Mercurial > repos > jdv > porechop

annotate porechop.xml @ 3:80408ff0c1f5 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
author jdv
date Sat, 14 Oct 2017 22:23:22 -0400
parents f84a33bc5c3e
children 40232a4e5a04
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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1 <tool id="porechop" name="Porechop" version="0.2.1">
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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3 <description>Demux and adapter removal</description>
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5 <!-- ***************************************************************** -->
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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7 <!-- not yet working with Bioconda
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8 <requirements>
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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9 <requirement type="package" version="0.2.1">porechop</requirement>
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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10 </requirements>
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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11 -->
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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13 <!-- ***************************************************************** -->
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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15 <version_command>porechop --version</version_command>
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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17 <!-- ***************************************************************** -->
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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19 <command detect_errors="aggressive">
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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20 <![CDATA[
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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22 #set filename = str($input.name)
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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24 mkdir out &&
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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26 porechop
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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28 --input ${input}
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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2
f84a33bc5c3e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 19e515145381f7a8b16662e33678df7087019f19
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30 --format ${out_format}
f84a33bc5c3e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 19e515145381f7a8b16662e33678df7087019f19
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31
0
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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32 #if str($demux_section.demux_options.demux) == "yes":
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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33 --barcode_dir out
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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34 #else:
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35 --output "out/$filename"
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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36 #end if
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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38 ##if $input.is_of_type('fastq')
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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39 --format fastq
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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40 ##else:
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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41 ##--format fasta
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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42 ##end if
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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44 --threads \${GALAXY_SLOTS:-1}
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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46 ##--Demultiplex Options--------------------------
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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48 #if str($demux_section.demux_options.demux) == "yes":
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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50 --barcode_threshold $demux_section.demux_options.barcode_threshold
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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51 --barcode_diff $demux_section.demux_options.barcode_diff
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52 $demux_section.demux_options.require_two_barcodes
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54 #end if
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56 ##--Adapter Trim Options--------------------------
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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58 #if str($trim_section.trim_options.trim) == "yes":
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60 --adapter_threshold $trim_section.trim_options.adapter_threshold
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61 --check_reads $trim_section.trim_options.check_reads
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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62 --scoring_scheme $trim_section.trim_options.scoring_scheme
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64 --end_size $trim_section.trim_options.end_size
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65 --end_threshold $trim_section.trim_options.end_threshold
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66 --min_trim_size $trim_section.trim_options.min_trim_size
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67 --extra_end_trim $trim_section.trim_options.extra_end_trim
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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69 $trim_section.trim_options.discard_middle
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70 --middle_threshold $trim_section.trim_options.middle_threshold
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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71 --extra_middle_trim_good_side $trim_section.trim_options.extra_middle_trim_good_side
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72 --extra_middle_trim_bad_side $trim_section.trim_options.extra_middle_trim_bad_side
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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73 --min_split_read_size $trim_section.trim_options.min_split_read_size
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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76 #else:
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77 --untrimmed
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79 #end if
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80
3
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81 | perl $__tool_directory__/porechop_summarize.pl
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82 > $result_table
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
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83
0
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84 ]]>
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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85 </command>
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87 <!-- ***************************************************************** -->
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88
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89 <inputs>
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90
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91 <param argument="--input" type="data" format="fastq,fasta" label="Input reads" />
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92
2
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93 <param name="out_format" type="select" label="Output format">
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94 <option value="fastq" selected="true">fastq</option>
f84a33bc5c3e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 19e515145381f7a8b16662e33678df7087019f19
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95 <option value="fasta">fasta</option>
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96 </param>
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97
0
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98 <section name="demux_section" title="Demultiplexing Options" expanded="True">
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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99 <conditional name="demux_options">
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100 <param name="demux" type="select" label="Perform demultiplexing" help="">
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101 <option value="no" selected="true">no</option>
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102 <option value="yes">yes</option>
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103 </param>
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104 <when value="no" />
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105 <when value="yes">
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106 <param argument="--barcode_threshold" size="5" type="float" value="75.0" min="0" max="100" label="Barcode threshold identity" />
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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107 <param argument="--barcode_diff" size="5" type="float" value="5.0" min="0" max="100" label="Barcode threshold difference" />
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108 <param argument="--require_two_barcodes" type="boolean" truevalue="--require_two_barcodes" falsevalue="" checked="false" label="Require two barcodes" />
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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109 </when>
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110 </conditional>
