Mercurial > repos > iuc > obi_annotate

annotate ngsfilter.xml.orig @ 4:d0f6ac976373 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:49:38 +0000
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4
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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1 <<<<<<< HEAD
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <tool id="obi_ngsfilter" name="NGSfilter" version="@TOOL_VERSION@" profile="@PROFILE@">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <description>Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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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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11
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12 ngsfilter
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13
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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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", $unident)]
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33 #end if
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34 @GENERATE_GALAXY_JSON@
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35 ]]></command>
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36 <inputs>
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37 <param name="inputextrafile" type="data" format="tabular" label="Parameter file" help="extrafile describing the DNA tags and primers sequences used for each sample" />
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38 <param name="input" type="data" format="@INPUT_FORMATS@" label="Read from file" help="file of Illumina pair-end reads assembled by illuminapairedend" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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39 <param name="mismatch" type="integer" value="2" label="Number of errors allowed for matching primers (default = 2)" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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40 <param name="bool" type="boolean" checked="true" label="Do you want to generate a file with unidentified sequences?" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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41 <expand macro="input_format_options_macro"/>
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42 <expand macro="out_format_macro"/>
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43 </inputs>
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44 <outputs>
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45 <data name="unident" format="auto" label="${tool.name} on ${on_string}: Unassigned sequences">
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46 <filter>bool is True</filter>
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47 </data>
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48 <data name="output" format="auto" label="${tool.name} on ${on_string}: Trimmed and annotated" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />
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53 <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsanger" />
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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>
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58 <test>
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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" />
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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.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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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
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83 by ngsfilter. Such erroneous sequences are not reported by the program unless specified by the appropriate option.
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84
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
85 --------
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
86
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
87 **Help**
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
88 Extrafile format:
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
89
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
90 a tab delimited tabular file with 8 columns.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
91
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
92 experiment_name sample_name oligo_tag(s) forward_primer reverse_primer F @ extra_information
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
93
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
94 ex:
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
95
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
96 laos_gh LA01E1a agcgacta:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01A;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
97
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
98 laos_gh LA01E1b tcagtgtc:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01B;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
99
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
100 laos_gh LA01E2a actctgct:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01C;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
101
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
102 laos_gh LA01E2b atatagcg:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01D;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
103
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
104 laos_gh LA01P1a ctatgcta:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01E;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
105
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
106 laos_gh LA01P1b tcgcgctg:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01F;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
107
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
108 laos_gh LA01P2a agcacagt:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01G;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
109
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
110 laos_gh LA01P2b tagctagt:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01H;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
111
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
112 laos_gh LA02E1a agcgacta:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02A;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
113
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
114 laos_gh LA02E1b tcagtgtc:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02B;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
115
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
116 laos_gh LA02E2a actctgct:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02C;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
117
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
118 @OBITOOLS_LINK@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
119
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
120
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
121 ]]>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
122
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
123 </help>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
124 <expand macro="citation" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
125
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
126 </tool>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
127 =======
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
128 <tool id="obi_ngsfilter" name="NGSfilter" version="@TOOL_VERSION@">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
129 <description>Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers</description>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
130 <expand macro="bio_tools"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
131 <macros>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
132 <import>macros.xml</import>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
133 </macros>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
134 <expand macro="requirements"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
135 <expand macro="stdio"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
136 <command>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
137 <![CDATA[
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
138
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
139 ngsfilter
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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140 -t '$inputextrafile' '$inputfastq'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
141 #if $bool
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
142 -u '$unident'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
143 #end if
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
144 -e '$mismatch' > '$output'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
145
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
146 ]]>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
147
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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148 </command>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
149
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
150 <inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
151 <param name="inputextrafile" type="data" format="tabular" label="Parameter file" help="extrafile describing the DNA tags and primers sequences used for each sample" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
152 <param name="inputfastq" type="data" format="fastq" label="Read from file" help="file of Illumina pair-end reads assembled by illuminapairedend" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
153 <param name="mismatch" type="integer" value="2" label="Number of errors allowed for matching primers (default = 2)" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
154 <param name="bool" type="boolean" checked="true" label="Do you want to generate a file with unidentified sequences?" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
155 </inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
156 <outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
157 <data format="fastq" name="unident" label="unidentified.fastq with ${tool.name} on ${on_string}">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
158 <filter>bool is True</filter>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
159 </data>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
160 <data format="fastq" name="output" label="${tool.name} on ${on_string}: Trimmed and annotated" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
161 </outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
162 <tests>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
163 <test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
164 <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
165 <param name="inputfastq" value="illuminapairedend.output.fastq" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
166 <param name="mismatch" value="2" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
167 <param name="bool" value="False" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
168 <output name="output" file="output_ngsfilter.fastq" ftype="fastq"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
169 </test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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170 <test>
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171 <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />
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172 <param name="inputfastq" value="illuminapairedend.output.fastq" />
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173 <param name="mismatch" value="3" />
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174 <param name="bool" value="True" />
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175 <output name="output" file="output_ngsfilter_error_3.fastq" ftype="fastq"/>
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176 <output name="unident" file="output_ngsfilter_unidentified.fastq" ftype="fastq"/>
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177 </test>
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178 </tests>
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179 <help><![CDATA[
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180
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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181 .. class:: infomark
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182
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183 **What it does**
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184
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185 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).
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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186 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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187 informations on the design of such tags) unique for each PCR products are concatenated to the PCR primers.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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188 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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189 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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190
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191 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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192
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193 The results consist of sequences trimmed of the primers and tags and annotated with the corresponding sample (and possibly some extra informations).
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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194 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
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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195 by ngsfilter. Such erroneous sequences are not reported by the program unless specified by the appropriate option.
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196
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197 --------
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198
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199 **Help**
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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200 Extrafile format:
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201
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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202 a tab delimited tabular file with 8 columns.
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203
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204 experiment_name sample_name oligo_tag(s) forward_primer reverse_primer F @ extra_information
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205
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206 ex:
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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207
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208 laos_gh LA01E1a agcgacta:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01A;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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209
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210 laos_gh LA01E1b tcagtgtc:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01B;
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211
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212 laos_gh LA01E2a actctgct:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01C;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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213
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214 laos_gh LA01E2b atatagcg:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01D;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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215
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216 laos_gh LA01P1a ctatgcta:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01E;
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217
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218 laos_gh LA01P1b tcgcgctg:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01F;
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219
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220 laos_gh LA01P2a agcacagt:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01G;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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221
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222 laos_gh LA01P2b tagctagt:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01H;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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223
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224 laos_gh LA02E1a agcgacta:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02A;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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225
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226 laos_gh LA02E1b tcagtgtc:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02B;
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227
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228 laos_gh LA02E2a actctgct:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02C;
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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229
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230 @OBITOOLS_LINK@
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231
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232
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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233 ]]>
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234
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235 </help>
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236 <expand macro="citation" />
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237
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238 </tool>
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239 >>>>>>> 7abad681f (add tools up until P)