Mercurial > repos > jjohnson > translate_bed_sequences
annotate translate_bed_sequences.xml @ 5:c626a939eef7 draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Tue, 12 Jan 2016 14:38:03 -0500 |
| parents | 3b526a780849 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 5 | 2 <tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.0"> |
| 0 | 3 <description>3 frame translation of BED augmented with a sequence column</description> |
| 1 | 4 <requirements> |
| 5 <requirement type="package" version="1.62">biopython</requirement> | |
| 6 <requirement type="python-module">Bio</requirement> | |
| 7 </requirements> | |
| 5 | 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 | |
| 0 | 19 #if $reference: |
| 20 --reference $reference | |
| 21 #else: | |
| 22 --reference ${input.metadata.dbkey} | |
| 23 #end if | |
| 5 | 24 #if $refsource: |
| 25 --refsource $refsource | |
| 26 #end if | |
| 0 | 27 #if $seqtype: |
| 28 --seqtype $seqtype | |
| 29 #end if | |
| 30 #if $score_name: | |
| 31 --score_name $score_name | |
| 32 #end if | |
| 33 #if $filter.filterseqs == 'yes': | |
| 34 #if $filter.leading_bp: | |
| 35 --leading_bp $filter.leading_bp | |
| 36 #end if | |
| 37 #if $filter.trailing_bp: | |
| 38 --trailing_bp $filter.trailing_bp | |
| 39 #end if | |
| 40 #else: | |
| 41 --unfiltered | |
| 42 #end if | |
| 43 #if $trim.trimseqs == 'no': | |
| 44 --untrimmed | |
| 5 | 45 #if str($trim.max_stop_codons) != '': |
| 0 | 46 --max_stop_codons $trim.max_stop_codons |
| 47 #end if | |
| 48 #end if | |
| 5 | 49 #if str($min_length) != '': |
| 0 | 50 --min_length $min_length |
| 51 #end if | |
| 5 | 52 --bed $translated_bed |
| 0 | 53 --output "$output" |
| 54 </command> | |
| 55 <inputs> | |
| 56 <param name="input" type="data" format="bed" label="BED file with added sequence column" | |
| 57 help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> | |
| 5 | 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=""/> | |
| 0 | 70 <param name="reference" type="text" value="" optional="true" label="Genome reference name" |
| 71 help="By default, the database metadata will be used."/> | |
| 72 <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines" | |
|
3
3b526a780849
Change default seqtype from pep:novel to pep:splice
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
73 help="For example: pep:splice"/> |
| 0 | 74 <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name" |
| 75 help="For example: with the tag name 'depth' and bed score 12: depth:12"/> | |
| 76 <conditional name="filter"> | |
| 77 <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site"> | |
| 78 <option value="yes" selected="true">Yes</option> | |
| 79 <option value="no">No</option> | |
| 80 </param> | |
| 81 <when value="yes"> | |
| 82 <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs" | |
| 83 help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/> | |
| 84 <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs" | |
| 85 help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/> | |
| 86 </when> | |
| 87 <when value="no"/> | |
| 88 </conditional> | |
| 89 <conditional name="trim"> | |
| 90 <param name="trimseqs" type="select" label="Trim translations to stop codons"> | |
| 91 <option value="yes" selected="true">Yes</option> | |
| 92 <option value="no">No</option> | |
| 93 </param> | |
| 94 <when value="no"> | |
| 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"/> | |
| 96 </when> | |
| 97 </conditional> | |
| 98 <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/> | |
| 99 </inputs> | |
| 100 <stdio> | |
| 101 <exit_code range="1:" level="fatal" description="Error" /> | |
| 102 </stdio> | |
| 103 <outputs> | |
| 5 | 104 <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed"> |
| 105 </data> | |
| 106 <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta"> | |
| 0 | 107 </data> |
| 108 </outputs> | |
| 109 <tests> | |
| 110 <test> | |
| 111 <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/> | |
| 112 <param name="reference" value="GRCh37"/> | |
| 113 <param name="seqtype" value="pep:novel"/> | |
| 114 <param name="score_name" value="depth"/> | |
| 115 <output name="output" file="translated_bed_sequences.fa"/> | |
| 116 </test> | |
| 117 </tests> | |
| 118 <help> | |
| 119 **Translate BED Sequences** | |
| 120 | |
| 121 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. | |
| 123 | |
| 124 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. | |
| 126 | |
| 127 </help> | |
| 128 </tool> |