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annotate seqprep.xml @ 0:8a0aa44e1e5b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
author iuc
date Thu, 15 Feb 2024 14:23:13 +0000
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0
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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1 <tool id="seqprep" name="Merging paired-end Illumina reads (SeqPrep)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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2 <description>Merge and Trim Adapter Sequences from Paired-End Illumina Reads</description>
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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3 <macros>
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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4 <import>macros.xml</import>
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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5 </macros>
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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6 <expand macro="biotools"/>
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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7 <expand macro="requirements"/>
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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8 <expand macro="creators"/>
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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9 <command detect_errors="exit_code"><![CDATA[
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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10 SeqPrep
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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11 -f '${input1}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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12 -r '${input2}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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13 -1 '${output1}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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14 -2 '${output2}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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15
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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16 #if $merge_reads
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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17 -s '${merged}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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18 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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19
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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20 ## General Arguments ##
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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21 #if $general_options.first_read_discarded
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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22 -3 '${general_options.first_read_discarded}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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23 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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24 #if $general_options.second_read_discarded
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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25 -4 '${general_options.second_read_discarded}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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26 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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27 #if $general_options.phred64
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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28 -6 '${general_options.phred64}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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29 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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30 #if $general_options.quality_cutoff
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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31 -q '${general_options.quality_cutoff}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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32 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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33 #if $general_options.min_length
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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34 -L '${general_options.min_length}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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35 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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36
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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37 ## Additional Adapter/Primer Trimming Arguments ##
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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38 #if $trimming_options.adapter_a
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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39 -A '${trimming_options.adapter_a}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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40 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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41 #if $trimming_options.adapter_b
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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42 -B '${trimming_options.adapter_b}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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43 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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44 #if $trimming_options.adapter_overlap
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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45 -O '${trimming_options.adapter_overlap}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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46 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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47 #if $trimming_options.max_mismatch_fraction
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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48 -M '${trimming_options.max_mismatch_fraction}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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49 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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50 #if $trimming_options.min_match_fraction
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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51 -N '${trimming_options.min_match_fraction}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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52 #end if
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53 #if $trimming_options.adapter_bandwidth
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54 -b '${trimming_options.adapter_bandwidth}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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55 #end if
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56 #if $trimming_options.gap_open
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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57 -Q '${trimming_options.gap_open}'
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58 #end if
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59 #if $trimming_options.gap_extend
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60 -t '${trimming_options.gap_extend}'
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61 #end if
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62 #if $trimming_options.gap_end
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63 -e '${trimming_options.gap_end}'
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64 #end if
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65 #if $trimming_options.local_alignment_score
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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66 -Z '${trimming_options.local_alignment_score}'
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67 #end if
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68 #if $trimming_options.read_alignment_bandwidth
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69 -w '${trimming_options.read_alignment_bandwidth}'
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70 #end if
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71 #if $trimming_options.read_alignment_gap_open
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72 -W '${trimming_options.read_alignment_gap_open}'
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73 #end if
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74 #if $trimming_options.read_alignment_gap_extend
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75 -p '${trimming_options.read_alignment_gap_extend}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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76 #end if
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77 #if $trimming_options.read_alignment_gap_end
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78 -P '${trimming_options.read_alignment_gap_end}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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79 #end if
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80 #if $trimming_options.read_alignment_max_gap_fraction
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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81 -X '${trimming_options.read_alignment_max_gap_fraction}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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82 #end if
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83
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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84 ## Additional Arguments for Merging ##
