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1 <tool id="samifier" name="Samifier" version="1.0.0">
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2 <description>Samifier vX.X</description>
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3 <command interpreter="bash">
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4 javaRunner.sh samifier.jar -c "/usr/local/galaxy-dist/tools/ap11/chromosome/" -g "$genome" -m "$mapping" -o "$output1" -r "$mascot"
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5 #if $score_thresold
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6 -s "$score_thresold"
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7 #end if
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8 #if $condition2.tool_option2 == "yes"
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9 -l "$output2"
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10 #end if
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11 #if $condition3.tool_option3 == "yes"
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12 -b "$output3"
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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="genome" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
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17 <param name="mascot" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" />
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18 <param name="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" />
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19 <param name="score_thresold" type="integer" label="Confidence Score thresold" help="Minimum confidence score for peptides to" optional="true"/>
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20
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21 <conditional name="condition2">
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22 <param name="tool_option2" type="select" label="Write log file" help="Create an output containing the logs">
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23 <option value="yes" selected="No">Yes</option>
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24 <option value="no" selected="Yes">No</option>
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25 </param>
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26 </conditional>
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27 <conditional name="condition3">
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28 <param name="tool_option3" type="select" label="Write output in bed format" help="Output to write IGV regions of interest">
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29 <option value="yes" selected="No">Yes</option>
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30 <option value="no" selected="Yes">No</option>
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31 </param>
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32 </conditional>
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33 </inputs>
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34 <outputs>
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35 <data format="sam" name="output1" />
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36 <data format="txt" name="output2" label="Samifier log file">
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37 <filter>condition2['tool_option2'] == "yes"</filter>
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38 </data>
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39 <data format="bed" name="output3" label="Samifier Bed">
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40 <filter>condition3['tool_option3'] == "yes"</filter>
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41 </data>
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42 </outputs>
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43 <help>
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44 </help>
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45 </tool>
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