Mercurial > repos > peterjc > fastq_paired_unpaired
annotate tools/fastq_paired_unpaired/fastq_paired_unpaired.xml @ 7:2709a0f065c9 draft
v0.1.4 Internal changes to command line handling
author | peterjc |
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date | Tue, 16 May 2017 08:53:57 -0400 |
parents | f396701fbf32 |
children | 8cbc866b72ce |
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7 | 1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.4"> |
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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="1.0.1">galaxy_sequence_utils</requirement> |
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5 <requirement type="package" version="1.67">biopython</requirement> |
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6 </requirements> |
7 | 7 <version_command> |
8 python $__tool_directory__/fastq_paired_unpaired.py --version | |
9 </version_command> | |
10 <command detect_errors="aggressive"> | |
11 python $__tool_directory__/fastq_paired_unpaired.py '$input_fastq.extension' '$input_fastq' | |
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12 #if $output_choice_cond.output_choice=="separate" |
7 | 13 '$output_forward' '$output_reverse' |
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14 #elif $output_choice_cond.output_choice=="interleaved" |
7 | 15 '$output_paired' |
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16 #end if |
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17 $output_singles |
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18 </command> |
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19 <inputs> |
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20 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/> |
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21 <conditional name="output_choice_cond"> |
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22 <param name="output_choice" type="select" label="How to output paired reads?"> |
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23 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option> |
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24 <option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option> |
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25 </param> |
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26 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml --> |
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27 <when value="separate" /> |
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28 <when value="interleaved" /> |
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29 </conditional> |
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30 </inputs> |
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31 <outputs> |
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32 <data name="output_singles" format_source="input_fastq" label="Orphan or single reads"/> |
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33 <data name="output_forward" format_source="input_fastq" label="Forward paired reads"> |
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34 <filter>output_choice_cond["output_choice"] == "separate"</filter> |
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35 </data> |
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36 <data name="output_reverse" format_source="input_fastq" label="Reverse 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_paired" format_source="input_fastq" label="Interleaved paired reads"> |
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40 <filter>output_choice_cond["output_choice"] == "interleaved"</filter> |
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41 </data> |
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42 </outputs> |
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43 <tests> |
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44 <test> |
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45 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/> |
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46 <param name="output_choice" value="separate"/> |
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47 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/> |
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48 <output name="output_forward" file="sanger-pairs-forward.fastq" ftype="fastq"/> |
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49 <output name="output_reverse" file="sanger-pairs-reverse.fastq" ftype="fastq"/> |
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50 </test> |
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51 <test> |
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52 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/> |
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53 <param name="output_choice" value="interleaved"/> |
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54 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/> |
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55 <output name="output_paired" file="sanger-pairs-interleaved.fastq" ftype="fastq"/> |
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56 </test> |
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57 </tests> |
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58 <help> |
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59 |
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60 **What it does** |
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61 |
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62 Using the common read name suffix conventions, it divides a FASTQ file into |
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63 paired reads, and orphan or single reads. |
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64 |
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65 The input file should be a valid FASTQ file which has been sorted so that |
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66 any partner forward+reverse reads are consecutive. The output files all |
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67 preserve this sort order. Pairing are recognised based on standard name |
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68 suffices. See below or run the tool with no arguments for more details. |
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69 |
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70 Any reads where the forward/reverse naming suffix used is not recognised |
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71 are treated as orphan reads. The tool supports the /1 and /2 convention |
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72 originally used by Illumina, .f and .r convention, the Sanger convention |
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73 (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details), |
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74 and the current Illumina convention where the reads get the same identifier |
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75 with the fragment number in the description, for example: |
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76 |
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77 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA |
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78 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA |
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79 |
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80 Note that this does support multiple forward and reverse reads per template |
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81 (which is quite common with Sanger sequencing), e.g. this which is sorted |
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82 alphabetically: |
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83 |
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84 * WTSI_1055_4p17.p1kapIBF |
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85 * WTSI_1055_4p17.p1kpIBF |
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86 * WTSI_1055_4p17.q1kapIBR |
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87 * WTSI_1055_4p17.q1kpIBR |
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88 |
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89 or this where the reads already come in pairs: |
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90 |
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91 * WTSI_1055_4p17.p1kapIBF |
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92 * WTSI_1055_4p17.q1kapIBR |
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93 * WTSI_1055_4p17.p1kpIBF |
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94 * WTSI_1055_4p17.q1kpIBR |
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95 |
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96 both become: |
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97 |
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98 * WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR |
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99 * WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR |
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100 |
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101 **References** |
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102 |
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103 If you use this Galaxy tool in work leading to a scientific publication please |
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104 cite the following paper: |
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105 |
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106 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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107 Galaxy tools and workflows for sequence analysis with applications |
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108 in molecular plant pathology. PeerJ 1:e167 |
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109 http://dx.doi.org/10.7717/peerj.167 |
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110 |
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111 This tool is available to install into other Galaxy Instances via the Galaxy |
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112 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired |
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113 </help> |
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114 <citations> |
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115 <citation type="doi">10.7717/peerj.167</citation> |
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116 </citations> |
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117 </tool> |