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1 <tool id="protmerger" name="Protein Merger" version="1.0.9">
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2 <description>Virtual Protein Merger</description>
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3 <command interpreter="bash">
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4 protein_merger.sh virtual_protein_merger.jar $chromosome_tar -g "$genomeFile" -o "$output1"
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5 -r "$searchResultsFile"
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6 #if $trans_tab_file
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7 -t "$trans_tab_file"
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8 #end if
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9 #if $confidence_score
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10 -s "$confidence_score"
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11 #end if
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12 </command>
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13 <inputs>
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14 <param name="chromosome_tar" type="data" format="tar" label="Select chromosome tar file" help="A Tar file containing all the chromosome files" />
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15 <param name="genomeFile" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
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16 <param name="searchResultsFile" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" />
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17 <param name="trans_tab_file" type="data" format="txt" label="Select Translation Table File" help="File containing a mapping of codons to amino acids, in the format used by NCBI." optional="True"/>
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18 <param name="confidence_score" type="integer" label="Confidence score thresold" help="Minimum confidence score for peptides to be included" optional="True" />
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19 </inputs>
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20 <outputs>
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21 <data format="sam" name="output1" />
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22 </outputs>
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23 <help>
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24 </help>
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25 </tool>
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