Mercurial > repos > galaxyp > map_peptides_to_bed
comparison 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 |
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0:51f8f9041724 | 1:db90662d26f9 |
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1 <tool id="map_peptides_to_bed" name="Map peptides to a bed file" version="0.1.0"> | 1 <tool id="map_peptides_to_bed" name="Map peptides to a bed file" version="0.1.0"> |
2 <description>for viewing in a genome browser</description> | |
2 <requirements> | 3 <requirements> |
3 <requirement type="package" version="1.62">biopython</requirement> | 4 <requirement type="package" version="1.62">biopython</requirement> |
4 </requirements> | 5 </requirements> |
5 <stdio> | 6 <stdio> |
6 <exit_code range="1:" /> | 7 <exit_code range="1:" /> |
20 #end if | 21 #end if |
21 $gffTags | 22 $gffTags |
22 --bed="$mapped_peptides" | 23 --bed="$mapped_peptides" |
23 ]]></command> | 24 ]]></command> |
24 <inputs> | 25 <inputs> |
25 <param name="translated_bed" type="data" format="bed" label="Translated bed with IDs to match in the input" help=""/> | 26 <param name="translated_bed" type="data" format="bed" label="Translated BED" |
26 <param name="input" type="data" format="tabular" label="Identified Peptides" help=""/> | 27 help="mapping Protein IDs from a Protein Search fasta to a reference genome"/> |
27 <param name="peptide_column" type="data_column" data_ref="input" label="peptide column" optional="true" | 28 <param name="input" type="data" format="tabular" label="Identified Peptides" |
28 help="Defaults to first column"/> | 29 help="Such as a PSM (Peptide Spectral Match) report from a Proteomics Search Application"/> |
29 <param name="name_column" type="data_column" data_ref="input" label="protein name column" optional="true" | 30 <param name="peptide_column" type="data_column" data_ref="input" label="PSM peptide column" optional="true" |
30 help="The name in this column must match the name column in the Translate bed"/> | 31 help="Contains the peptide amino acid sequence. Defaults to first column"/> |
31 <param name="start_column" type="data_column" data_ref="input" label="peptide offset column" optional="true" | 32 <param name="name_column" type="data_column" data_ref="input" label="PSM protein name column" optional="true" |
32 help="The offset in AnimoAcids of the peptide from the start of the protein sequence"/> | 33 help="The name in this column must match the name column in the Translate BED input. Defaults to second column." /> |
33 <param name="gffTags" type="boolean" truevalue="--gffTags" falsevalue="" checked="true" label="Use #gffTags in output" help=""/> | 34 <param name="start_column" type="data_column" data_ref="input" label="PSM peptide offset column (optional)" optional="true"> |
35 <help>The offset in AnimoAcids of the peptide from the start of the protein sequence. | |
36 If this column is not available, the application will expect the Translated BED file | |
37 to have a 13th column with the protein sequence from which to determine the offset | |
38 </help> | |
39 </param> | |
40 <param name="gffTags" type="boolean" truevalue="--gffTags" falsevalue="" checked="true" label="Use #gffTags in output" | |
41 help="and use the peptide as the display name for the entry"/> | |
34 </inputs> | 42 </inputs> |
35 <outputs> | 43 <outputs> |
36 <data name="mapped_peptides" format="bed" /> | 44 <data name="mapped_peptides" format="bed" /> |
37 </outputs> | 45 </outputs> |
38 <tests> | 46 <tests> |
43 <param name="name_column" value="1"/> | 51 <param name="name_column" value="1"/> |
44 <output name="mapped_peptides" file="mapped_peptides.bed"/> | 52 <output name="mapped_peptides" file="mapped_peptides.bed"/> |
45 </test> | 53 </test> |
46 </tests> | 54 </tests> |
47 <help><![CDATA[ | 55 <help><![CDATA[ |
48 Usage: map_peptides_to_bed.py [options] | 56 **Map peptides to a bed file** |
57 | |
58 This tool is intended to map peptides identified by Mass Spectrometry relative to the protein sequence in the Proteomics Search database. | |
59 | |
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. | |
61 | |
62 | |
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. | |
64 | |
65 The other input is a BED file decribing the location of protein sequences relative to a reference genome. | |
66 This file can be produced by the Translate BED Sequences tool when generating the fasta file of translations. | |
67 | |
68 The output is a BED file with lines from the input BED file that had peptide matches. | |
69 The ID, thichStart, and thickEnd fields are changed to reflect the peptide match to that protein entry. | |
70 | |
71 | |
72 Inputs: | |
73 | |
74 - A BED file for the Proteins contained in a Proteomics Search Database. | |
75 (Should have a 13th column with the protein sequence.) | |
76 | |
77 - A tabular file (Pepetide Spectral Matach report) that includes columns that contain the protein identifer and the peptide sequence. | |
78 | |
79 | |
80 Output: | |
81 | |
82 - A BED file with an entry from the input BED file for each mapped input peptide, | |
83 with the ID, thichStart, and thickEnd fields are changed to reflect the peptide. | |
84 | |
85 | |
86 Example: | |
87 | |
88 Input BED file :: | |
89 | |
90 track name="novel_junction_peptides" type=bedDetail description="test" | |
91 5 90931315 90932985 JUNC00034987_3 1 + 90931315 90932985 255,0,0 2 118,74 0,1596 AWRRGPAASRCSGAVWAEGLCEPRASPSARGAASGAAAGGPAERRDSIFQRLPLSASPFSHLFK | |
92 X 157593859 157598461 JUNC00080388_3 11 - 157593859 157598461 255,0,0 2 14,151 0,4451 SPGLVRMVLCRPRPFLFPFGVSAPGREPLRAPAASACALPRGASVRPSKEIICVF | |
93 | |
94 | |
95 Input PSM (Peptide Spectral Match) file :: | |
96 | |
97 25895 JUNC00034987_3 ASPSARGAASGAAAGGPAER | |
98 15253 JUNC00080388_3 APAASACALPR | |
99 | |
100 | |
101 Output BED file:: | |
102 | |
103 track name="novel_junction_peptides" type=bedDetail description="test" | |
104 #gffTags | |
105 5 90931315 90932985 ID=JUNC00034987_3;Name=ASPSARGAASGAAAGGPAER 1 + 90931387 90932925 255,0,0 2 118,74 0,1596 ASPSARGAASGAAAGGPAER AWRRGPAASRCSGAVWAEGLCEPRASPSARGAASGAAAGGPAERRDSIFQRLPLSASPFSHLFK | |
106 X 157593859 157598461 ID=JUNC00080388_3;Name=APAASACALPR 11 - 157598338 157598371 255,0,0 2 14,151 0,4451 APAASACALPR SPGLVRMVLCRPRPFLFPFGVSAPGREPLRAPAASACALPRGASVRPSKEIICVF | |
107 | |
108 | |
109 Usage: map_peptides_to_bed.py [options] | |
49 | 110 |
50 Options: | 111 Options: |
51 -h, --help show this help message and exit | 112 -h, --help show this help message and exit |
52 -t TRANSLATED_BED, --translated_bed=TRANSLATED_BED | 113 -t TRANSLATED_BED, --translated_bed=TRANSLATED_BED |
53 A bed file with added 13th column having a translation | 114 A bed file with added 13th column having a translation |