Mercurial > repos > galaxyp > map_peptides_to_bed
annotate map_peptides_to_bed.xml @ 1:db90662d26f9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
author | galaxyp |
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date | Mon, 22 Feb 2016 17:30:45 -0500 |
parents | 51f8f9041724 |
children | 78b8213e122d |
rev | line source |
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51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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1 <tool id="map_peptides_to_bed" name="Map peptides to a bed file" version="0.1.0"> |
1
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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2 <description>for viewing in a genome browser</description> |
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51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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3 <requirements> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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4 <requirement type="package" version="1.62">biopython</requirement> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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5 </requirements> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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6 <stdio> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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7 <exit_code range="1:" /> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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8 </stdio> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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9 <command interpreter="python"><![CDATA[ |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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10 map_peptides_to_bed.py |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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11 --translated_bed="$translated_bed" |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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12 --input="$input" |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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13 #if $peptide_column: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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14 --peptide_column=$peptide_column |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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15 #end if |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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16 #if $name_column: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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17 --name_column=$name_column |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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18 #end if |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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19 #if $start_column: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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20 --start_column=$start_column |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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21 #end if |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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22 $gffTags |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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23 --bed="$mapped_peptides" |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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24 ]]></command> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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25 <inputs> |
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db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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26 <param name="translated_bed" type="data" format="bed" label="Translated BED" |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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27 help="mapping Protein IDs from a Protein Search fasta to a reference genome"/> |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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28 <param name="input" type="data" format="tabular" label="Identified Peptides" |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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29 help="Such as a PSM (Peptide Spectral Match) report from a Proteomics Search Application"/> |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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30 <param name="peptide_column" type="data_column" data_ref="input" label="PSM peptide column" optional="true" |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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31 help="Contains the peptide amino acid sequence. Defaults to first column"/> |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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32 <param name="name_column" type="data_column" data_ref="input" label="PSM protein name column" optional="true" |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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33 help="The name in this column must match the name column in the Translate BED input. Defaults to second column." /> |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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34 <param name="start_column" type="data_column" data_ref="input" label="PSM peptide offset column (optional)" optional="true"> |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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35 <help>The offset in AnimoAcids of the peptide from the start of the protein sequence. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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36 If this column is not available, the application will expect the Translated BED file |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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37 to have a 13th column with the protein sequence from which to determine the offset |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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38 </help> |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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39 </param> |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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40 <param name="gffTags" type="boolean" truevalue="--gffTags" falsevalue="" checked="true" label="Use #gffTags in output" |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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41 help="and use the peptide as the display name for the entry"/> |
0
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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42 </inputs> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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43 <outputs> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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44 <data name="mapped_peptides" format="bed" /> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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45 </outputs> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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46 <tests> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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47 <test> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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48 <param name="translated_bed" type="data" ftype="bed" value="translated_bed_sequences.bed"/> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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49 <param name="input" type="data" ftype="tabular" value="peptides.tsv"/> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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50 <param name="peptide_column" value="2"/> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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51 <param name="name_column" value="1"/> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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52 <output name="mapped_peptides" file="mapped_peptides.bed"/> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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53 </test> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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54 </tests> |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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55 <help><![CDATA[ |
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db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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56 **Map peptides to a bed file** |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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57 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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58 This tool is intended to map peptides identified by Mass Spectrometry relative to the protein sequence in the Proteomics Search database. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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59 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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60 It generates a BED file that maps the location of peptides within proteins mapped to a reference genome so that they can be displayed in a genome browser. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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61 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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62 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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63 The input is a tabular file that has columns containing: peptide, protein ID, and optionally the offset of the peptide from the start of the protein sequence. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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64 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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65 The other input is a BED file decribing the location of protein sequences relative to a reference genome. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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66 This file can be produced by the Translate BED Sequences tool when generating the fasta file of translations. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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67 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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68 The output is a BED file with lines from the input BED file that had peptide matches. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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69 The ID, thichStart, and thickEnd fields are changed to reflect the peptide match to that protein entry. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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70 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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71 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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72 Inputs: |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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73 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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74 - A BED file for the Proteins contained in a Proteomics Search Database. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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75 (Should have a 13th column with the protein sequence.) |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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76 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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77 - A tabular file (Pepetide Spectral Matach report) that includes columns that contain the protein identifer and the peptide sequence. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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78 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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79 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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80 Output: |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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81 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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82 - A BED file with an entry from the input BED file for each mapped input peptide, |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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83 with the ID, thichStart, and thickEnd fields are changed to reflect the peptide. |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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84 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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85 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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86 Example: |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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87 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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88 Input BED file :: |
db90662d26f9
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89 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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90 track name="novel_junction_peptides" type=bedDetail description="test" |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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91 5 90931315 90932985 JUNC00034987_3 1 + 90931315 90932985 255,0,0 2 118,74 0,1596 AWRRGPAASRCSGAVWAEGLCEPRASPSARGAASGAAAGGPAERRDSIFQRLPLSASPFSHLFK |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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92 X 157593859 157598461 JUNC00080388_3 11 - 157593859 157598461 255,0,0 2 14,151 0,4451 SPGLVRMVLCRPRPFLFPFGVSAPGREPLRAPAASACALPRGASVRPSKEIICVF |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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93 |
db90662d26f9
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94 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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95 Input PSM (Peptide Spectral Match) file :: |
db90662d26f9
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96 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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97 25895 JUNC00034987_3 ASPSARGAASGAAAGGPAER |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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98 15253 JUNC00080388_3 APAASACALPR |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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99 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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100 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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101 Output BED file:: |
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102 |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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103 track name="novel_junction_peptides" type=bedDetail description="test" |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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104 #gffTags |
db90662d26f9
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105 5 90931315 90932985 ID=JUNC00034987_3;Name=ASPSARGAASGAAAGGPAER 1 + 90931387 90932925 255,0,0 2 118,74 0,1596 ASPSARGAASGAAAGGPAER AWRRGPAASRCSGAVWAEGLCEPRASPSARGAASGAAAGGPAERRDSIFQRLPLSASPFSHLFK |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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106 X 157593859 157598461 ID=JUNC00080388_3;Name=APAASACALPR 11 - 157598338 157598371 255,0,0 2 14,151 0,4451 APAASACALPR SPGLVRMVLCRPRPFLFPFGVSAPGREPLRAPAASACALPRGASVRPSKEIICVF |
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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107 |
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108 |
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109 Usage: map_peptides_to_bed.py [options] |
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110 |
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111 Options: |
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112 -h, --help show this help message and exit |
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113 -t TRANSLATED_BED, --translated_bed=TRANSLATED_BED |
51f8f9041724
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114 A bed file with added 13th column having a translation |
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115 -i INPUT, --input=INPUT |
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116 Tabular file with peptide_sequence column |
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117 -p PEPTIDE_COLUMN, --peptide_column=PEPTIDE_COLUMN |
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118 column ordinal with peptide sequence |
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119 -n NAME_COLUMN, --name_column=NAME_COLUMN |
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120 column ordinal with protein name |
51f8f9041724
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121 -s START_COLUMN, --start_column=START_COLUMN |
51f8f9041724
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122 column with peptide start position in protein |
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123 -B BED, --bed=BED Output a bed file with added 13th column having |
51f8f9041724
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124 translation |
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125 -T, --gffTags Add #gffTags to bed output for IGV |
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126 -d, --debug Turn on wrapper debugging to stderr |
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127 |
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128 ]]></help> |
51f8f9041724
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129 </tool> |