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85 #if $merging_options.maximum_quality_score
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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86 -y '${merging_options.maximum_quality_score}'
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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87 #end if
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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88 #if $merging_options.print_overhang
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89 -g '${merging_options.print_overhang}'
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90 #end if
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91 #if $merging_options.min_base_pair_overlap
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92 -o '${merging_options.min_base_pair_overlap}'
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93 #end if
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94 #if $merging_options.max_mismatch_fraction
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95 -m '${merging_options.max_mismatch_fraction}'
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96 #end if
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97 #if $merging_options.min_match_fraction
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98 -n '${merging_options.min_match_fraction}'
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99 #end if
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100 ]]></command>
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101 <inputs>
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102 <param name="input1" type="data" format="fastq" label="First Read Input" help="Select the FASTQ file containing the first set of paired-end reads." />
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103 <param name="input2" type="data" format="fastq" label="Second Read Input" help="Select the FASTQ file containing the second set of paired-end reads." />
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104 <param name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Merge Reads" help="Enable this to merge overlapping reads from the provided paired-end FASTQ files." />
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105
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106 <!-- Section for General Arguments -->
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107 <section name="general_options" title="General Arguments (Optional)" expanded="false">
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108 <param name="first_read_discarded" argument="-3" type="text" optional="true" label="First Read Discarded FASTQ Filename" help="first read discarded fastq filename" />
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109 <param name="second_read_discarded" argument="-4" type="text" optional="true" label="Second Read Discarded FASTQ Filename" help="second read discarded fastq filename" />
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110 <param name="phred64" argument="-6" type="boolean" truevalue="-6" falsevalue="" checked="false" label="Input Sequence is in Phred+64 Format" help="Input sequence is in phred+64 rather than phred+33 format, the output will still be phred+33"/>
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111 <param name="quality_cutoff" argument="-q" type="integer" optional="true" value="13" label="Quality Score Cutoff" help="Quality score cutoff for mismatches to be counted in overlap" />
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112 <param name="min_length" argument="-L" type="integer" optional="true" value="30" label="Minimum Length of Reads" help="Minimum length of a trimmed or merged read to print it" />
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113 </section>
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114
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115 <!-- Section for Additional Adapter/Primer Trimming Arguments -->
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116 <section name="trimming_options" title="Additional Adapter/Primer Trimming Arguments" expanded="false">
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117 <param name="adapter_a" argument="-A" label="Adapter Sequence A" type="text" optional="true" value="AGATCGGAAGAGCGGTTCAG" help="Forward read primer/adapter sequence to trim as it would appear at the end of a read" />
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118 <param name="adapter_b" argument="-B" label="Adapter Sequence B" type="text" optional="true" value="AGATCGGAAGAGCGTCGTGT" help="Reverse read primer/adapter sequence to trim as it would appear at the end of a read" />
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119 <param name="adapter_overlap" argument="-O" label="Minimum Overall Base Pair Overlap with Adapter" type="integer" value="10" optional="true" help="minimum overall base pair overlap with adapter sequence to trim" />
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120 <param name="max_mismatch_fraction" argument="-M" label="Maximum Fraction of Good Quality Mismatching Bases" type="float" value="0.02" optional="true" help="maximum fraction of good quality mismatching bases for primer/adapter overlap" />
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121 <param name="min_match_fraction" argument="-N" label="Minimum Fraction of Matching Bases" type="float" value="0.87" optional="true" help="minimum fraction of matching bases for primer/adapter overlap" />
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122 <param name="adapter_bandwidth" argument="-b" label="Adapter Alignment Band-width" type="integer" value="50" optional="true" />
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123 <param name="gap_open" argument="-Q" label="Adapter Alignment Gap-Open" type="integer" value="8" optional="true" />
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124 <param name="gap_extend" argument="-t" label="Adapter Alignment Gap-Extension" type="integer" value="2" optional="true" />
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125 <param name="gap_end" argument="-e" label="Adapter Alignment Gap-End" type="integer" value="2" optional="true" />
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126 <param name="local_alignment_score" argument="-Z" label="Minimum Local Alignment Score Cutoff" type="integer" value="26" optional="true" help="Adapter alignment minimum local alignment score cutoff [roughly (2*num_hits) - (num_gaps*gap_open) - (num_gaps*gap_close) - (gap_len*gap_extend) - (2*num_mismatches)]" />
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127 <param name="read_alignment_bandwidth" argument="-w" label="Read Alignment Band-width" type="integer" value="50" optional="true" />
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128 <param name="read_alignment_gap_open" argument="-W" label="Read Alignment Gap-Open" type="integer" value="26" optional="true" />
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129 <param name="read_alignment_gap_extend" argument="-p" label="Read Alignment Gap-Extension" type="integer" value="9" optional="true" />
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130 <param name="read_alignment_gap_end" argument="-P" label="Read Alignment Gap-End" type="integer" value="5" optional="true" help="read alignment maximum fraction gap cutoff" />
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131 <param name="read_alignment_max_gap_fraction" argument="-X" label="Read Alignment Maximum Fraction Gap Cutoff" type="float" value="0.125" optional="true" />
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132 </section>
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133
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134 <!-- Section for Optional Arguments for Merging: -->
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135 <section name="merging_options" title="Optional Arguments for Merging" expanded="false">
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136 <param name="maximum_quality_score" argument="-y" label="Maximum Quality Score in Output" type="text" optional="true" help="Maximum quality score in output (phred 33), default = ']'"/>
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137 <param name="print_overhang" argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print Overhang When Adapters Are Present and Stripped" help="Use this if reads are different lengths"/>
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138 <param name="min_base_pair_overlap" argument="-o" type="integer" optional="true" value="15" label="Minimum Overall Base Pair Overlap" help="Minimum overall base pair overlap to merge two reads"/>
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139 <param name="max_mismatch_fraction" argument="-m" type="float" optional="true" value="0.02" label="Maximum Fraction of Good Quality Mismatching Bases" help="Maximum fraction of good quality mismatching bases to overlap reads"/>
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140 <param name="min_match_fraction" argument="-n" type="float" optional="true" value="0.9" label="Minimum Fraction of Matching Bases" help="Minimum fraction of matching bases to overlap reads"/>
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141 </section>
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142 </inputs>
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143 <outputs>
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144 <data format="fastq.gz" name="output1" label="${tool.name} on ${on_string}: First Read Output">
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145 <filter>output_all</filter>
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146 </data>
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147 <data format="fastq.gz" name="output2" label="${tool.name} on ${on_string}: Second Read Output">
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148 <filter>output_all</filter>
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149 </data>
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150 <data format="fastq.gz" name="merged" label="${tool.name} on ${on_string}: Merged Reads">
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151 <filter>merge_reads</filter>
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152 </data>
