Mercurial > repos > iuc > porechop

annotate porechop.xml @ 1:93d623d9979c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 4155cc1e26dd6e647d882a550b5278141ab39314
author iuc
date Wed, 19 Sep 2018 08:35:02 -0400
parents 24822689acf8
children 5f76b20953e5
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24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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1 <tool id="porechop" name="Porechop" version="0.2.3">
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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2 <description>adapter trimmer for Oxford Nanopore reads</description>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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3 <requirements>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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4 <requirement type="package" version="0.2.3_seqan2.1.1">porechop</requirement>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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5 </requirements>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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6 <version_command>porechop --version</version_command>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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7 <command detect_errors="exit_code"><![CDATA[
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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8 porechop
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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9 -i '$input_file'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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10 --format '$format'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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11 --barcode_threshold '$barcode_binning_settings.barcode_threshold'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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12 --barcode_diff '$barcode_binning_settings.barcode_diff'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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13 $barcode_binning_settings.require_two_barcodes
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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14 $barcode_binning_settings.discard_unassigned
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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15 --adapter_threshold '$adapter_search_settings.adapter_threshold'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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16 --check_reads '$adapter_search_settings.check_reads'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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17 --scoring_scheme '$adapter_search_settings.scoring_scheme'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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18 --end_size '$end_adapter_settings.end_size'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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19 --min_trim_size '$end_adapter_settings.min_trim_size'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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20 --extra_end_trim '$end_adapter_settings.extra_end_trim'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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21 --end_threshold '$end_adapter_settings.end_threshold'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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22 $middle_adapter_settings.no_split
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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23 $middle_adapter_settings.discard_middle
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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24 --middle_threshold '$middle_adapter_settings.middle_threshold'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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25 --extra_middle_trim_good_side '$middle_adapter_settings.extra_middle_trim_good_side'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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26 --extra_middle_trim_bad_side '$middle_adapter_settings.extra_middle_trim_bad_side'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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27 --min_split_read_size '$middle_adapter_settings.min_split_read_size'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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28 -o 'out.$format'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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29
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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30 ]]></command>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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31 <inputs>
1
93d623d9979c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 4155cc1e26dd6e647d882a550b5278141ab39314
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32 <param name="input_file" type="data" format="fasta,fastqsanger" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" />
93d623d9979c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 4155cc1e26dd6e647d882a550b5278141ab39314
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33 <param name="format" type="select" label="Output format for the reads" help="Output format for the reads">
93d623d9979c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 4155cc1e26dd6e647d882a550b5278141ab39314
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34 <option selected="True" value="fasta">fasta</option>
93d623d9979c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 4155cc1e26dd6e647d882a550b5278141ab39314
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35 <option value="fastq">fastq</option>
93d623d9979c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 4155cc1e26dd6e647d882a550b5278141ab39314
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36 <option value="fasta.gz">fasta.gz</option>
93d623d9979c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 4155cc1e26dd6e647d882a550b5278141ab39314
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37 <option value="fastq.gz">fastq.gz</option>
0
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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38 </param>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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39 <section name="barcode_binning_settings" title="Barcode binning settings">
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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40 <param argument="--barcode_threshold" type="float" min="0" max="100" value="75.0" optional="True" label="Percent identity for binning"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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41 help="A read must have at least this percent identity to a barcode to be binned (default: 75.0)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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42 <param argument="--barcode_diff" type="float" min="0" max="100" value="5.0" optional="True" label="Minimum difference in identity"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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43 help="If the difference between a read's best barcode identity and its second-best barcode identity is less than this value, it will not be put in a barcode bin (to exclude cases which are too close to call) (default: 5.0)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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44 <param argument="--require_two_barcodes" type="boolean" checked="false" truevalue="--require_two_barcodes" falsevalue="" label="Require two matches for binning"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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45 help="Reads will only be put in barcode bins if they have a strong match for the barcode on both their start and end (default: a read can be binned with a match at its start or end)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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46 <param argument="--discard_unassigned" type="boolean" checked="false" truevalue="--discard_unassigned" falsevalue="" label="Discard unassigned reads"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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47 help="Discard unassigned reads (instead of creating a 'none' bin) (default: False)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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48 </section>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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49 <section name="adapter_search_settings" title="Adapter search settings">
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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50 <param argument="--adapter_threshold" type="float" min="0" max="100" value="90.0" optional="True" label="Minimum identity"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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51 help="An adapter set has to have at least this percent identity to be labelled as present and trimmed off (0 to 100) (default: 90.0)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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52 <param argument="--check_reads" type="integer" min="0" value="10000" optional="True" label="Number of alligned reads"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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53 help="This many reads will be aligned to all possible adapters to determine which adapter sets are present (default: 10000)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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54 <param argument="--scoring_scheme" type="text" value="3,-6,-5,-2" label="Scoring scheme"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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55 help="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend">
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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56 <validator type="regex" message="Scoring scheme must be comma-separated string of four positive/negative integers">^((-?\d+[,]){3})-?\d+$</validator>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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57 </param>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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58 </section>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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59 <section name="end_adapter_settings" title="End adapter settings">
