Mercurial > repos > jjohnson > translate_bed_sequences
annotate translate_bed_sequences.xml @ 3:3b526a780849
Change default seqtype from pep:novel to pep:splice
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 23 Jan 2014 09:10:16 -0600 |
| parents | 359addb9b9d4 |
| children | c626a939eef7 |
| rev | line source |
|---|---|
| 0 | 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> | |
| 1 | 4 <requirements> |
| 5 <requirement type="package" version="1.62">biopython</requirement> | |
| 6 <requirement type="python-module">Bio</requirement> | |
| 7 </requirements> | |
| 0 | 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 | |
|
2
359addb9b9d4
Do not include the stop codon when filtering
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
32 #if $trim.max_stop_codons.__str__ != '': |
| 0 | 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" | |
|
3
3b526a780849
Change default seqtype from pep:novel to pep:splice
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
47 help="For example: pep:splice"/> |
| 0 | 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> |