Mercurial > repos > iracooke > protxml_to_gff
comparison protxml_to_gff.xml @ 0:04dc24d06ddb draft default tip
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| author | iracooke |
|---|---|
| date | Sat, 14 Jun 2014 18:18:41 -0400 |
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| -1:000000000000 | 0:04dc24d06ddb |
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| 1 <tool id="protxml_to_gff" name="ProtXML to GFF" version="1.0.1"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.3">protk</requirement> | |
| 4 <requirement type="package" version="2.2.29">blast+</requirement> | |
| 5 </requirements> | |
| 6 | |
| 7 <description>Map peptides from a protXML file to genomic coordinates</description> | |
| 8 | |
| 9 <command> | |
| 10 protxml_to_gff.rb -p $protxml_file | |
| 11 | |
| 12 -g $genome_fasta_file | |
| 13 | |
| 14 -d $protein_fasta_file | |
| 15 | |
| 16 -o $output | |
| 17 | |
| 18 --threshold $peptide_threshold | |
| 19 | |
| 20 --prot-threshold $protein_threshold | |
| 21 | |
| 22 $stack_charges | |
| 23 | |
| 24 </command> | |
| 25 | |
| 26 | |
| 27 | |
| 28 | |
| 29 <stdio> | |
| 30 <exit_code range="1:" level="fatal" description="Failure" /> | |
| 31 </stdio> | |
| 32 | |
| 33 <inputs> | |
| 34 <param name="protxml_file" type="data" format="protxml" help="ProtXML containing combined results from all searches" label="ProtXML File" /> | |
| 35 <param name="genome_fasta_file" type="data" format="fasta" help="The genome against which peptides will be mapped" label="Genome fasta file" /> | |
| 36 <param name="protein_fasta_file" type="data" format="fasta" help="The database used for ms/ms searches (must have genomic coords encoded in the fasta header)" label="Protein fasta file" /> | |
| 37 | |
| 38 <param name="peptide_threshold" help="Peptide Probability Threshold" type="float" value="0.95" min="0" max="1" label="Peptide Probability Threshold" /> | |
| 39 <param name="protein_threshold" help="Protein Probability Threshold" type="float" value="0.99" min="0" max="1" label="Protein Probability Threshold" /> | |
| 40 | |
| 41 <param name="stack_charges" type="boolean" label="Stack Charges" help="Different peptide charge states get separate gff entries" truevalue="--stack-charge-states" falsevalue=""/> | |
| 42 | |
| 43 <param name="collapse_redundant_proteins" type="boolean" label="Collapse Redundant Proteins" help="Proteins that cover genomic regions already covered will be skipped" truevalue="--collapse-redundant-proteins" falsevalue=""/> | |
| 44 | |
| 45 </inputs> | |
| 46 | |
| 47 <outputs> | |
| 48 <data format="gff3" name="output" /> | |
| 49 </outputs> | |
| 50 | |
| 51 | |
| 52 <help> | |
| 53 | |
| 54 **What it does** | |
| 55 | |
| 56 Generates a gff file containing genomic coordinates for peptides present in a protXML file. | |
| 57 | |
| 58 In order for this tool to work the inputs must satisfy certain requirements. | |
| 59 | |
| 60 1. The genome fasta should encode the scaffold numbers as in the following example | |
| 61 | |
| 62 >scaffoldXXX | |
| 63 | |
| 64 or | |
| 65 | |
| 66 >scaffold_XXX | |
| 67 | |
| 68 where XXX represent digits encoding the scaffold number. Any number of digits are allowed | |
| 69 | |
| 70 2. The protXML should have been generated by searching a database generated using the protk Generate 6 frame translation tool and the extract proteins from gff3 tool. Both those tools should be run with the genomics coordinates included in the output file. | |
| 71 | |
| 72 | |
| 73 | |
| 74 ---- | |
| 75 | |
| 76 **References** | |
| 77 | |
| 78 | |
| 79 </help> | |
| 80 | |
| 81 </tool> |