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1 <tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="1.3">protk</requirement>
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4 </requirements>
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5
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6 <description>
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7 Generate random protein sequences with the same AA composition as input sequences
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8 </description>
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9
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10 <command>
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11 make_decoy.rb $fasta_file -o $output -P $prefix_string $append
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12 </command>
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13
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14 <stdio>
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15 <exit_code range="1:" level="fatal" description="Failure" />
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16 </stdio>
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17
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18 <inputs>
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19 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
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20 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>
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21 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
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22 </inputs>
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23
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24 <outputs>
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25 <data format="fasta" name="output" />
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26 </outputs>
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27
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28
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29 <help>
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30
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31 **What it does**
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32
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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
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34
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35
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36 </help>
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37
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38 </tool>
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