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153 </outputs>
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154 <tests>
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155 <!-- Test default inputs #1 -->
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156 <test expect_num_outputs="3">
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157 <param name="input1" value="input1.fq" />
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158 <param name="input2" value="input2.fq" />
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159 <param name="merge_reads" value="true" />
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160
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161 <!-- Section for General Arguments -->
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162 <section name="general_options" >
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163 <param name="quality_cutoff" value="13" />
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164 <param name="min_length" value="30" />
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165 </section>
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166
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iuc
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diff changeset
167 <!-- Section for Additional Adapter/Primer Trimming Arguments -->
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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168 <section name="trimming_options">
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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169 <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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170 <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
parents:
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171 <param name="adapter_overlap" value="10" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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172 <param name="max_mismatch_fraction" value="0.02" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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173 <param name="min_match_fraction" value="0.87" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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174 <param name="adapter_bandwidth" value="50" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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175 <param name="gap_open" value="8" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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176 <param name="gap_extend" value="2" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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177 <param name="gap_end" value="2" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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178 <param name="local_alignment_score" value="26" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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179 <param name="read_alignment_bandwidth" value="50" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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180 <param name="read_alignment_gap_open" value="26" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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181 <param name="read_alignment_gap_extend" value="9" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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182 <param name="read_alignment_gap_end" value="5" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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183 <param name="read_alignment_max_gap_fraction" value="0.125" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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184 </section>
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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185 <output name="output1" file="output1.fq.gz" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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186 <output name="output2" file="output2.fq.gz" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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187 <output name="merged" file="merged_output.fq.gz" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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188 </test>
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189
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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190 <!-- Without Merging, Two Outputs #2 -->
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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191 <test expect_num_outputs="2">
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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192 <param name="input1" value="input1.fq" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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193 <param name="input2" value="input2.fq" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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194 <param name="merge_reads" value="false" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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195
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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196 <!-- Section for General Arguments -->
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iuc
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197 <section name="general_options" >
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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198 <param name="quality_cutoff" value="13" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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199 <param name="min_length" value="30" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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200 </section>
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201
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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202 <!-- Section for Additional Adapter/Primer Trimming Arguments -->
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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203 <section name="trimming_options">
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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204 <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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205 <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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206 <param name="adapter_overlap" value="10" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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207 <param name="max_mismatch_fraction" value="0.02" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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208 <param name="min_match_fraction" value="0.87" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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209 <param name="adapter_bandwidth" value="50" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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210 <param name="gap_open" value="8" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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211 <param name="gap_extend" value="2" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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212 <param name="gap_end" value="2" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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213 <param name="local_alignment_score" value="26" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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214 <param name="read_alignment_bandwidth" value="50" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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215 <param name="read_alignment_gap_open" value="26" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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216 <param name="read_alignment_gap_extend" value="9" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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217 <param name="read_alignment_gap_end" value="5" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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218 <param name="read_alignment_max_gap_fraction" value="0.125" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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219 </section>
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iuc
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220 <output name="output1" file="outputNoMerge1.fq.gz" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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221 <output name="output2" file="outputNoMerge2.fq.gz" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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222 </test>
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iuc
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223 <!-- Test with Empty Input Files #3 -->
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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224 <test expect_num_outputs="3">
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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225 <param name="input1" value="empty1.fq" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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226 <param name="input2" value="empty2.fq" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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227 <param name="merge_reads" value="true" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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228
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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229 <!-- Section for General Arguments -->
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iuc
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230 <section name="general_options" >