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111 </section>
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112
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113 <section name="trim_section" title="Trimming Options" expanded="True">
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114 <conditional name="trim_options">
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115 <param name="trim" type="select" label="Perform adapter trimming" help="">
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116 <option value="no" selected="true">no</option>
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117 <option value="yes">yes</option>
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118 </param>
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119 <when value="no" />
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120 <when value="yes">
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121 <param argument="--adapter_threshold" size="4" type="float" value="90.0" min="0" max="100" label="Adapter set threshold identity" />
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122 <param argument="--check_reads" size="7" type="integer" value="10000" label="Number of reads to check to determine adapter sets" />
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123 <param argument="--barcode_diff" size="4" type="float" value="5.0" min="0" max="100" label="Barcode threshold difference" />
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124 <param argument="--scoring_scheme" type="text" value="3,-6,-5,-2" label="Scoring scheme" />
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125 <param argument="--end_size" size="4" type="integer" value="150" label="Number of terminal bases to search" />
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126 <param argument="--min_trim_size" size="4" type="integer" value="4" label="Minimum adapter match length" />
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127 <param argument="--extra_end_trim" size="4" type="integer" value="2" label="Adjacent bases to trim " />
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128 <param argument="--end_threshold" size="4" type="float" value="75.0" min="0" max="100" label="End adapter trim threshold identity" />
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129
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130 <param argument="--discard_middle" type="boolean" truevalue="--discard_middle" falsevalue="" checked="false" label="Discard reads with middle adapters" />
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131 <param argument="--middle_threshold" size="4" type="float" value="85.0" min="0" max="100" label="Middle adapter trim threshold identity" />
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132 <param argument="--extra_middle_trim_good_side" size="4" type="integer" value="10" label="Adjacent bases to trim on good side" />
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133 <param argument="--extra_middle_trim_bad_side" size="4" type="integer" value="100" label="Adjacent bases to trim on bad side" />
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134 <param argument="--min_split_read_size" size="4" type="integer" value="1000" label="Minimum length of split reads to keep" />
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135 </when>
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136 </conditional>
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137 </section>
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138
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139 </inputs>
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140
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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141 <!-- ***************************************************************** -->
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142
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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143 <outputs>
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144
2
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145 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}">
f84a33bc5c3e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 19e515145381f7a8b16662e33678df7087019f19
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146 <filter>out_format == 'fastq'</filter>
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147 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fastqsanger" />
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148 </collection>
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149 <collection type="list" name="output_collection_fasta" label="${tool.name} on ${on_string}">
f84a33bc5c3e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 19e515145381f7a8b16662e33678df7087019f19
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150 <filter>out_format == 'fasta'</filter>
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151 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fasta" />
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152 </collection>
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153
3
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
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154 <data format="table" name="result_table" label="${tool.name} on ${on_string} (summary)" />
0
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155 </outputs>
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156
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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157 <!-- ***************************************************************** -->
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158
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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159 <tests>
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160 <test>
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161 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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162 <param name="demux" value="yes" />
2
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163 <output_collection name="output_collection_fastq" type="list">
0
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164 <element name="BC01.fastq" file="bar1/BC01.fastq" compare="diff" decompress="true"/>
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165 <element name="BC02.fastq" file="bar1/BC02.fastq" compare="diff" decompress="true"/>
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166 <element name="BC03.fastq" file="bar1/BC03.fastq" compare="diff" decompress="true"/>
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167 <element name="none.fastq" file="bar1/none.fastq" compare="diff" decompress="true"/>
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168 </output_collection>
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169 </test>
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170 <test>
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171 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
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172 <param name="demux" value="yes" />
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173 <param name="require_two_barcodes" value="True" />
2
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174 <output_collection name="output_collection_fastq" type="list">
0
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175 <element name="BC01.fastq" file="bar2/BC01.fastq" compare="diff" decompress="true"/>
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176 <element name="BC02.fastq" file="bar2/BC02.fastq" compare="diff" decompress="true"/>
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177 <element name="BC03.fastq" file="bar2/BC03.fastq" compare="diff" decompress="true"/>
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178 <element name="none.fastq" file="bar2/none.fastq" compare="diff" decompress="true"/>
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179 </output_collection>
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180 </test>
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181 <test>
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182 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
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183 <param name="demux" value="yes" />
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184 <param name="trim" value="yes" />
2
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185 <output_collection name="output_collection_fastq" type="list">
0
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186 <element name="BC01.fastq" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/>
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187 <element name="BC02.fastq" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/>
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188 <element name="BC03.fastq" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>
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189 <element name="none.fastq" file="bar1_trim/none.fastq" compare="diff" decompress="true"/>
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190 </output_collection>
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191 </test>
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192 </tests>
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193
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194 <!-- ***************************************************************** -->
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195
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196 <help>
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197 <![CDATA[
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198
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199 **Description**
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200
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201 Porechop is a tool for finding and removing adapters from Oxford Nanopore
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202 reads. Adapters on the ends of reads are trimmed off, and when a read has an
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203 adapter in its middle, it is treated as chimeric and chopped into separate
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204 reads. Porechop performs thorough alignments to effectively find adapters,
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205 even at low sequence identity.
