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1 <tool id="rtg_cgmap" name="CG map">
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2 <description>reads with rtg cg map</description>
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3 <command interpreter="bash">galaxy-rtg-map-wrapper.sh paired $output1 $output2 $__new_file_path__
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4 cgmap -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 --min-insert-size $minlength --max-insert-size $maxlength
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8 --max-mated-score $maxscore --max-unmated-score $maxuscore
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9 </command>
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10 <inputs>
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11 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
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12 <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/>
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13 <param name="repeat" type="text" value="90%" label="Repeat frequency">
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14 <sanitizer sanitize="False"/>
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15 </param>
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16
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17 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for mated reads">
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18 <sanitizer sanitize="False"/>
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19 </param>
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20 <param name="maxuscore" type="text" value="10%" label="Maximum alignment score for umated reads">
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21 <sanitizer sanitize="False"/>
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22 </param>
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23 <param name="minlength" type="integer" value="0" label="Minimum insert size"/>
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24 <param name="maxlength" type="integer" value="1000" label="Maximum insert size"/>
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25
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26 </inputs>
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27 <outputs>
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28 <data name="output1" format="samix" label="Cgmap mated on reads data ${reads.hid} and template data ${template.hid}"/>
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29 <data name="output2" format="samix" label="Cgmap unmated on reads data ${reads.hid} and template data ${template.hid}"/>
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30 </outputs>
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31
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32 <help>
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33 This tool performs a NGS read mapping using rtg cgmap
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34 </help>
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35
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36 </tool>
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