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annotate tools/fastq/fastq_paired_unpaired.xml @ 1:7ed81e36fc1c

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Uploaded v0.0.5 which handles Illumina 1.8 style pair naming.
author peterjc
date Mon, 12 Dec 2011 11:33:10 -0500
parents 72e9fcaec61f
children 95a632a71951
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7ed81e36fc1c Uploaded v0.0.5 which handles Illumina 1.8 style pair naming.
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1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.5">
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2 <description>using the read name suffices</description>
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3 <command interpreter="python">
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4 fastq_paired_unpaired.py $input_fastq.extension $input_fastq
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5 #if $output_choice_cond.output_choice=="separate"
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6 $output_forward $output_reverse
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7 #elif $output_choice_cond.output_choice=="interleaved"
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8 $output_paired
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9 #end if
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10 $output_singles
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11 </command>
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12 <inputs>
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13 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>
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14 <conditional name="output_choice_cond">
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15 <param name="output_choice" type="select" label="How to output paired reads?">
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16 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option>
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17 <option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option>
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18 </param>
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19 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
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20 <when value="separate" />
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21 <when value="interleaved" />
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22 </conditional>
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23 </inputs>
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24 <outputs>
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25 <data name="output_singles" format="input" label="Orphan or single reads"/>
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26 <data name="output_forward" format="input" label="Forward paired reads">
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27 <filter>output_choice_cond["output_choice"] == "separate"</filter>
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28 </data>
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29 <data name="output_reverse" format="input" label="Reverse paired reads">
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30 <filter>output_choice_cond["output_choice"] == "separate"</filter>
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31 </data>
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32 <data name="output_paired" format="input" label="Interleaved paired reads">
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33 <filter>output_choice_cond["output_choice"] == "interleaved"</filter>
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34 </data>
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35 </outputs>
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36 <tests>
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37 </tests>
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38 <requirements>
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39 <requirement type="python-module">Bio</requirement>
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40 </requirements>
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41 <help>
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42
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43 **What it does**
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44
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45 Using the common read name suffix conventions, it divides a FASTQ file into
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46 paired reads, and orphan or single reads.
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47
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48 The input file should be a valid FASTQ file which has been sorted so that
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49 any partner forward+reverse reads are consecutive. The output files all
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50 preserve this sort order. Pairing are recognised based on standard name
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51 suffices. See below or run the tool with no arguments for more details.
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52
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53 Any reads where the forward/reverse naming suffix used is not recognised
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54 are treated as orphan reads. The tool supports the /1 and /2 convention
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7ed81e36fc1c Uploaded v0.0.5 which handles Illumina 1.8 style pair naming.
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55 originally used by Illumina, .f and .r convention, the Sanger convention
7ed81e36fc1c Uploaded v0.0.5 which handles Illumina 1.8 style pair naming.
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56 (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details),
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57 and the current Illumina convention where the reads get the same identifier
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58 with the fragment number in the description, for example:
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59
7ed81e36fc1c Uploaded v0.0.5 which handles Illumina 1.8 style pair naming.
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60 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA
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61 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA
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62
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63 Note that this does support multiple forward and reverse reads per template
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64 (which is quite common with Sanger sequencing), e.g. this which is sorted
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65 alphabetically:
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66
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67 * WTSI_1055_4p17.p1kapIBF
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68 * WTSI_1055_4p17.p1kpIBF
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69 * WTSI_1055_4p17.q1kapIBR
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70 * WTSI_1055_4p17.q1kpIBR
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71
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72 or this where the reads already come in pairs:
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73
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74 * WTSI_1055_4p17.p1kapIBF
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75 * WTSI_1055_4p17.q1kapIBR
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76 * WTSI_1055_4p17.p1kpIBF
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77 * WTSI_1055_4p17.q1kpIBR
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78
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79 both become:
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80
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81 * WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR
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82 * WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR
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83
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84 </help>
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85 </tool>