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1 <tool id="resanalyser" name="Result Analyser" version="1.0.1">
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2 <description>Result Analyser</description>
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3 <command interpreter="bash">
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4 result_analyser.sh results_analyser.jar $chromosome_tar -g "$genomeFile" -m "$mapping" -o "$output1" -r "$searchResultsFile"
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5 #if $reportId
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6 -rep "$reportId"
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7 #end if
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8 #if $reportList
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9 -replist "$reportList"
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10 #end if
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11 #if $sqlQuery
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12 -sql "$sqlQuery"
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13 #end if
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14 </command>
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15 <inputs>
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16 <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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17 <param name="genomeFile" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
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18 <param name="searchResultsFile" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" />
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19 <param name="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" />
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20
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21 <param name="reportId" optional="true" type="data" format="txt" label="Select reportId" help="Access a built in report query" />
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22 <param name="reportList" optional="true" type="data" format="txt" label="Select reportList" help="A file containing all the pre-built SQL queries" />
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23 <param name="sqlQuery" optional="true" type="data" format="txt" label="Select SQL Query" help="Filters the result through the use of a SQL statement to the output file" />
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24
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25 </inputs>
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26 <outputs>
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27 <data format="sam" name="output1" />
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28 </outputs>
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29 <help>
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30 </help>
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31 </tool>
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