Mercurial > repos > peterjc > fastq_paired_unpaired

annotate tools/fastq/fastq_paired_unpaired.xml @ 3:528ba9c896e0 draft

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Uploaded v0.0.8, MIT licence and reST for README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:13:27 -0400
parents 95a632a71951
children
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1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.7">
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2 <description>using the read name suffices</description>
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3 <version_command interpreter="python">fastq_paired_unpaired.py --version</version_command>
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4 <command interpreter="python">
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5 fastq_paired_unpaired.py $input_fastq.extension $input_fastq
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6 #if $output_choice_cond.output_choice=="separate"
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7 $output_forward $output_reverse
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8 #elif $output_choice_cond.output_choice=="interleaved"
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9 $output_paired
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10 #end if
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11 $output_singles
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12 </command>
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13 <stdio>
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14 <!-- Anything other than zero is an error -->
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15 <exit_code range="1:" />
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16 <exit_code range=":-1" />
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17 </stdio>
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18 <inputs>
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19 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>
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20 <conditional name="output_choice_cond">
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21 <param name="output_choice" type="select" label="How to output paired reads?">
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22 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option>
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23 <option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option>
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24 </param>
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25 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
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26 <when value="separate" />
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27 <when value="interleaved" />
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28 </conditional>
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29 </inputs>
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30 <outputs>
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31 <data name="output_singles" format="input" label="Orphan or single reads"/>
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32 <data name="output_forward" format="input" label="Forward paired reads">
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33 <filter>output_choice_cond["output_choice"] == "separate"</filter>
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34 </data>
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35 <data name="output_reverse" format="input" label="Reverse paired reads">
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36 <filter>output_choice_cond["output_choice"] == "separate"</filter>
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37 </data>
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38 <data name="output_paired" format="input" label="Interleaved paired reads">
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39 <filter>output_choice_cond["output_choice"] == "interleaved"</filter>
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40 </data>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/>
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45 <param name="output_choice" value="separate"/>
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46 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/>
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47 <output name="output_forward" file="sanger-pairs-forward.fastq" ftype="fastq"/>
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48 <output name="output_reverse" file="sanger-pairs-reverse.fastq" ftype="fastq"/>
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49 </test>
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50 <test>
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51 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/>
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52 <param name="output_choice" value="interleaved"/>
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53 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/>
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54 <output name="output_paired" file="sanger-pairs-interleaved.fastq" ftype="fastq"/>
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55 </test>
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56 </tests>
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57 <help>
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58
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59 **What it does**
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60
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61 Using the common read name suffix conventions, it divides a FASTQ file into
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62 paired reads, and orphan or single reads.
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63
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64 The input file should be a valid FASTQ file which has been sorted so that
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65 any partner forward+reverse reads are consecutive. The output files all
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66 preserve this sort order. Pairing are recognised based on standard name
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67 suffices. See below or run the tool with no arguments for more details.
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68
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69 Any reads where the forward/reverse naming suffix used is not recognised
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70 are treated as orphan reads. The tool supports the /1 and /2 convention
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71 originally used by Illumina, .f and .r convention, the Sanger convention
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72 (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details),
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73 and the current Illumina convention where the reads get the same identifier
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74 with the fragment number in the description, for example:
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75
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76 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA
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77 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA
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78
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79 Note that this does support multiple forward and reverse reads per template
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80 (which is quite common with Sanger sequencing), e.g. this which is sorted
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81 alphabetically:
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82
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83 * WTSI_1055_4p17.p1kapIBF
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84 * WTSI_1055_4p17.p1kpIBF
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85 * WTSI_1055_4p17.q1kapIBR
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86 * WTSI_1055_4p17.q1kpIBR
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87
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88 or this where the reads already come in pairs:
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89
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90 * WTSI_1055_4p17.p1kapIBF
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91 * WTSI_1055_4p17.q1kapIBR
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92 * WTSI_1055_4p17.p1kpIBF
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93 * WTSI_1055_4p17.q1kpIBR
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94
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95 both become:
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96
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97 * WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR
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98 * WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR
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99
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100 **References**
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101
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102 If you use this Galaxy tool in work leading to a scientific publication please
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103 cite the following paper:
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104
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105 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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106 Galaxy tools and workflows for sequence analysis with applications
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107 in molecular plant pathology. PeerJ 1:e167
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108 http://dx.doi.org/10.7717/peerj.167
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109
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110 This tool is available to install into other Galaxy Instances via the Galaxy
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111 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
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112 </help>
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113 </tool>