Mercurial > repos > iuc > seqtk

annotate seqtk_mergepe.xml @ 5:a09586d5149a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
author iuc
date Fri, 11 Jan 2019 05:15:20 -0500
parents ecf1c30da3a2
children 58c8ece95b53
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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 <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 seqtk mergepe
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11 '$in_fq1'
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12 '$in_fq2'
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13 #echo "| pigz --no-name --no-time" if $in_fq1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
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14 ]]></command>
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15 <inputs>
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16 <param name="in_fq1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
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17 <param name="in_fq2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
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18 </inputs>
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19 <outputs>
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20 <data name="default" format_source="in_fq1" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
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21 </outputs>
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22 <tests>
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23 <test>
4
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24 <param name="in_fq1" value="paired_dat1.fq" ftype="fastqsanger"/>
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25 <param name="in_fq2" value="paired_dat2.fq" ftype="fastqsanger"/>
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26 <output name="default" file="paired_dat.fq" ftype="fastqsanger"/>
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27 </test>
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28 <test>
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29 <param name="in_fq1" value="paired_dat1.fq.gz" ftype="fastqsanger.gz"/>
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30 <param name="in_fq2" value="paired_dat2.fq.gz" ftype="fastqsanger.gz"/>
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31 <output name="default" file="paired_dat.fq.gz" ftype="fastqsanger.gz"/>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 **What it does**
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36
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37 Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file
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38
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39 ::
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40
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41 # r1.fq
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42 @test-6/1
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43 AGCTTGACGC
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44 +
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45 ?.HCF@C>>F
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46
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47 # r2.fq
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48 @test-6/2
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49 TGCGAAGACC
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50 +
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51 >2?A?A@@7?
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52
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53 will produce the following paired file:
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54
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55 ::
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56
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57 @test-6/1
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58 AGCTTGACGC
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59 +
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60 ?.HCF@C>>F
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61 @test-6/2
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62 TGCGAAGACC
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63 +
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64 >2?A?A@@7?
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65
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66 While this may not have been an illuminating example, it is important to note
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67 that this tool will properly interleave data. For example if you have the ids:
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68
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69 ::
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70
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71 @r-1/1
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72 @r-2/1
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73 @r-3/1
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74 @r-4/1
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75
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76 and
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77
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78 ::
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79
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80 @r-1/2
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81 @r-2/2
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82 @r-3/2
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83 @r-4/2
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84
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85 These will be interleaved as
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86
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87 ::
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88
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89 @r-1/1
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90 @r-1/2
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91 @r-2/1
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92 @r-2/2
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93 @r-3/1
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94 @r-3/2
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95 @r-4/1
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96 @r-4/2
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98 @ATTRIBUTION@
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99 ]]></help>
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100 <expand macro="citation" />
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101 </tool>