Mercurial > repos > iuc > seqtk

annotate seqtk_mergepe.xml @ 3:bc7d99f46a5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_mergepe" name="seqtk_mergepe" version="@WRAPPER_VERSION@.0">
3
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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>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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6 </macros>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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7 <expand macro="requirements"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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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 > '$default'
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14 ]]></command>
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15 <inputs>
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16 <param name="in_fq1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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17 <param name="in_fq2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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18 </inputs>
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19 <outputs>
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20 <data name="default" format_source="in_fq1" label="$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>
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24 <param name="in_fq1" value="paired_dat1.fq"/>
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25 <param name="in_fq2" value="paired_dat2.fq"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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26 <output name="default" file="paired_dat.fq" ftype="fastq"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 **What it does**
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31
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32 Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file
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33
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34 ::
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35
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36 # r1.fq
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37 @test-6/1
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38 AGCTTGACGC
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39 +
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40 ?.HCF@C>>F
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41
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42 # r2.fq
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43 @test-6/2
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44 TGCGAAGACC
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45 +
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46 >2?A?A@@7?
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47
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48 will produce the following paired file:
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49
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50 ::
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51
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52 @test-6/1
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53 AGCTTGACGC
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54 +
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55 ?.HCF@C>>F
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56 @test-6/2
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57 TGCGAAGACC
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58 +
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59 >2?A?A@@7?
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60
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61 While this may not have been an illuminating example, it is important to note
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62 that this tool will properly interleave data. For example if you have the ids:
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63
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64 ::
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65
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66 @r-1/1
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67 @r-2/1
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68 @r-3/1
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69 @r-4/1
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70
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71 and
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72
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73 ::
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74
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75 @r-1/2
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76 @r-2/2
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77 @r-3/2
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78 @r-4/2
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79
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80 These will be interleaved as
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81
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82 ::
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83
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84 @r-1/1
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85 @r-1/2
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86 @r-2/1
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87 @r-2/2
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88 @r-3/1
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89 @r-3/2
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90 @r-4/1
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91 @r-4/2
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92
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93 @ATTRIBUTION@
3
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94 ]]></help>
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95 <expand macro="citation" />
0
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96 </tool>