Mercurial > repos > galaxyp > translate_bed_sequences

annotate translate_bed_sequences.xml @ 0:d723eb657f1d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
author galaxyp
date Mon, 25 Jan 2016 12:21:21 -0500
parents
children 6bbce76c78c1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
1 <?xml version="1.0"?>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
2 <tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.0">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
3 <description>3 frame translation of BED augmented with a sequence column</description>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
4 <requirements>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
5 <requirement type="package" version="1.62">biopython</requirement>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
6 <requirement type="python-module">Bio</requirement>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
7 </requirements>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
8 <command interpreter="python">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
9 translate_bed_sequences.py --input "$input"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
10 #if $fa_db:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
11 --fa_db='$fa_db'
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
12 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
13 #if $fa_sep:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
14 --fa_sep='$fa_sep'
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
15 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
16 #if $id_prefix:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
17 --id_prefix='$id_prefix'
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
18 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
19 #if $reference:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
20 --reference $reference
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
21 #else:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
22 --reference ${input.metadata.dbkey}
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
23 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
24 #if $refsource:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
25 --refsource $refsource
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
26 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
27 #if $seqtype:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
28 --seqtype $seqtype
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
29 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
30 #if $score_name:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
31 --score_name $score_name
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
32 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
33 #if $filter.filterseqs == 'yes':
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
34 #if $filter.leading_bp:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
35 --leading_bp $filter.leading_bp
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
36 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
37 #if $filter.trailing_bp:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
38 --trailing_bp $filter.trailing_bp
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
39 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
40 #else:
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
41 --unfiltered
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
42 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
43 #if $trim.trimseqs == 'no':
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
44 --untrimmed
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
45 #if str($trim.max_stop_codons) != '':
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
46 --max_stop_codons $trim.max_stop_codons
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
47 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
48 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
49 #if str($min_length) != '':
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
50 --min_length $min_length
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
51 #end if
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
52 --bed $translated_bed
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
53 --output "$output"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
54 </command>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
55 <inputs>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
56 <param name="input" type="data" format="bed" label="BED file with added sequence column"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
57 help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
58 <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
59 help="Any Compomics application such as PeptideShaker, requires a source">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
60 </param>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
61 <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
62 help="Only used when a fasta ID source is given, defaults to the pipe character">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
63 </param>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
64 <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
65 help="Can be used to distinguish samples">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
66 <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
67 </param>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
68 <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
69 help=""/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
70 <param name="reference" type="text" value="" optional="true" label="Genome reference name"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
71 help="By default, the database metadata will be used."/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
72 <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
73 help="For example: pep:splice"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
74 <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
75 help="For example: with the tag name 'depth' and bed score 12: depth:12"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
76 <conditional name="filter">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
77 <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
78 <option value="yes" selected="true">Yes</option>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
79 <option value="no">No</option>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
80 </param>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
81 <when value="yes">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
82 <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
83 help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
84 <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs"
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
85 help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
86 </when>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
87 <when value="no"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
88 </conditional>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
89 <conditional name="trim">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
90 <param name="trimseqs" type="select" label="Trim translations to stop codons">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
91 <option value="yes" selected="true">Yes</option>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
92 <option value="no">No</option>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
93 </param>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
94 <when value="no">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
95 <param name="max_stop_codons" type="integer" value="" min="0" optional="true" label="Maximum number of stop codons allowed in a translation to be reported"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
96 </when>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
97 </conditional>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
98 <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
99 </inputs>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
100 <stdio>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
101 <exit_code range="1:" level="fatal" description="Error" />
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
102 </stdio>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
103 <outputs>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
104 <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
105 </data>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
106 <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta">
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
107 </data>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
108 </outputs>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
109 <tests>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
110 <test>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
111 <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
112 <param name="reference" value="GRCh37"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
113 <param name="seqtype" value="pep:novel"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
114 <param name="score_name" value="depth"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
115 <output name="output" file="translated_bed_sequences.fa"/>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
116 </test>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
117 </tests>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
118 <help>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
119 **Translate BED Sequences**
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
120
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
121 This tool takes a BED input file that has been processed
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
122 by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
123
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
124 It generates a peptide fasta file with the 3-frame translations of the spliced sequence
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
125 defined by each entry in the input BED file.
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
126
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
127 </help>
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
128 </tool>