Mercurial > repos > galaxyp > map_peptides_to_bed
comparison map_peptides_to_bed.xml @ 0:51f8f9041724 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
author | galaxyp |
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date | Mon, 25 Jan 2016 15:32:49 -0500 |
parents | |
children | db90662d26f9 |
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-1:000000000000 | 0:51f8f9041724 |
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1 <tool id="map_peptides_to_bed" name="Map peptides to a bed file" version="0.1.0"> | |
2 <requirements> | |
3 <requirement type="package" version="1.62">biopython</requirement> | |
4 </requirements> | |
5 <stdio> | |
6 <exit_code range="1:" /> | |
7 </stdio> | |
8 <command interpreter="python"><![CDATA[ | |
9 map_peptides_to_bed.py | |
10 --translated_bed="$translated_bed" | |
11 --input="$input" | |
12 #if $peptide_column: | |
13 --peptide_column=$peptide_column | |
14 #end if | |
15 #if $name_column: | |
16 --name_column=$name_column | |
17 #end if | |
18 #if $start_column: | |
19 --start_column=$start_column | |
20 #end if | |
21 $gffTags | |
22 --bed="$mapped_peptides" | |
23 ]]></command> | |
24 <inputs> | |
25 <param name="translated_bed" type="data" format="bed" label="Translated bed with IDs to match in the input" help=""/> | |
26 <param name="input" type="data" format="tabular" label="Identified Peptides" help=""/> | |
27 <param name="peptide_column" type="data_column" data_ref="input" label="peptide column" optional="true" | |
28 help="Defaults to first column"/> | |
29 <param name="name_column" type="data_column" data_ref="input" label="protein name column" optional="true" | |
30 help="The name in this column must match the name column in the Translate bed"/> | |
31 <param name="start_column" type="data_column" data_ref="input" label="peptide offset column" optional="true" | |
32 help="The offset in AnimoAcids of the peptide from the start of the protein sequence"/> | |
33 <param name="gffTags" type="boolean" truevalue="--gffTags" falsevalue="" checked="true" label="Use #gffTags in output" help=""/> | |
34 </inputs> | |
35 <outputs> | |
36 <data name="mapped_peptides" format="bed" /> | |
37 </outputs> | |
38 <tests> | |
39 <test> | |
40 <param name="translated_bed" type="data" ftype="bed" value="translated_bed_sequences.bed"/> | |
41 <param name="input" type="data" ftype="tabular" value="peptides.tsv"/> | |
42 <param name="peptide_column" value="2"/> | |
43 <param name="name_column" value="1"/> | |
44 <output name="mapped_peptides" file="mapped_peptides.bed"/> | |
45 </test> | |
46 </tests> | |
47 <help><![CDATA[ | |
48 Usage: map_peptides_to_bed.py [options] | |
49 | |
50 Options: | |
51 -h, --help show this help message and exit | |
52 -t TRANSLATED_BED, --translated_bed=TRANSLATED_BED | |
53 A bed file with added 13th column having a translation | |
54 -i INPUT, --input=INPUT | |
55 Tabular file with peptide_sequence column | |
56 -p PEPTIDE_COLUMN, --peptide_column=PEPTIDE_COLUMN | |
57 column ordinal with peptide sequence | |
58 -n NAME_COLUMN, --name_column=NAME_COLUMN | |
59 column ordinal with protein name | |
60 -s START_COLUMN, --start_column=START_COLUMN | |
61 column with peptide start position in protein | |
62 -B BED, --bed=BED Output a bed file with added 13th column having | |
63 translation | |
64 -T, --gffTags Add #gffTags to bed output for IGV | |
65 -d, --debug Turn on wrapper debugging to stderr | |
66 | |
67 ]]></help> | |
68 </tool> |