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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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1
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3 <container type="docker">iracooke/protk-1.4.1</container>
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4 <requirement type="package" version="1.4">protk</requirement>
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5 </requirements>
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6
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7 <description>
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8 Generate random protein sequences with the same AA composition as input sequences
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9 </description>
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10
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11 <command>
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12 make_decoy.rb $fasta_file -o $output -P $prefix_string $append
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13 </command>
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14
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15 <stdio>
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16 <exit_code range="1:" level="fatal" description="Failure" />
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17 </stdio>
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18
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19 <inputs>
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20 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
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21 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>
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22 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
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23 </inputs>
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24
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25 <outputs>
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26 <data format="fasta" name="output" />
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27 </outputs>
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28
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29 <tests>
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30 <test>
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31 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
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32 <output name="output" format="fasta">
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33 <assert_contents>
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34 <has_text text="decoy_rp3" />
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35 </assert_contents>
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36 </output>
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37 </test>
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38 </tests>
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39
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40
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41
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42 <help>
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43
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44 **What it does**
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45
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46 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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47
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48
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49 </help>
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50
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51 </tool>
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