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comparison result_analyser.xml @ 0:cafda610cf4b draft default tip

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author przemyslaw
date Thu, 27 Jun 2013 20:38:20 -0400
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1 <tool id="resanalyser" name="Result Analyser" version="1.0.8">
2 <description>Result Analyser</description>
3 <command interpreter="bash">
4 result_analyser.sh results_analyser.jar $chromosome_tar -g "$genomeFile" -m "$mapping" -o "$output1" -r "$searchResultsFile"
5 #if $reportId
6 -rep "$reportId"
7 #end if
8 #if $reportList
9 -replist "$reportList"
10 #end if
11 #if $sqlQuery
12 -sql "$sqlQuery"
13 #end if
14 </command>
15 <inputs>
16 <param name="chromosome_tar" type="data" format="tar" label="Select chromosome tar file" help="A Tar file containing all the chromosome files" />
17 <param name="genomeFile" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
18 <param name="searchResultsFile" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" />
19 <param name="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" />
20
21 <param name="reportId" optional="true" type="data" format="txt" label="Select reportId" help="Access a built in report query" />
22 <param name="reportList" optional="true" type="data" format="txt" label="Select reportList" help="A file containing all the pre-built SQL queries" />
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" />
24
25 </inputs>
26 <outputs>
27 <data format="sam" name="output1" />
28 </outputs>
29 <help>
30 </help>
31 </tool>