Mercurial > repos > iracooke > make_protein_decoys
comparison make_decoy.xml @ 0:a90539d8e409 draft
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| author | iracooke |
|---|---|
| date | Fri, 13 Jun 2014 18:10:03 -0400 |
| parents | |
| children | 354e820eb485 |
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| -1:000000000000 | 0:a90539d8e409 |
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| 1 <tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.3">protk</requirement> | |
| 4 </requirements> | |
| 5 | |
| 6 <description> | |
| 7 Generate random protein sequences with the same AA composition as input sequences | |
| 8 </description> | |
| 9 | |
| 10 <command> | |
| 11 make_decoy.rb $fasta_file -o $output -P $prefix_string $append | |
| 12 </command> | |
| 13 | |
| 14 <stdio> | |
| 15 <exit_code range="1:" level="fatal" description="Failure" /> | |
| 16 </stdio> | |
| 17 | |
| 18 <inputs> | |
| 19 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" /> | |
| 20 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/> | |
| 21 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" /> | |
| 22 </inputs> | |
| 23 | |
| 24 <outputs> | |
| 25 <data format="fasta" name="output" /> | |
| 26 </outputs> | |
| 27 | |
| 28 | |
| 29 <help> | |
| 30 | |
| 31 **What it does** | |
| 32 | |
| 33 Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches | |
| 34 | |
| 35 | |
| 36 </help> | |
| 37 | |
| 38 </tool> |