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comparison translate_bed_sequences.xml @ 5:c626a939eef7 draft default tip

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author jjohnson
date Tue, 12 Jan 2016 14:38:03 -0500
parents 3b526a780849
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4:aa93f7910259 5:c626a939eef7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.0.1"> 2 <tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.0">
3 <description>3 frame translation of BED augmented with a sequence column</description> 3 <description>3 frame translation of BED augmented with a sequence column</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.62">biopython</requirement> 5 <requirement type="package" version="1.62">biopython</requirement>
6 <requirement type="python-module">Bio</requirement> 6 <requirement type="python-module">Bio</requirement>
7 </requirements> 7 </requirements>
8 <command interpreter="python">translate_bed_sequences.py --input "$input" 8 <command interpreter="python">
9 translate_bed_sequences.py --input "$input"
10 #if $fa_db:
11 --fa_db='$fa_db'
12 #end if
13 #if $fa_sep:
14 --fa_sep='$fa_sep'
15 #end if
16 #if $id_prefix:
17 --id_prefix='$id_prefix'
18 #end if
9 #if $reference: 19 #if $reference:
10 --reference $reference 20 --reference $reference
11 #else: 21 #else:
12 --reference ${input.metadata.dbkey} 22 --reference ${input.metadata.dbkey}
23 #end if
24 #if $refsource:
25 --refsource $refsource
13 #end if 26 #end if
14 #if $seqtype: 27 #if $seqtype:
15 --seqtype $seqtype 28 --seqtype $seqtype
16 #end if 29 #end if
17 #if $score_name: 30 #if $score_name:
27 #else: 40 #else:
28 --unfiltered 41 --unfiltered
29 #end if 42 #end if
30 #if $trim.trimseqs == 'no': 43 #if $trim.trimseqs == 'no':
31 --untrimmed 44 --untrimmed
32 #if $trim.max_stop_codons.__str__ != '': 45 #if str($trim.max_stop_codons) != '':
33 --max_stop_codons $trim.max_stop_codons 46 --max_stop_codons $trim.max_stop_codons
34 #end if 47 #end if
35 #end if 48 #end if
36 #if $min_length: 49 #if str($min_length) != '':
37 --min_length $min_length 50 --min_length $min_length
38 #end if 51 #end if
52 --bed $translated_bed
39 --output "$output" 53 --output "$output"
40 </command> 54 </command>
41 <inputs> 55 <inputs>
42 <param name="input" type="data" format="bed" label="BED file with added sequence column" 56 <param name="input" type="data" format="bed" label="BED file with added sequence column"
43 help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> 57 help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/>
58 <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic"
59 help="Any Compomics application such as PeptideShaker, requires a source">
60 </param>
61 <param name="fa_sep" type="text" value="" optional="true" label="fasta ID source, e.g. generic"
62 help="Only used when a fasta ID source is given, default to the pipe character">
63 </param>
64 <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs"
65 help="Can be used to distinguish samples">
66 <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator>
67 </param>
68 <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source"
69 help=""/>
44 <param name="reference" type="text" value="" optional="true" label="Genome reference name" 70 <param name="reference" type="text" value="" optional="true" label="Genome reference name"
45 help="By default, the database metadata will be used."/> 71 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" 72 <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"/> 73 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" 74 <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
73 </inputs> 99 </inputs>
74 <stdio> 100 <stdio>
75 <exit_code range="1:" level="fatal" description="Error" /> 101 <exit_code range="1:" level="fatal" description="Error" />
76 </stdio> 102 </stdio>
77 <outputs> 103 <outputs>
78 <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string}"> 104 <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed">
79 <filter>'found' in str(outputs)</filter> 105 </data>
106 <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta">
80 </data> 107 </data>
81 </outputs> 108 </outputs>
82 <tests> 109 <tests>
83 <test> 110 <test>
84 <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/> 111 <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>
95 by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence. 122 by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.
96 123
97 It generates a peptide fasta file with the 3-frame translations of the spliced sequence 124 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. 125 defined by each entry in the input BED file.
99 126
100
101 </help> 127 </help>
102 </tool> 128 </tool>