Mercurial > repos > iuc > obi_ngsfilter

annotate ngsfilter.xml @ 5:983c8c46184f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
author iuc
date Thu, 30 Oct 2025 16:02:48 +0000
parents d46e95113e9e
children
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1 <tool id="obi_ngsfilter" name="NGSfilter" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
5
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6 <expand macro="bio_tools"/>
4
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
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10 @GUNZIP_INPUT@
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12 ngsfilter
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13
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14 --without-progress-bar
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15 -t '$inputextrafile'
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16 #if $bool
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17 -u unident
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18 #end if
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19 -e '$mismatch'
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20 @INPUT_FORMAT@
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21 @OUT_FORMAT@
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22 input
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23 @GZIP_OUTPUT@
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24 > '$output'
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25
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26 #if $bool
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27 #if $input.ext.endswith(".gz")
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28 && gzip -c unident > '$unident'
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29 #else
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30 && mv unident '$unident'
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31 #end if
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32 #set outputs = [("output", $output), ("unident", $unident)]
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33 #end if
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34 @GENERATE_GALAXY_JSON@
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35 ]]></command>
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36 <inputs>
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37 <param name="inputextrafile" type="data" format="tabular" label="Parameter file" help="extrafile describing the DNA tags and primers sequences used for each sample"/>
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38 <param name="input" type="data" format="@INPUT_FORMATS@" label="Read from file" help="file of Illumina pair-end reads assembled by illuminapairedend"/>
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39 <param name="mismatch" type="integer" value="2" label="Number of errors allowed for matching primers (default = 2)"/>
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40 <param name="bool" type="boolean" checked="true" label="Do you want to generate a file with unidentified sequences?"/>
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41 <expand macro="input_format_options_macro"/>
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42 <expand macro="out_format_macro"/>
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43 </inputs>
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44 <outputs>
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45 <data name="unident" format="auto" label="${tool.name} on ${on_string}: Unassigned sequences">
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46 <filter>bool is True</filter>
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47 </data>
5
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48 <data name="output" format="auto" label="${tool.name} on ${on_string}: Trimmed and annotated"/>
4
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49 </outputs>
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50 <tests>
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51 <test expect_num_outputs="1">
4
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52 <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />
5
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53 <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsanger"/>
4
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54 <param name="mismatch" value="2" />
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55 <param name="bool" value="False" />
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56 <output name="output" file="output_ngsfilter.fastq" ftype="fastqsanger"/>
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57 </test>
5
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58 <test expect_num_outputs="2">
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59 <param name="inputextrafile" value="input_ngsfilter_extrafile.txt"/>
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60 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz"/>
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61 <param name="mismatch" value="3"/>
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62 <param name="bool" value="True"/>
4
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63 <output name="output" file="output_ngsfilter_error_3.fastq" ftype="fastqsanger.gz" decompress="true"/>
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64 <output name="unident" file="output_ngsfilter_unidentified.fastq" ftype="fastqsanger.gz" decompress="true"/>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68
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69 .. class:: infomark
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70
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71 **What it does**
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72
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73 A DNA metabarcoding experiment can be considered as a set a PCR products mixed together and sequenced using a next generation sequencer ({i.e.} a solexa or a 454).
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74 To distinguish between this different PCR products, pairs of small DNA sequences (call tags, see the oligoTag command and its associated paper for more
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75 informations on the design of such tags) unique for each PCR products are concatenated to the PCR primers.
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76 As they are amplified during the PCR, these tags should be recognizable, together with their respective primers, at the beginning and the end of the reads.
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77 The first step in data analysis is thus to demultiplex the large resulting sequence file by identifying these DNA tags and the primers.
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78
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79 Usually the results of sequencing are stored in one or more files formatted according to the fasta or fastq format. ngsfilter take as input such sequence file and an extra file describing the DNA tags and primers sequences used for each sample.
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80
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81 The results consist of sequences trimmed of the primers and tags and annotated with the corresponding sample (and possibly some extra informations).
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82 Sequences for which the tags and primers have not been well identified, and which are thus unassigned to any sample, are tagged as erroneous sequences
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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83 by ngsfilter. Such erroneous sequences are not reported by the program unless specified by the appropriate option.
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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84
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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85 --------
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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86
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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87 **Help**
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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88 Extrafile format:
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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89
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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90 a tab delimited tabular file with 8 columns.
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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91
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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92 experiment_name sample_name oligo_tag(s) forward_primer reverse_primer F @ extra_information
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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93
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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94 ex:
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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95
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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96 laos_gh LA01E1a agcgacta:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01A;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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97
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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98 laos_gh LA01E1b tcagtgtc:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01B;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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99
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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100 laos_gh LA01E2a actctgct:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01C;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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101
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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102 laos_gh LA01E2b atatagcg:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01D;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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103
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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104 laos_gh LA01P1a ctatgcta:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01E;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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105
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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106 laos_gh LA01P1b tcgcgctg:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01F;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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107
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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108 laos_gh LA01P2a agcacagt:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01G;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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109
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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110 laos_gh LA01P2b tagctagt:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01H;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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111
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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112 laos_gh LA02E1a agcgacta:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02A;
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113
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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114 laos_gh LA02E1b tcagtgtc:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02B;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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115
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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116 laos_gh LA02E2a actctgct:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02C;
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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117
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118 @OBITOOLS_LINK@
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119
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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120
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121 ]]>
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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122
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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123 </help>
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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124 <expand macro="citation" />
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125
d46e95113e9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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126 </tool>