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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60 <param argument="--end_size" type="integer" min="0" value="150" optional="True" label="Number of bases"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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61 help="The number of base pairs at each end of the read which will be searched for adapter sequences (default: 150)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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62 <param argument="--min_trim_size" type="integer" min="0" value="4" optional="True" label="Minimum trim length"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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63 help="Adapter alignments smaller than this will be ignored (default: 4)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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64 <param argument="--extra_end_trim" type="integer" min="0" value="2" optional="True" label="Extra bases trimmed"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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65 help="This many additional bases will be removed next to adapters found at the ends of reads (default: 2)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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66 <param argument="--end_threshold" type="float" min="0" max="100" value="75.0" optional="True" label="Minimum percent identity"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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67 help="Adapters at the ends of reads must have at least this percent identity to be removed (0 to 100) (default: 75.0)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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68 </section>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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69 <section name="middle_adapter_settings" title="Middle adapter settings">
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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70 <param argument="--no_split" type="boolean" checked="false" truevalue="--no_split" falsevalue="" label="Skip splitting"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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71 help="Skip splitting reads based on middle adapters (default: split reads when an adapter is found in the middle)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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72 <param argument="--discard_middle" type="boolean" checked="false" truevalue="--discard_middle" falsevalue="" label="Discard reads with middle adapter"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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73 help="Reads with middle adapters will be discarded (default: reads with middle adapters are split) (required for reads to be used with Nanopolish, this option is on by default when outputting reads into barcode bins)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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74 <param argument="--middle_threshold" type="float" min="0" max="100" value="85.0" optional="True" label="Minimum percent identity"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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75 help="Adapters in the middle of reads must have at least this percent identity to be found (0 to 100) (default: 85.0)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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76 <param argument="--extra_middle_trim_good_side" type="integer" min="0" value="10" optional="True" label="Extra trimming good side"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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77 help="This many additional bases will be removed next to middle adapters on their 'good' side (default: 10)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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78 <param argument="--extra_middle_trim_bad_side" type="integer" min="0" value="100" optional="True" label="Extra trimming bad side"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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79 help="This many additional bases will be removed next to middle adapters on their 'bad' side (default: 100)"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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80 <param argument="--min_split_read_size" type="integer" min="0" value="1000" optional="True" label="Minimum length reads post-split"
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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81 help="Post-split read pieces smaller than this many base pairs will not be outputted (default: 1000)"/>
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82 </section>
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83 </inputs>
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84 <outputs>
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85 <data name="outfile" format="fasta" from_work_dir="out.*" label="${tool.name} on ${on_string}: Trimmed">
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86 <change_format>
1
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87 <when input="format" value="fastq" format="fastqsanger"/>
0
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88 <when input="format" value="fasta.gz" format="fasta.gz"/>
1
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89 <when input="format" value="fastq.gz" format="fastqsanger.gz"/>
0
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90 </change_format>
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91 </data>
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92 </outputs>
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93 <tests>
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94 <test>
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95 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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96 <param name="format" value="fasta"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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97 <output name="outfile" ftype="fasta" file="out.fasta"/>
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98 </test>
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99 <test>
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100 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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101 <param name="format" value="fastq"/>
1
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102 <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
0
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103 </test>
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104 <test>
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105 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
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106 <param name="format" value="fasta.gz"/>
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107 <output name="outfile" ftype="fasta.gz" file="out.fasta.gz" compare="sim_size"/>
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108 </test>
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109 <test>
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110 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
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111 <param name="format" value="fastq.gz"/>
1
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112 <output name="outfile" ftype="fastqsanger.gz" file="out.fastq.gz" compare="sim_size"/>
0
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113 </test>
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114 <test>
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115 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
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116 <param name="format" value="fasta"/>
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117 <param name="barcode_threshold" value="70"/>
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118 <param name="barcode_diff" value="4"/>
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119 <param name="require_two_barcodes" value="True"/>
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120 <param name="discard_unassigned" value="True"/>
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121 <param name="end_size" value="100"/>
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122 <param name="min_trim_size" value="2"/>
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123 <param name="extra_end_trim" value="1"/>
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124 <param name="end_threshold" value="80"/>
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125 <param name="discard_middle" value="True"/>
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126 <param name="middle_threshold" value="90"/>
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127 <param name="extra_middle_trim_good_size" value="3"/>
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128 <param name="extra_middle_trim_bad_size" value="30"/>
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129 <param name="min_split_read_size" value="1500"/>
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130 <output name="outfile" ftype="fasta" file="out_advanced.fasta"/>
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131 </test>
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132 </tests>
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133 <help><![CDATA[
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134 Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.
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135 Adapters on the ends of reads are trimmed off, and when a read has an adapter in
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136 its middle, it is treated as chimeric and chopped into separate reads. Porechop
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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137 performs thorough alignments to effectively find adapters, even at low sequence identity.
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138
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139 Porechop also supports demultiplexing of Nanopore reads that were barcoded with
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140 the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.
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141 ]]></help>
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142 <citations>
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143 <citation type="bibtex">
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144 @misc{rrwick2017,
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145 author = {Wick, Ryan},
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146 year = {2017},
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147 title = {Porechop},
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148 publisher = {GitHub},
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149 journal = {GitHub repository},
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150 url = {https://github.com/rrwick/Porechop},
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151 }
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152 </citation>
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153 </citations>
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154 </tool>