Mercurial > repos > iuc > seqtk

annotate seqtk_mergepe.xml @ 8:3da72230c066 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"
author iuc
date Thu, 14 Oct 2021 09:22:39 +0000
parents 58c8ece95b53
children 4b494533146a
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_mergepe" name="seqtk_mergepe" version="@TOOL_VERSION@.1">
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3 <description>interleave two unpaired FASTA/Q files for a paired-end file</description>
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4 <expand macro="bio_tools"/>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 seqtk mergepe
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12 '$in_fq1'
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13 '$in_fq2'
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14 #echo "| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time" if $in_fq1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
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15 ]]></command>
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16 <inputs>
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17 <param name="in_fq1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
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18 <param name="in_fq2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
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19 </inputs>
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20 <outputs>
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21 <data name="default" format_source="in_fq1" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
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22 </outputs>
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23 <tests>
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24 <test>
4
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25 <param name="in_fq1" value="paired_dat1.fq" ftype="fastqsanger"/>
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26 <param name="in_fq2" value="paired_dat2.fq" ftype="fastqsanger"/>
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27 <output name="default" file="paired_dat.fq" ftype="fastqsanger"/>
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28 </test>
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29 <test>
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30 <param name="in_fq1" value="paired_dat1.fq.gz" ftype="fastqsanger.gz"/>
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31 <param name="in_fq2" value="paired_dat2.fq.gz" ftype="fastqsanger.gz"/>
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32 <output name="default" file="paired_dat.fq.gz" ftype="fastqsanger.gz"/>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 **What it does**
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37
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38 Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file
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39
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40 ::
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41
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42 # r1.fq
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43 @test-6/1
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44 AGCTTGACGC
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45 +
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46 ?.HCF@C>>F
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47
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48 # r2.fq
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49 @test-6/2
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50 TGCGAAGACC
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51 +
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52 >2?A?A@@7?
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53
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54 will produce the following paired file:
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55
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56 ::
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57
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58 @test-6/1
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59 AGCTTGACGC
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60 +
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61 ?.HCF@C>>F
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62 @test-6/2
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63 TGCGAAGACC
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64 +
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65 >2?A?A@@7?
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66
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67 While this may not have been an illuminating example, it is important to note
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68 that this tool will properly interleave data. For example if you have the ids:
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69
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70 ::
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71
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72 @r-1/1
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73 @r-2/1
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74 @r-3/1
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75 @r-4/1
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77 and
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79 ::
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80
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81 @r-1/2
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82 @r-2/2
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83 @r-3/2
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84 @r-4/2
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85
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86 These will be interleaved as
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88 ::
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89
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90 @r-1/1
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91 @r-1/2
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92 @r-2/1
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99 @ATTRIBUTION@
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100 ]]></help>
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101 <expand macro="citation" />
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102 </tool>