Mercurial > repos > iuc > seqtk

annotate seqtk_dropse.xml @ 16:48a51c72f5e7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:58:58 -0400
parents 16f2535c08bf
children 069c8f0695ee
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_dropse" name="seqtk_dropse" version="@WRAPPER_VERSION@.0">
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3 <description>drop unpaired from interleaved Paired End FASTA/Q</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 dropse
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11 '$in_file'
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12 @CONDITIONAL_GZIP_OUT@
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13 ]]></command>
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14 <inputs>
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15 <expand macro="in_faq"/>
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16 </inputs>
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17 <outputs>
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18 <data name="default" format_source="in_file" label="Only paired-end reads from $in_file.name"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="in_file" value="seqtk_dropse.fq" ftype="fastqsanger"/>
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23 <output name="default" file="seqtk_dropse.out" ftype="fastqsanger"/>
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24 </test>
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25 <test>
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26 <param name="in_file" value="seqtk_dropse.fq.gz" ftype="fastqsanger.gz"/>
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27 <output name="default" file="seqtk_dropse.out.gz" ftype="fastqsanger.gz"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31 **What it does**
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32
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33 Remove unpaired reads in an interleaved paired-end FASTA/Q file. Given a fastq file with unpaired reads:
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34
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35 ::
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36
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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 @test-6/2
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42 TGCGAAGACC
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43 +
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44 >2?A?A@@7?
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45 @test-4/1
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46 CTTGACGCTG
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47 +
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48 I@>3EFCG@C
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49 @test-2/1
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50 AGACCAAAAT
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51 +
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52 ??><6E?IFC
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53 @test-2/2
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54 CTGGCGAATT
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55 +
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56 ?=?*?A?<?@
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57
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58 This tool will remove the offending reads (test-4/1), leaving just the paired data.
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59
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60 ::
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61
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62 @test-6/1
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63 AGCTTGACGC
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64 +
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65 ?.HCF@C>>F
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66 @test-6/2
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67 TGCGAAGACC
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68 +
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69 >2?A?A@@7?
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70 @test-2/1
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71 AGACCAAAAT
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72 +
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73 ??><6E?IFC
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74 @test-2/2
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75 CTGGCGAATT
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76 +
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77 ?=?*?A?<?@
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78
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79 @ATTRIBUTION@
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80 ]]></help>
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81 <expand macro="citation" />
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82 </tool>