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author jjohnson
date Wed, 05 Feb 2014 09:27:54 -0500
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1 <?xml version="1.0"?>
2 <tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.0.1">
3 <description>3 frame translation of BED augmented with a sequence column</description>
4 <requirements>
5 <requirement type="package" version="1.62">biopython</requirement>
6 <requirement type="python-module">Bio</requirement>
7 </requirements>
8 <command interpreter="python">translate_bed_sequences.py --input "$input"
9 #if $reference:
10 --reference $reference
11 #else:
12 --reference ${input.metadata.dbkey}
13 #end if
14 #if $seqtype:
15 --seqtype $seqtype
16 #end if
17 #if $score_name:
18 --score_name $score_name
19 #end if
20 #if $filter.filterseqs == 'yes':
21 #if $filter.leading_bp:
22 --leading_bp $filter.leading_bp
23 #end if
24 #if $filter.trailing_bp:
25 --trailing_bp $filter.trailing_bp
26 #end if
27 #else:
28 --unfiltered
29 #end if
30 #if $trim.trimseqs == 'no':
31 --untrimmed
32 #if $trim.max_stop_codons.__str__ != '':
33 --max_stop_codons $trim.max_stop_codons
34 #end if
35 #end if
36 #if $min_length:
37 --min_length $min_length
38 #end if
39 --output "$output"
40 </command>
41 <inputs>
42 <param name="input" type="data" format="bed" label="BED file with added sequence column"
43 help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/>
44 <param name="reference" type="text" value="" optional="true" label="Genome reference name"
45 help="By default, the database metadata will be used."/>
46 <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
47 help="For example: pep:splice"/>
48 <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
49 help="For example: with the tag name 'depth' and bed score 12: depth:12"/>
50 <conditional name="filter">
51 <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">
52 <option value="yes" selected="true">Yes</option>
53 <option value="no">No</option>
54 </param>
55 <when value="yes">
56 <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs"
57 help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/>
58 <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs"
59 help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/>
60 </when>
61 <when value="no"/>
62 </conditional>
63 <conditional name="trim">
64 <param name="trimseqs" type="select" label="Trim translations to stop codons">
65 <option value="yes" selected="true">Yes</option>
66 <option value="no">No</option>
67 </param>
68 <when value="no">
69 <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"/>
70 </when>
71 </conditional>
72 <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/>
73 </inputs>
74 <stdio>
75 <exit_code range="1:" level="fatal" description="Error" />
76 </stdio>
77 <outputs>
78 <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string}">
79 <filter>'found' in str(outputs)</filter>
80 </data>
81 </outputs>
82 <tests>
83 <test>
84 <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>
85 <param name="reference" value="GRCh37"/>
86 <param name="seqtype" value="pep:novel"/>
87 <param name="score_name" value="depth"/>
88 <output name="output" file="translated_bed_sequences.fa"/>
89 </test>
90 </tests>
91 <help>
92 **Translate BED Sequences**
93
94 This tool takes a BED input file that has been processed
95 by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.
96
97 It generates a peptide fasta file with the 3-frame translations of the spliced sequence
98 defined by each entry in the input BED file.
99
100
101 </help>
102 </tool>