Mercurial > repos > iuc > obi_illumina_pairend

annotate illuminapairedend.xml @ 3:83fbdf93d51e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author iuc
date Mon, 10 May 2021 19:36:09 +0000
parents 0c9296704212
children 8cb6bd511879
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83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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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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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command>
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9 <![CDATA[
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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10 #if $inputfastq3p.ext.endswith(".gz")
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11 gunzip -c '$inputfastq3p' > fastq3p.fastq &&
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12 gunzip -c '$inputfastq5p' > fastq5p.fastq &&
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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13 #else
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14 ln -s '$inputfastq3p' fastq3p.fastq &&
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15 ln -s '$inputfastq5p' fastq5p.fastq &&
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16 #end if
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17
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18 illuminapairedend
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19 ##--index-file=
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20 #if $inputfastq3p.ext.startswith("fastqsolexa")
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21 ##input file is in fastq nucleic format produced by solexa sequencer
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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22 --solexa
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23 #else if $inputfastq3p.ext.startswith("fastqillumina")
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24 ##input file is in fastq nucleic format produced by solexa sequencer
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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25 --illumina
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26 #else
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27 ## input file is in sanger fastq nucleic format (standard fastq)
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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28 --sanger
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29 #end if
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30 --without-progress-bar
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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31 --score-min='$score'
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32 -r fastq3p.fastq
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33 fastq5p.fastq
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34 #if $inputfastq3p.ext.endswith(".gz")
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35 | gzip -c
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36 #end if
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37 > '$output'
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38 ]]>
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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39 </command>
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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40 <inputs>
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41 <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)" />
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42 <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)" />
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43 <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>
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44 </inputs>
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45 <outputs>
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46 <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" />
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47 </outputs>
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48
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49 <tests>
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50 <test>
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51 <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" />
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52 <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" />
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53 <param name="score" value="40.0" />
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54 <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" />
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55 </test>
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56 <test>
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57 <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" />
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58 <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" />
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59 <param name="score" value="40.0" />
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60 <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
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61 </test>
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62 </tests>
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63
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64 <help><![CDATA[
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65
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66 .. class:: warning
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67
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68 **Warning:**
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69 Sequence records corresponding to the same read pair must be in the same order in the two files
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70
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71 --------
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72
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73 .. class:: infomark
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74
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75 **What it does**
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76
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77 illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform :
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78
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79 \* If the two reads overlap, it returns the consensus sequence together with its quality
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80 \* Otherwise, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
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81
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82 The program uses as input one or two fastq sequences reads files.
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83
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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84 \* 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.
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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85 \* 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.
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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86
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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87 illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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88
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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89 @OBITOOLS_LINK@
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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90
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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91 ]]>
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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92 </help>
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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93 <expand macro="citation" />
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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94
83fbdf93d51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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95 </tool>