Mercurial > repos > jjohnson > translate_bed_sequences
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author | jjohnson |
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date | Wed, 08 Jan 2014 18:33:29 -0500 |
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children | 639ee511d552 |
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<?xml version="1.0"?> <tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.0.1"> <description>3 frame translation of BED augmented with a sequence column</description> <command interpreter="python">translate_bed_sequences.py --input "$input" #if $reference: --reference $reference #else: --reference ${input.metadata.dbkey} #end if #if $seqtype: --seqtype $seqtype #end if #if $score_name: --score_name $score_name #end if #if $filter.filterseqs == 'yes': #if $filter.leading_bp: --leading_bp $filter.leading_bp #end if #if $filter.trailing_bp: --trailing_bp $filter.trailing_bp #end if #else: --unfiltered #end if #if $trim.trimseqs == 'no': --untrimmed #if $trim.max_stop_codons != None: --max_stop_codons $trim.max_stop_codons #end if #end if #if $min_length: --min_length $min_length #end if --output "$output" </command> <inputs> <param name="input" type="data" format="bed" label="BED file with added sequence column" help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> <param name="reference" type="text" value="" optional="true" label="Genome reference name" help="By default, the database metadata will be used."/> <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines" help="For example: pep:novel"/> <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name" help="For example: with the tag name 'depth' and bed score 12: depth:12"/> <conditional name="filter"> <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site"> <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> <when value="yes"> <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs" help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/> <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs" help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/> </when> <when value="no"/> </conditional> <conditional name="trim"> <param name="trimseqs" type="select" label="Trim translations to stop codons"> <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> <when value="no"> <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"/> </when> </conditional> <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/> </inputs> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> <outputs> <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string}"> <filter>'found' in str(outputs)</filter> </data> </outputs> <tests> <test> <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/> <param name="reference" value="GRCh37"/> <param name="seqtype" value="pep:novel"/> <param name="score_name" value="depth"/> <output name="output" file="translated_bed_sequences.fa"/> </test> </tests> <help> **Translate BED Sequences** This tool takes a BED input file that has been processed by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence. It generates a peptide fasta file with the 3-frame translations of the spliced sequence defined by each entry in the input BED file. </help> </tool>