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1 <tool id="rtg_mapx" name="MapX">
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2 <description>protein reads with rtg mapx</description>
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3 <command interpreter="bash">galaxy-rtg-mapx-wrapper.sh $output1 $__new_file_path__
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4 mapx -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 --max-alignment-score $maxscore
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8 </command>
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9 <inputs>
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10 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
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11 <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/>
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12 <param name="repeat" type="text" value="90%" label="Repeat frequency">
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13 <sanitizer sanitize="False"/>
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14 </param>
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15
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16 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for reads (percentages do not work ATM)">
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17 <sanitizer sanitize="False"/>
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18 </param>
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19
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20 </inputs>
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21 <outputs>
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22 <data name="output1" format="tabular" />
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23 </outputs>
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24
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25 <help>
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26 This tool performs a NGS protein read mapping using rtg mapx
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27 </help>
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28
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29 </tool>
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