Mercurial > repos > iuc > obi_illumina_pairend

annotate illuminapairedend.xml @ 4:8cb6bd511879 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:17:09 +0000
parents 83fbdf93d51e
children
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4
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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1 <tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>Construct consensus reads from Illumina pair-end reads</description>
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iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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5 </macros>
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iuc
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6 <expand macro="bio_tools"/>
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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9 <command>
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10 <![CDATA[
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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11 #if $inputfastq3p.ext.endswith(".gz")
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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12 gunzip -c '$inputfastq3p' > fastq3p.fastq &&
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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13 gunzip -c '$inputfastq5p' > fastq5p.fastq &&
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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14 #else
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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15 ln -s '$inputfastq3p' fastq3p.fastq &&
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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16 ln -s '$inputfastq5p' fastq5p.fastq &&
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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17 #end if
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18
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19 illuminapairedend
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20 ##--index-file=
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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21 #if $inputfastq3p.ext.startswith("fastqsolexa")
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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22 ##input file is in fastq nucleic format produced by solexa sequencer
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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23 --solexa
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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24 #else if $inputfastq3p.ext.startswith("fastqillumina")
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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25 ##input file is in fastq nucleic format produced by solexa sequencer
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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26 --illumina
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27 #else
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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28 ## input file is in sanger fastq nucleic format (standard fastq)
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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29 --sanger
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30 #end if
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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31 --without-progress-bar
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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32 --score-min='$score'
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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33 -r fastq3p.fastq
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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34 fastq5p.fastq
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35 #if $inputfastq3p.ext.endswith(".gz")
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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36 | gzip -c
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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37 #end if
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38 > '$output'
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39 ]]>
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40 </command>
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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41 <inputs>
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42 <param name="inputfastq3p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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43 <param name="inputfastq5p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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44 <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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45 </inputs>
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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46 <outputs>
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47 <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" />
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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48 </outputs>
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49
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50 <tests>
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51 <test expect_num_outputs="1">
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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52 <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" />
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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53 <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" />
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54 <param name="score" value="40.0" />
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55 <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" />
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56 </test>
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57 <test expect_num_outputs="1">
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58 <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" />
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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59 <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" />
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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60 <param name="score" value="40.0" />
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61 <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
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62 </test>
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63 </tests>
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64
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65 <help><![CDATA[
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66
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67 .. class:: warning
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68
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69 **Warning:**
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70 Sequence records corresponding to the same read pair must be in the same order in the two files
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71
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72 --------
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73
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74 .. class:: infomark
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75
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76 **What it does**
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77
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78 illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform :
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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79
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80 \* If the two reads overlap, it returns the consensus sequence together with its quality
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81 \* Otherwise, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
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82
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83 The program uses as input one or two fastq sequences reads files.
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84
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85 \* If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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86 \* If just one file is provided, sequence records are supposed to be all of the same length. The first half of th e sequence is used as forward read, the second half is used as the reverse read.
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87
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88 illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.
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89
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90 @OBITOOLS_LINK@
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91
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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92 ]]>
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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93 </help>
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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94 <expand macro="citation" />
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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96 </tool>
8cb6bd511879 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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97