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annotate tools/dada2-filter-and-trim.xml @ 0:44579a4814b7 draft

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planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
author dfornika
date Tue, 01 May 2018 19:10:14 -0400
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44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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1 <tool id="dada2-filter-and-trim" name="dada2: Filter and Trim" version="1.8">
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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2 <description>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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3 Filters and trims an input fastq file(s) (can be compressed) based on several user-definable criteria, and outputs fastq file(s) (compressed by default) containing those trimmed reads which passed the filters. Corresponding forward and reverse fastq file(s) can be provided as input, in which case filtering is performed on the forward and reverse reads independently, and both reads must pass for the read pair to be output.
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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4 </description>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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5 <requirements>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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6 <requirement type="package" version="1.8">bioconductor-dada2</requirement>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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7 <requirement type="package" version="1.3.2">r-optparse</requirement>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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8 </requirements>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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9 <edam_operations>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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10 <edam_operation>operation_3192</edam_operation>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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11 <edam_operation>operation_3695</edam_operation>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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12 </edam_operations>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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13 <command detect_errors="exit_code"><![CDATA[
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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14 Rscript dada2-filter-and-trim.R \
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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15 --fwd '$fwd' \
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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16 --rev '$rev' \
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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17 --filt '$filt' \
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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18 --filt.rev '$filt.rev' \
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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19 ]]></command>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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20 <inputs>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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21 <param name="fwd" type="data" multiple="True"/>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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22 <param name="rev" type="data" multiple="True"/>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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23 </inputs>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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24 <outputs>
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25 <data name="filt" format="fastqsanger.gz" />
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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26 <data name="filt.rev" format="fastqsanger.gz" />
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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27 </outputs>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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28 <citations>
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29 <citation type="doi">10.1038/nmeth.3869</citation>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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30 </citations>
44579a4814b7 planemo upload for repository https://github.com/dfornika/dada2-galaxy commit a2ae309ba8ff0ef18a1e4abbe5d1ef412e4f69a9
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31 </tool>