Mercurial > repos > iuc > seqtk

annotate seqtk_dropse.xml @ 20:8f26884c60b6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:36:24 +0000
parents 069c8f0695ee
children f2a792351212
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_dropse" name="seqtk_dropse" version="@TOOL_VERSION@.1">
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3 <description>drop unpaired from interleaved Paired End FASTA/Q</description>
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8f26884c60b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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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 dropse
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12 '$in_file'
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13 @CONDITIONAL_GZIP_OUT@
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14 ]]></command>
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15 <inputs>
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16 <expand macro="in_faq"/>
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17 </inputs>
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18 <outputs>
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19 <data name="default" format_source="in_file" label="Only paired-end reads from $in_file.name"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="in_file" value="seqtk_dropse.fq" ftype="fastqsanger"/>
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24 <output name="default" file="seqtk_dropse.out" ftype="fastqsanger"/>
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25 </test>
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26 <test>
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27 <param name="in_file" value="seqtk_dropse.fq.gz" ftype="fastqsanger.gz"/>
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28 <output name="default" file="seqtk_dropse.out.gz" ftype="fastqsanger.gz"/>
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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32 **What it does**
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33
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34 Remove unpaired reads in an interleaved paired-end FASTA/Q file. Given a fastq file with unpaired reads:
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35
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36 ::
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37
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38 @test-6/1
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39 AGCTTGACGC
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40 +
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41 ?.HCF@C>>F
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42 @test-6/2
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43 TGCGAAGACC
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44 +
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45 >2?A?A@@7?
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46 @test-4/1
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47 CTTGACGCTG
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48 +
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49 I@>3EFCG@C
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50 @test-2/1
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51 AGACCAAAAT
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52 +
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53 ??><6E?IFC
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54 @test-2/2
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55 CTGGCGAATT
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56 +
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57 ?=?*?A?<?@
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58
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59 This tool will remove the offending reads (test-4/1), leaving just the paired data.
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60
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61 ::
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62
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63 @test-6/1
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64 AGCTTGACGC
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65 +
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66 ?.HCF@C>>F
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67 @test-6/2
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68 TGCGAAGACC
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69 +
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70 >2?A?A@@7?
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71 @test-2/1
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72 AGACCAAAAT
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73 +
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74 ??><6E?IFC
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75 @test-2/2
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76 CTGGCGAATT
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77 +
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78 ?=?*?A?<?@
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79
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80 @ATTRIBUTION@
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81 ]]></help>
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82 <expand macro="citation" />
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83 </tool>