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comparison translate_bed_sequences.xml @ 1:6bbce76c78c1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 7025b29e8113049e5f21389ce67858c18af6611b
author galaxyp
date Thu, 15 Dec 2016 18:41:21 -0500
parents d723eb657f1d
children 4221664a2bd0
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0:d723eb657f1d 1:6bbce76c78c1
1 <?xml version="1.0"?> 1 <tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.1">
2 <tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.0"> 2 <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> 3 <requirements>
4 <requirements> 4 <requirement type="package" version="1.62">biopython</requirement>
5 <requirement type="package" version="1.62">biopython</requirement> 5 </requirements>
6 <requirement type="python-module">Bio</requirement> 6 <stdio>
7 </requirements> 7 <exit_code range="1:" level="fatal" description="Error" />
8 <command interpreter="python"> 8 </stdio>
9 translate_bed_sequences.py --input "$input" 9 <command>
10 #if $fa_db: 10 python '$__tool_directory__/translate_bed_sequences.py'
11 --fa_db='$fa_db' 11 --input '$input'
12 #end if 12 #if $fa_db:
13 #if $fa_sep: 13 --fa_db='$fa_db'
14 --fa_sep='$fa_sep' 14 #end if
15 #end if 15 #if $fa_sep:
16 #if $id_prefix: 16 --fa_sep='$fa_sep'
17 --id_prefix='$id_prefix' 17 #end if
18 #end if 18 #if $id_prefix:
19 #if $reference: 19 --id_prefix='$id_prefix'
20 --reference $reference 20 #end if
21 #else: 21 #if $reference:
22 --reference ${input.metadata.dbkey} 22 --reference $reference
23 #end if 23 #else:
24 #if $refsource: 24 --reference ${input.metadata.dbkey}
25 --refsource $refsource 25 #end if
26 #end if 26 #if $refsource:
27 #if $seqtype: 27 --refsource $refsource
28 --seqtype $seqtype 28 #end if
29 #end if 29 #if $seqtype:
30 #if $score_name: 30 --seqtype $seqtype
31 --score_name $score_name 31 #end if
32 #end if 32 #if $score_name:
33 #if $filter.filterseqs == 'yes': 33 --score_name $score_name
34 #if $filter.leading_bp: 34 #end if
35 --leading_bp $filter.leading_bp 35 #if $filter.filterseqs == 'yes':
36 #end if 36 #if $filter.leading_bp:
37 #if $filter.trailing_bp: 37 --leading_bp $filter.leading_bp
38 --trailing_bp $filter.trailing_bp 38 #end if
39 #end if 39 #if $filter.trailing_bp:
40 #else: 40 --trailing_bp $filter.trailing_bp
41 --unfiltered 41 #end if
42 #end if 42 #else:
43 #if $trim.trimseqs == 'no': 43 --unfiltered
44 --untrimmed 44 #end if
45 #if str($trim.max_stop_codons) != '': 45 #if $trim.trimseqs == 'no':
46 --max_stop_codons $trim.max_stop_codons 46 --untrimmed
47 #end if 47 #if str($trim.max_stop_codons) != '':
48 #end if 48 --max_stop_codons $trim.max_stop_codons
49 #if str($min_length) != '': 49 #end if
50 --min_length $min_length 50 #end if
51 #end if 51 #if str($min_length) != '':
52 --bed $translated_bed 52 --min_length $min_length
53 --output "$output" 53 #end if
54 </command> 54 --bed $translated_bed
55 <inputs> 55 --output '$output'
56 <param name="input" type="data" format="bed" label="BED file with added sequence column" 56 </command>
57 help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> 57 <inputs>
58 <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic" 58 <param name="input" type="data" format="bed" label="BED file with added sequence column"
59 help="Any Compomics application such as PeptideShaker, requires a source"> 59 help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/>
60 </param> 60 <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic"
61 <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character" 61 help="Any Compomics application such as PeptideShaker, requires a source">
62 help="Only used when a fasta ID source is given, defaults to the pipe character"> 62 </param>
63 </param> 63 <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character"
64 <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs" 64 help="Only used when a fasta ID source is given, defaults to the pipe character">
65 help="Can be used to distinguish samples"> 65 </param>
66 <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator> 66 <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs"
67 </param> 67 help="Can be used to distinguish samples">
68 <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source" 68 <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator>
69 help=""/> 69 </param>
70 <param name="reference" type="text" value="" optional="true" label="Genome reference name" 70 <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source"
71 help="By default, the database metadata will be used."/> 71 help=""/>
72 <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines" 72 <param name="reference" type="text" value="" optional="true" label="Genome reference name"
73 help="For example: pep:splice"/> 73 help="By default, the database metadata will be used."/>
74 <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="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
75 help="For example: with the tag name 'depth' and bed score 12: depth:12"/> 75 help="For example: pep:splice"/>
76 <conditional name="filter"> 76 <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
77 <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site"> 77 help="For example: with the tag name 'depth' and bed score 12: depth:12"/>
78 <option value="yes" selected="true">Yes</option> 78 <conditional name="filter">
79 <option value="no">No</option> 79 <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">
80 </param> 80 <option value="yes" selected="true">Yes</option>
81 <when value="yes"> 81 <option value="no">No</option>
82 <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs" 82 </param>
83 help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/> 83 <when value="yes">
84 <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs" 84 <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs"
85 help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/> 85 help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/>
86 </when> 86 <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs"
87 <when value="no"/> 87 help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/>
88 </conditional> 88 </when>
89 <conditional name="trim"> 89 <when value="no"/>
90 <param name="trimseqs" type="select" label="Trim translations to stop codons"> 90 </conditional>
91 <option value="yes" selected="true">Yes</option> 91 <conditional name="trim">
92 <option value="no">No</option> 92 <param name="trimseqs" type="select" label="Trim translations to stop codons">
93 </param> 93 <option value="yes" selected="true">Yes</option>
94 <when value="no"> 94 <option value="no">No</option>
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"/> 95 </param>
96 </when> 96 <when value="no">
97 </conditional> 97 <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"/>
98 <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/> 98 </when>
99 </inputs> 99 </conditional>
100 <stdio> 100 <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/>
101 <exit_code range="1:" level="fatal" description="Error" /> 101 </inputs>
102 </stdio> 102 <outputs>
103 <outputs> 103 <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed" />
104 <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed"> 104 <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta" />
105 </data> 105 </outputs>
106 <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta"> 106 <tests>
107 </data> 107 <test>
108 </outputs> 108 <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>
109 <tests> 109 <param name="reference" value="GRCh37"/>
110 <test> 110 <param name="seqtype" value="pep:novel"/>
111 <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/> 111 <param name="score_name" value="depth"/>
112 <param name="reference" value="GRCh37"/> 112 <output name="output" file="translated_bed_sequences.fa"/>
113 <param name="seqtype" value="pep:novel"/> 113 </test>
114 <param name="score_name" value="depth"/> 114 </tests>
115 <output name="output" file="translated_bed_sequences.fa"/> 115 <help>
116 </test>
117 </tests>
118 <help>
119 **Translate BED Sequences** 116 **Translate BED Sequences**
120 117
121 This tool takes a BED input file that has been processed 118 This tool takes a BED input file that has been processed
122 by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence. 119 by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.
123 120
124 It generates a peptide fasta file with the 3-frame translations of the spliced sequence 121 It generates a peptide fasta file with the 3-frame translations of the spliced sequence
125 defined by each entry in the input BED file. 122 defined by each entry in the input BED file.
126 123
127 </help> 124 </help>
128 </tool> 125 </tool>