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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231 <param name="quality_cutoff" value="13" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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232 <param name="min_length" value="30" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
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233 </section>
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234
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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235 <!-- Section for Additional Adapter/Primer Trimming Arguments -->
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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236 <section name="trimming_options">
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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237 <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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238 <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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239 <param name="adapter_overlap" value="10" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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240 <param name="max_mismatch_fraction" value="0.02" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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241 <param name="min_match_fraction" value="0.87" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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242 <param name="adapter_bandwidth" value="50" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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243 <param name="gap_open" value="8" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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244 <param name="gap_extend" value="2" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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245 <param name="gap_end" value="2" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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246 <param name="local_alignment_score" value="26" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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247 <param name="read_alignment_bandwidth" value="50" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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248 <param name="read_alignment_gap_open" value="26" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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249 <param name="read_alignment_gap_extend" value="9" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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250 <param name="read_alignment_gap_end" value="5" />
8a0aa44e1e5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep commit 06828a419d1bf8546382b7c687a76b65a577e736
iuc
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251 <param name="read_alignment_max_gap_fraction" value="0.125" />
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252 </section>
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253 <output name="output1" file="empty_output1.fq.gz" />
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254 <output name="output2" file="empty_output2.fq.gz" />
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255 <output name="merged" file="empty_merged_output.fq.gz" />
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256 </test>
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257
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258 <!-- Advanced Functional Tests -->
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259 <!-- General Arguments Test #4 -->
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260 <test expect_num_outputs="2">
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261 <param name="input1" value="input1.fq" />
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262 <param name="input2" value="input2.fq" />
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263 <param name="merge_reads" value="false" />
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264
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265 <param name="quality_cutoff" value="15" />
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266 <param name="min_length" value="25" />
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267 <output name="output1" file="output1_general_args.fq.gz" />
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268 <output name="output2" file="output2_general_args.fq.gz" />
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269 </test>
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270
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271 <!-- Adapter/Primer Trimming Arguements Test #5 -->
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272 <test expect_num_outputs="2">
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273 <param name="input1" value="input1.fq" />
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274 <param name="input2" value="input2.fq" />
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275 <param name="merge_reads" value="false" />
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276 <section name="trimming_options">
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277 <param name="adapter_a" value="ACTGACTG" />
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278 <param name="adapter_b" value="GTGACTGA" />
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279 <param name="adapter_overlap" value="12" />
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280 <param name="max_mismatch_fraction" value="0.03" />
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281 <param name="min_match_fraction" value="0.85" />
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282 <param name="adapter_bandwidth" value="55" />
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283 <param name="gap_open" value="10" />
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284 <param name="gap_extend" value="3" />
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285 <param name="gap_end" value="3" />
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286 <param name="local_alignment_score" value="28" />
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287 </section>
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288 <output name="output1" file="output1_adapter_trim.fq.gz" />
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289 <output name="output2" file="output2_adapter_trim.fq.gz" />
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290 </test>
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291 <!-- Test with gzipped input files #6 -->
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292 <test expect_num_outputs="3">
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293 <param name="input1" value="input1.fastq.gz" />
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294 <param name="input2" value="input2.fastq.gz" />
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295 <param name="merge_reads" value="true" />
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296 <output name="output1" file="output1_from_gzipped.fq.gz" />
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297 <output name="output2" file="output2_from_gzipped.fq.gz" />
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298 <output name="merged" file="merged_output_from_gzipped.fq.gz" />
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299 </test>
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300 </tests>
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301 <help><![CDATA[
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302 **SeqPrep**
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303
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304 SeqPrep is a versatile tool designed for merging overlapping paired-end Illumina reads into a single, longer read. Additionally, it offers the functionality to trim adapter sequences from reads, making it
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305 a needful tool for preprocessing Illumina sequencing data.
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306
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307 **Usage**
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308
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309 To utilize SeqPrep, start by selecting your input FASTQ files: one for the first set of reads and another for the second set. SeqPrep provides several options to customize your data processing:
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310
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311 - **Adapter Sequences:** You can provide specific sequences for adapter trimming if they are known. SeqPrep will remove these sequences from the reads.
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312 - **Quality Score Cutoff:** Set a threshold for the quality score. Reads with quality scores below this threshold can be discarded or trimmed.
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313 - **Minimum Read Length:** Define the minimum length for reads to be retained after trimming. Reads shorter than this length will be discarded.
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314
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315 If the merging feature is enabled, SeqPrep will combine overlapping reads into longer sequences, thereby enhancing the data quality for downstream analysis.
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316
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317 **Outputs**
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318
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319 SeqPrep generates outputs in gzipped FASTQ format.
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320
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321 See more details on SeqPrep github repository: https://github.com/jstjohn/SeqPrep
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322
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323 ]]></help>
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324 <expand macro="citations"/>
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325 </tool>