Mercurial > repos > iuc > porechop

annotate porechop.xml @ 4:a2899db6bd6e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
author iuc
date Sun, 09 Feb 2025 20:38:35 +0000
parents 543cbeef3949
children
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a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
iuc
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1 <tool id="porechop" name="Porechop" version="@WRAPPER_VERSION@+galaxy1" profile="20.01">
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2 <description>adapter trimmer for Oxford Nanopore reads</description>
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5f76b20953e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit e68e5869f08e66fbe2787f23b58c1d66e61d9df2"
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3 <macros>
5f76b20953e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit e68e5869f08e66fbe2787f23b58c1d66e61d9df2"
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4 <token name="@WRAPPER_VERSION@">0.2.4</token>
5f76b20953e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit e68e5869f08e66fbe2787f23b58c1d66e61d9df2"
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5 </macros>
0
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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6 <requirements>
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5f76b20953e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit e68e5869f08e66fbe2787f23b58c1d66e61d9df2"
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7 <requirement type="package" version="@WRAPPER_VERSION@">porechop</requirement>
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24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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8 </requirements>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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9 <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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10 <command detect_errors="exit_code"><![CDATA[
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a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
iuc
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11 #import re
a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
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a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
iuc
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13 #set file_path = re.sub('[^\s\w\-.]', '_', str($input_file.element_identifier))
a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
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a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
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15 ln -s '$input_file' '$file_path' &&
a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
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16
0
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17 porechop
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a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
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18 -i '$file_path'
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19 --format '$format'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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20 --barcode_threshold '$barcode_binning_settings.barcode_threshold'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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21 --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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22 $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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23 $barcode_binning_settings.discard_unassigned
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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24 --adapter_threshold '$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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25 --check_reads '$adapter_search_settings.check_reads'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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26 --scoring_scheme '$adapter_search_settings.scoring_scheme'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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27 --end_size '$end_adapter_settings.end_size'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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28 --min_trim_size '$end_adapter_settings.min_trim_size'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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29 --extra_end_trim '$end_adapter_settings.extra_end_trim'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
iuc
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30 --end_threshold '$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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31 $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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32 $middle_adapter_settings.discard_middle
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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33 --middle_threshold '$middle_adapter_settings.middle_threshold'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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34 --extra_middle_trim_good_side '$middle_adapter_settings.extra_middle_trim_good_side'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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35 --extra_middle_trim_bad_side '$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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36 --min_split_read_size '$middle_adapter_settings.min_split_read_size'
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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37 -o 'out.$format'
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38 #if $log_file
a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
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39 > '$log_output'
a2899db6bd6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
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40 #end if
0
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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41
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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42 ]]></command>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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43 <inputs>
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44 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" />
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45 <param name="format" type="select" label="Output format for the reads" help="Output format for the reads">
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46 <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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47 <option value="fastq">fastq</option>
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48 <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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49 <option value="fastq.gz">fastq.gz</option>
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50 </param>
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51 <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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52 <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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53 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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54 <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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55 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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56 <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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57 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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58 <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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59 help="Discard unassigned reads (instead of creating a 'none' bin) (default: False)"/>
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60 </section>
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61 <section name="adapter_search_settings" title="Adapter search settings">
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62 <param argument="--adapter_threshold" type="float" min="0" max="100" value="90.0" optional="True" label="Minimum identity"
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63 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)"/>
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64 <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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65 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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66 <param argument="--scoring_scheme" type="text" value="3,-6,-5,-2" label="Scoring scheme"
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67 help="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend">
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68 <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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69 </param>
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70 </section>
24822689acf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit b8cc84454aedcdbe22d385c1d7067fab599b9090
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71 <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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72 <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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73 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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74 <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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75 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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76 <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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77 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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78 <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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79 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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80 </section>
