Mercurial > repos > galaxyp > bed_to_protein_map

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
author galaxyp
date Tue, 07 Apr 2020 11:33:11 -0400
parents 024ed7b0ad93
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a7c58b43cbaa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
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1 <tool id="bed_to_protein_map" name="bed to protein map" version="0.2.0">
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2 <description>genomic location of proteins for MVP</description>
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3 <requirements>
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a7c58b43cbaa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
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4 <requirement type="package" version="3.7">python</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 python '$__tool_directory__/bed_to_protein_map.py' '$input' '$output'
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11 ]]></command>
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12 <inputs>
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13 <param name="input" type="data" format="bed" label="A BED file with 12 columns, thickStart and thickEnd define protein coding region"/>
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14 </inputs>
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15 <outputs>
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16 <data name="output" format="tabular">
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17 <actions>
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18 <action name="column_names" type="metadata" default="name,chrom,start,end,strand,cds_start,cds_end"/>
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19 </actions>
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20 </data>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" ftype="bed" value="input.bed"/>
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25 <output name="output" file="output.tabular"/>
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP).
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31 Example input BED dataset::
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33 X 276352 291629 ENST00000430923 20 + 284187 291629 80,80,80 5 42,148,137,129,131 0,7814,12380,14295,15146
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34 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
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37 Output::
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38
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39 name chrom start end strand cds_start cds_end
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40 ENST00000430923 X 284187 284314 + 0 127
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41 ENST00000430923 X 288732 288869 + 127 264
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42 ENST00000430923 X 290647 290776 + 264 393
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43 ENST00000430923 X 291498 291629 + 393 524
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44 ENST00000326153 X 318438 318787 - 0 349
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45 ENST00000326153 X 316913 317051 - 349 487
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46 ENST00000326153 X 315228 315299 - 487 558
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47 ENST00000326153 X 314889 315020 - 558 689
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48 ENST00000326153 X 314149 314217 - 689 757
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49 ENST00000326153 X 312765 312924 - 757 916
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50 ENST00000326153 X 311418 311627 - 916 1125
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51 ENST00000326153 X 307731 307880 - 1125 1274
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52 ENST00000326153 X 307359 307512 - 1274 1427
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53 ENST00000326153 X 305073 305197 - 1427 1551
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56 The tabular output can be converted to a sqlite database using the Query_Tabular_ tool.
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57
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58 The sqlite table should be named: feature_cds_map
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59 The names for the columns should be: name,chrom,start,end,strand,cds_start,cds_end
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61 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)::
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62
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63 SELECT distinct chrom, CASE WHEN strand = '+' THEN start + cds_offset - cds_start ELSE end - cds_offset - cds_start END as "pos"
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64 FROM feature_cds_map
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65 WHERE name = acc_name AND cds_offset >= cds_start AND cds_offset < cds_end
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68 .. _Query_Tabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/1ea4e668bf73
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70 ]]></help>
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71 </tool>