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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
author dfornika
date Tue, 10 Mar 2020 15:20:39 +0000
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1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
dfornika
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1 <tool id="readucks" name="readucks" version="@TOOL_VERSION@+galaxy0">
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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2 <description>Nanopore read de-multiplexer</description>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
dfornika
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3 <macros>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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4 <token name="@TOOL_VERSION@">0.0.2</token>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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5 </macros>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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6 <requirements>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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7 <requirement type="package" version="@TOOL_VERSION@">readucks</requirement>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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8 </requirements>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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9 <command detect_errors="exit_code">
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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10 <![CDATA[
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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11 mkdir demuxed &&
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
dfornika
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12 readucks
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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13 -t \${GALAXY_SLOTS:-1}
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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14 -i ${input_fastq}
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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15 --threshold '${barcode_identity_threshold}'
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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16 --bin_barcodes
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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17 --native_barcodes
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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18 -o demuxed
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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19 ]]>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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20 </command>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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21 <inputs>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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22 <param format="fastq,fastqsanger" name="input_fastq" type="data" label="FASTQ Input" help="FASTQ dataset"/>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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23 <outputs>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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24 <data name="barcode_NB01" format="fastq" from_work_dir="demuxed/NB01.fastq" label="${tool.name} on ${on_string}: Barcode 01"/>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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25 <data name="barcode_NB02" format="fastq" from_work_dir="demuxed/NB02.fastq" label="${tool.name} on ${on_string}: Barcode 02"/>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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26 <data name="barcode_NB03" format="fastq" from_work_dir="demuxed/NB02.fastq" label="${tool.name} on ${on_string}: Barcode 03"/>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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27 <data name="barcode_NB04" format="fastq" from_work_dir="demuxed/NB02.fastq" label="${tool.name} on ${on_string}: Barcode 04"/>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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28 <data name="unassigned" format="fastq" from_work_dir="demuxed/unassigned.fastq" label="${tool.name} on ${on_string}: Unassigned"/>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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29 </outputs>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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30 <tests>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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31 <test>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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32 <param name="input_fastq" value="simulated_badreads_1_first100reads.fastq" />
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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33 <output name="barcode_NB02" ftype="fastq" file="demuxed/NB02.fastq" />
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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34 </test>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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35 </tests>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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36 <help>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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37 <![CDATA[
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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38 ]]>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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39 </help>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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40 <citations>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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41 </citations>
1710fc590220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/readucks commit 5803dd6efc58e812f3181261b290039bfe011602-dirty"
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42 </tool>