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1 <tool id="rtg_map" name="Map">
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2 <description>reads with rtg map</description>
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3 <command interpreter="bash">galaxy-rtg-map-wrapper.sh $paired.sPaired $output1 $output2 $__new_file_path__
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4 map -t ${template.extra_files_path}
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5 --repeat-freq ${repeat}
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6 -i ${reads.extra_files_path}
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7 #if $paired.sPaired == "paired":
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8 --min-insert-size $paired.minlength --max-insert-size $paired.maxlength
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9 --max-mated-score $paired.maxscore --max-unmated-score $paired.maxuscore
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10 #else:
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11 --max-alignment-score $paired.maxscore
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12 #end if
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13 </command>
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14 <inputs>
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15 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
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16 <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/>
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17 <param name="repeat" type="text" value="90%" label="Repeat frequency">
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18 <sanitizer sanitize="False"/>
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19 </param>
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20
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21 <conditional name="paired">
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22 <param name="sPaired" type="select" label="Are you mapping paired-end reads?">
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23 <option value="paired">Paired-end</option>
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24 <option value="single">Single-end</option>
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25 </param>
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26 <when value="single">
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27 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for reads (percentages do not work ATM)">
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28 <sanitizer sanitize="False"/>
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29 </param>
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30 </when>
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31 <when value="paired">
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32 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for mated reads">
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33 <sanitizer sanitize="False"/>
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34 </param>
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35 <param name="maxuscore" type="text" value="10%" label="Maximum alignment score for umated reads">
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36 <sanitizer sanitize="False"/>
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37 </param>
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38 <param name="minlength" type="integer" value="200" label="Minimum insert size"/>
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39 <param name="maxlength" type="integer" value="400" label="Maximum insert size"/>
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40 </when>
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41 </conditional>
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42
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43 </inputs>
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44 <outputs>
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45 <data name="output1" format="samix" />
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46 <data name="output2" format="samix" >
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47 <filter>paired['sPaired'] == "paired"</filter>
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48 </data>
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49 </outputs>
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50
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51 <help>
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52 This tool performs a NGS read mapping using rtg map
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53 </help>
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54
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55 </tool>
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