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206
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207 Porechop also supports demultiplexing of Nanopore reads that were barcoded
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208 with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.
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209
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210 **Options**
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211 ::
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212
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213 *** Barcode binning settings ***
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214
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215 -b BARCODE_DIR, --barcode_dir BARCODE_DIR
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216 Reads will be binned based on their barcode and saved to separate
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217 files in this directory (incompatible with --output)
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218 --barcode_threshold BARCODE_THRESHOLD
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219 A read must have at least this percent identity to a barcode to be
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220 binned (default: 75.0)
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221 --barcode_diff BARCODE_DIFF If the difference between a read's best barcode identity and its
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222 second-best barcode identity is less than this value, it will not be
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223 put in a barcode bin (to exclude cases which are too close to call)
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224 (default: 5.0)
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225 --require_two_barcodes Reads will only be put in barcode bins if they have a strong match for
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226 the barcode on both their start and end (default: a read can be binned
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227 with a match at its start or end)
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228 --untrimmed Bin reads but do not trim the ends (appropriate if reads are to be
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229 used with Nanopolish) (default: False)
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230
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231 *** Adapter search settings ***
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232
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233 --adapter_threshold ADAPTER_THRESHOLD
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234 An adapter set has to have at least this percent identity to be
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235 labelled as present and trimmed off (0 to 100) (default: 90.0)
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236 --check_reads CHECK_READS This many reads will be aligned to all possible adapters to determine
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237 which adapter sets are present (default: 10000)
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238 --scoring_scheme SCORING_SCHEME Comma-delimited string of alignment scores: match,mismatch, gap open,
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239 gap extend (default: 3,-6,-5,-2)
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240
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241 *** End adapter settings ***
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242
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243 --end_size END_SIZE The number of base pairs at each end of the read which will be
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244 searched for adapter sequences (default: 150)
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245 --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ignored (default: 4)
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246 --extra_end_trim EXTRA_END_TRIM This many additional bases will be removed next to adapters found at
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247 the ends of reads (default: 2)
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248 --end_threshold END_THRESHOLD Adapters at the ends of reads must have at least this percent identity
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249 to be removed (0 to 100) (default: 75.0)
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250
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251 *** Middle adapter settings ***
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252
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253 --discard_middle Reads with middle adapters will be discarded (default: reads with
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254 middle adapters are split) (this option is on by default when
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255 outputting reads into barcode bins)
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256 --middle_threshold MIDDLE_THRESHOLD
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257 Adapters in the middle of reads must have at least this percent
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258 identity to be found (0 to 100) (default: 85.0)
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259 --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE
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260 This many additional bases will be removed next to middle adapters on
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261 their "good" side (default: 10)
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262 --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE
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263 This many additional bases will be removed next to middle adapters on
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264 their "bad" side (default: 100)
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265 --min_split_read_size MIN_SPLIT_READ_SIZE
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266 Post-split read pieces smaller than this many base pairs will not be
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267 outputted (default: 1000)
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268
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269
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270 ]]>
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271 </help>
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272
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273 <!-- ***************************************************************** -->
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274
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275 <citations>
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276 </citations>
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277
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278 </tool>