Mercurial > repos > peterjc > fastq_paired_unpaired
annotate tools/fastq_paired_unpaired/fastq_paired_unpaired.xml @ 4:09f9f0e29e47 draft
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author | peterjc |
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date | Wed, 05 Aug 2015 11:06:38 -0400 |
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1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.1"> |
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2 <description>using the read name suffices</description> |
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3 <requirements> |
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4 <requirement type="package" version="1.64">biopython</requirement> |
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5 <requirement type="python-module">Bio</requirement> |
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6 </requirements> |
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7 <stdio> |
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8 <!-- Anything other than zero is an error --> |
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9 <exit_code range="1:" /> |
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10 <exit_code range=":-1" /> |
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11 </stdio> |
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12 <version_command interpreter="python">fastq_paired_unpaired.py --version</version_command> |
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13 <command interpreter="python"> |
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14 fastq_paired_unpaired.py $input_fastq.extension $input_fastq |
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15 #if $output_choice_cond.output_choice=="separate" |
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16 $output_forward $output_reverse |
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17 #elif $output_choice_cond.output_choice=="interleaved" |
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18 $output_paired |
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19 #end if |
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20 $output_singles |
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21 </command> |
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22 <inputs> |
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23 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/> |
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24 <conditional name="output_choice_cond"> |
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25 <param name="output_choice" type="select" label="How to output paired reads?"> |
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26 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option> |
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27 <option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option> |
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28 </param> |
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29 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml --> |
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30 <when value="separate" /> |
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31 <when value="interleaved" /> |
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32 </conditional> |
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33 </inputs> |
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34 <outputs> |
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35 <data name="output_singles" format_source="input_fastq" label="Orphan or single reads"/> |
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36 <data name="output_forward" format_source="input_fastq" label="Forward paired reads"> |
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37 <filter>output_choice_cond["output_choice"] == "separate"</filter> |
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38 </data> |
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39 <data name="output_reverse" format_source="input_fastq" label="Reverse paired reads"> |
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40 <filter>output_choice_cond["output_choice"] == "separate"</filter> |
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41 </data> |
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42 <data name="output_paired" format_source="input_fastq" label="Interleaved paired reads"> |
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43 <filter>output_choice_cond["output_choice"] == "interleaved"</filter> |
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44 </data> |
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45 </outputs> |
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46 <tests> |
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47 <test> |
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48 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/> |
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49 <param name="output_choice" value="separate"/> |
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50 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/> |
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51 <output name="output_forward" file="sanger-pairs-forward.fastq" ftype="fastq"/> |
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52 <output name="output_reverse" file="sanger-pairs-reverse.fastq" ftype="fastq"/> |
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53 </test> |
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54 <test> |
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55 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/> |
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56 <param name="output_choice" value="interleaved"/> |
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57 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/> |
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58 <output name="output_paired" file="sanger-pairs-interleaved.fastq" ftype="fastq"/> |
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59 </test> |
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60 </tests> |
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61 <help> |
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62 |
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63 **What it does** |
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64 |
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65 Using the common read name suffix conventions, it divides a FASTQ file into |
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66 paired reads, and orphan or single reads. |
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67 |
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68 The input file should be a valid FASTQ file which has been sorted so that |
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69 any partner forward+reverse reads are consecutive. The output files all |
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70 preserve this sort order. Pairing are recognised based on standard name |
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71 suffices. See below or run the tool with no arguments for more details. |
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72 |
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73 Any reads where the forward/reverse naming suffix used is not recognised |
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74 are treated as orphan reads. The tool supports the /1 and /2 convention |
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75 originally used by Illumina, .f and .r convention, the Sanger convention |
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76 (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details), |
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77 and the current Illumina convention where the reads get the same identifier |
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78 with the fragment number in the description, for example: |
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79 |
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80 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA |
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81 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA |
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82 |
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83 Note that this does support multiple forward and reverse reads per template |
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84 (which is quite common with Sanger sequencing), e.g. this which is sorted |
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85 alphabetically: |
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86 |
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87 * WTSI_1055_4p17.p1kapIBF |
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88 * WTSI_1055_4p17.p1kpIBF |
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89 * WTSI_1055_4p17.q1kapIBR |
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90 * WTSI_1055_4p17.q1kpIBR |
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91 |
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92 or this where the reads already come in pairs: |
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93 |
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94 * WTSI_1055_4p17.p1kapIBF |
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95 * WTSI_1055_4p17.q1kapIBR |
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96 * WTSI_1055_4p17.p1kpIBF |
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97 * WTSI_1055_4p17.q1kpIBR |
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98 |
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99 both become: |
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100 |
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101 * WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR |
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102 * WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR |
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103 |
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104 **References** |
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105 |
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106 If you use this Galaxy tool in work leading to a scientific publication please |
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107 cite the following paper: |
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108 |
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109 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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110 Galaxy tools and workflows for sequence analysis with applications |
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111 in molecular plant pathology. PeerJ 1:e167 |
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112 http://dx.doi.org/10.7717/peerj.167 |
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113 |
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114 This tool is available to install into other Galaxy Instances via the Galaxy |
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115 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired |
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116 </help> |
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117 <citations> |
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118 <citation type="doi">10.7717/peerj.167</citation> |
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119 </citations> |
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120 </tool> |