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81 <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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82 <param argument="--no_split" type="boolean" checked="false" truevalue="--no_split" falsevalue="" label="Skip splitting"
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83 help="Skip splitting reads based on middle adapters (default: split reads when an adapter is found in the middle)"/>
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84 <param argument="--discard_middle" type="boolean" checked="false" truevalue="--discard_middle" falsevalue="" label="Discard reads with middle adapter"
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85 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)"/>
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86 <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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87 help="Adapters in the middle of reads must have at least this percent identity to be found (0 to 100) (default: 85.0)"/>
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88 <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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89 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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90 <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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91 help="This many additional bases will be removed next to middle adapters on their 'bad' side (default: 100)"/>
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92 <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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93 help="Post-split read pieces smaller than this many base pairs will not be outputted (default: 1000)"/>
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94 </section>
4
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95 <param name="log_file" type="boolean" label="Generate log file" help="Generates a log file out of stdout, which can be used as MultiQC input"/>
0
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96 </inputs>
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97 <outputs>
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98 <data name="outfile" format="fasta" from_work_dir="out.*" label="${tool.name} on ${on_string}: Trimmed">
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99 <change_format>
1
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100 <when input="format" value="fastq" format="fastqsanger"/>
0
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101 <when input="format" value="fasta.gz" format="fasta.gz"/>
1
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102 <when input="format" value="fastq.gz" format="fastqsanger.gz"/>
0
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103 </change_format>
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104 </data>
4
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105 <data name="log_output" format="txt" label="Porechop log file">
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106 <filter>log_file</filter>
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107 </data>
0
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108 </outputs>
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109 <tests>
4
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110 <test expect_num_outputs="2">
0
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111 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
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112 <param name="format" value="fasta"/>
4
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113 <param name="log_file" value="true"/>
0
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114 <output name="outfile" ftype="fasta" file="out.fasta"/>
4
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115 <output name="log_output" ftype="txt">
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116 <assert_contents>
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117 <has_line line=" PCR adapters 2 66.7 63.6"/>
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118 <has_line line=" Barcode 1 (reverse) 59.4 66.7"/>
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119 <has_line line="4 / 9 reads had adapters trimmed from their start (74 bp removed)"/>
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120 <has_line line="3 / 9 reads had adapters trimmed from their end (49 bp removed)"/>
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121 </assert_contents>
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122 </output>
0
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123 </test>
4
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124 <test expect_num_outputs="1">
2
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125 <param name="input_file" ftype="fastqsanger.gz" value="test_format.fastq.gz"/>
0
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126 <param name="format" value="fastq"/>
1
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127 <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
0
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128 </test>
4
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129 <test expect_num_outputs="1">
3
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130 <param name="input_file" ftype="fastq.gz" value="test_format.fastq.gz"/>
543cbeef3949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 6ea6e816d7c92599628ab3c0a0826fb7476270b0"
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131 <param name="format" value="fastq"/>
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132 <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
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133 </test>
4
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134 <test expect_num_outputs="1">
0
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135 <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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136 <param name="format" value="fasta.gz"/>
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137 <output name="outfile" ftype="fasta.gz" file="out.fasta.gz" compare="sim_size"/>
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138 </test>
4
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139 <test expect_num_outputs="1">
0
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140 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
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141 <param name="format" value="fastq.gz"/>
1
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142 <output name="outfile" ftype="fastqsanger.gz" file="out.fastq.gz" compare="sim_size"/>
0
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143 </test>
4
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144 <test expect_num_outputs="1">
0
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145 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
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146 <param name="format" value="fasta"/>
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147 <param name="barcode_threshold" value="70"/>
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148 <param name="barcode_diff" value="4"/>
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149 <param name="require_two_barcodes" value="True"/>
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150 <param name="discard_unassigned" value="True"/>
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151 <param name="end_size" value="100"/>
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152 <param name="min_trim_size" value="2"/>
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153 <param name="extra_end_trim" value="1"/>
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154 <param name="end_threshold" value="80"/>
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155 <param name="discard_middle" value="True"/>
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156 <param name="middle_threshold" value="90"/>
4
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157 <param name="extra_middle_trim_good_side" value="3"/>
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158 <param name="extra_middle_trim_bad_side" value="30"/>
0
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159 <param name="min_split_read_size" value="1500"/>
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160 <output name="outfile" ftype="fasta" file="out_advanced.fasta"/>
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161 </test>
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162 </tests>
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163 <help><![CDATA[
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164 Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.
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165 Adapters on the ends of reads are trimmed off, and when a read has an adapter in
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166 its middle, it is treated as chimeric and chopped into separate reads. Porechop
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167 performs thorough alignments to effectively find adapters, even at low sequence identity.
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168
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169 Porechop also supports demultiplexing of Nanopore reads that were barcoded with
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170 the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.
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171 ]]></help>
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172 <citations>
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173 <citation type="bibtex">
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174 @misc{rrwick2017,
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175 author = {Wick, Ryan},
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176 year = {2017},
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177 title = {Porechop},
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178 publisher = {GitHub},
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179 journal = {GitHub repository},
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180 url = {https://github.com/rrwick/Porechop},
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181 }
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182 </citation>
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183 </citations>
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184 </tool>