Mercurial > repos > devteam > fastq_paired_end_joiner

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
author iuc
date Fri, 04 Oct 2024 10:33:45 +0000
parents 9ffd7cf6bc37
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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88c5637a57e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
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1 <!-- TODO as soon as possible adapt the TOOL VERSION macro token .. so far only bump minor versions -->
88c5637a57e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
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2 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1.1+galaxy1" profile="@PROFILE@">
4
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3 <description>on paired end reads</description>
7
9ffd7cf6bc37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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4 <macros>
9ffd7cf6bc37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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5 <import>macros.xml</import>
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6 </macros>
6
8a372f389ced "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_topics>
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8 <edam_topic>topic_0622</edam_topic>
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9 </edam_topics>
8a372f389ced "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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10 <edam_operations>
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11 <edam_operation>operation_3436</edam_operation>
8a372f389ced "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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12 </edam_operations>
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88c5637a57e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
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13 <expand macro="requirements"/>
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14 <command><![CDATA[
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15 gx-fastq-paired-end-joiner '$input1_file' '${input1_file.extension[len('fastq'):]}' '$input2_file' '${input2_file.extension[len('fastq'):]}' '$output_file' $style '${paste_sequence}'
bce792b8e239 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit f2582539542b33240234e8ea6093e25d0aee9b6a
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16 ]]></command>
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17 <inputs>
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18 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Left-hand Reads" />
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19 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Right-hand Reads" />
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20 <param name="style" type="select" label="FASTQ Header Style">
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21 <option value="old" selected="true">old</option>
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22 <option value="new">new</option>
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23 </param>
bce792b8e239 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit f2582539542b33240234e8ea6093e25d0aee9b6a
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24 <param name="paste_sequence" type="text" value="" label="Bases to insert between joined reads" help="Values are in Base-space and quality scores of maximal value will be used"/>
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25 </inputs>
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26 <outputs>
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27 <data name="output_file" format_source="input1_file" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
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32 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
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33 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger" />
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34 </test>
5
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35 <test>
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36 <param name="input1_file" value="split_pair_reads_1.fastqsanger.gz" ftype="fastqsanger.gz" />
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37 <param name="input2_file" value="split_pair_reads_2.fastqsanger.gz" ftype="fastqsanger.gz" />
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38 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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39 </test>
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40 <test>
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41 <param name="input1_file" value="split_pair_reads_1.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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42 <param name="input2_file" value="split_pair_reads_2.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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43 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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44 </test>
4
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45 </tests>
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46 <help><![CDATA[
0
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47 **What it does**
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48
1
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49 This tool joins paired end FASTQ reads from two separate files into a
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50 single read in one file. The join is performed using sequence
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51 identifiers, allowing the two files to contain differing ordering. If
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52 a sequence identifier does not appear in both files, it is excluded
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53 from the output.
0
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54
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55 -----
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56
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57 **Input formats**
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58
1
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59 Both old and new (from recent Illumina software) style FASTQ headers
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60 are supported. The following example uses the "old" style.
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61
0
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62 Left-hand Read::
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63
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64 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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65 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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66 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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67 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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68
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69 Right-hand Read::
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70
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71 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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72 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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73 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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74 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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75
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76 -----
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77
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78 **Output**
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79
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80 A multiple-fastq file, for example::
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81
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82 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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83 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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84 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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85 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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86
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87 ------
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88
1
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89 **The "new" style**
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90
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91 Recent Illumina FASTQ headers are structured as follows::
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92
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93 @COORDS FLAGS
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94 COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y
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95 FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE
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96
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97 where the whitespace character between COORDS and FLAGS can be either
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98 a space or a tab.
0
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99
1
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100 ------
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101
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102 **Credits**
0
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103
4
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104 New style header support added by Simone Leo <simone.leo@crs4.it> .
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105 ]]></help>
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106 <citations>
bce792b8e239 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit f2582539542b33240234e8ea6093e25d0aee9b6a
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107 <citation type="doi">10.1093/bioinformatics/btq281</citation>
bce792b8e239 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit f2582539542b33240234e8ea6093e25d0aee9b6a
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108 </citations>
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d86b8db06e05 Imported from capsule None
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109 </tool>