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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
author bgruening
date Thu, 09 Mar 2017 08:31:30 -0500
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4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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1 <tool id="hicup_deduplicator" name="Hicup Deduplicator" version="0.1.0">
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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2 <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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3 <macros>
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4 <import>hicup_macros.xml</import>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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5 </macros>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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6 <expand macro="requirements_hicup" />
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7 <expand macro="stdio" />
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8
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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9 <command><![CDATA[
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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10 hicup_deduplicator --quiet '$input_file'
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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11 && mv *.dedup.* dataset.dedup_result
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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12 && mv hicup_deduplicator_summary*.txt hicup_deduplicator_summary.txt
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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13 && mv *deduplicator_cis_trans_piechart.svg deduplicator_cis_trans_piechart.svg
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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14 && mv *deduplicator_uniques_barchart.svg deduplicator_uniques_barchart.svg
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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15 ]]></command>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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16 <inputs>
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17 <param name="input_file" type="data" format="bam,sam" label="Input file(s)" help="Input files in bam or sam format."/>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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18 </inputs>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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19 <outputs>
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20 <data name="dedup_result" format="bam,sam" label="Deduplicator Result" from_work_dir="dataset.dedup_result" />
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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21 <expand macro="deduplicator_output" />
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input_file" value="dataset.filt.sam" ftype="sam"/>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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26 <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" />
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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27 <output name="cis_trans_piechart" file="deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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28 <output name="uniques_barchart" file="deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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29 <output name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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30 </test>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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31 </tests>
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32 <help><![CDATA[
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4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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34 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
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4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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36 To get more information about the deduplicator visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Deduplicator
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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37 ]]></help>
4c58b834686f planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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38 <expand macro="citation_hicup" />
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39 </tool>