 X 312765 312924 - 757 916
49 ENST00000326153 X 311418 311627 - 916 1125
50 ENST00000326153 X 307731 307880 - 1125 1274
51 ENST00000326153 X 307359 307512 - 1274 1427
52 ENST00000326153 X 305073 305197 - 1427 1551
53
54
55 The tabular output can be converted to a sqlite database using the Query_Tabular_ tool.
56
57 The sqlite table should be named: feature_cds_map
58 The names for the columns should be: name,chrom,start,end,strand,cds_start,cds_end
59
60 This SQL query will return the genomic location for a peptide sequence in a protein (multiply the animo acid position by 3 for the cds location)::
61
62 SELECT distinct chrom, CASE WHEN strand = '+' THEN start + cds_offset - cds_start ELSE end - cds_offset - cds_start END as "pos"
63 FROM feature_cds_map
64 WHERE name = acc_name AND cds_offset >= cds_start AND cds_offset < cds_end
65
66
67 .. _Query_Tabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/1ea4e668bf73
68
69 ]]></help>
70 </tool>