Mercurial > repos > devteam > fastq_paired_end_joiner

annotate fastq_paired_end_joiner.xml @ 7:c885369b207b draft

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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 d4ced60a941c4c4a2fe95de9c09a10086810b387"
author iuc
date Wed, 19 Feb 2020 12:33:37 -0500
parents 09a2199cd356
children 8d958759cf2a
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rev   line source
7
c885369b207b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 6
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1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1.1+galaxy0">
4
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2 <description>on paired end reads</description>
7
c885369b207b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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3 <macros>
c885369b207b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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4 <import>macros.xml</import>
c885369b207b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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5 </macros>
c885369b207b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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6 <expand macro="requirements"/>
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09a2199cd356 "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>
09a2199cd356 "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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9 </edam_topics>
09a2199cd356 "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>
09a2199cd356 "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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11 <edam_operation>operation_3436</edam_operation>
09a2199cd356 "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>
4
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13 <command><![CDATA[
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14 gx-fastq-paired-end-joiner '$input1_file' '${input1_file.extension[len('fastq'):]}' '$input2_file' '${input2_file.extension[len('fastq'):]}' '$output_file' $style '${paste_sequence}'
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15 ]]></command>
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16 <inputs>
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17 <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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18 <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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19 <param name="style" type="select" label="FASTQ Header Style">
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20 <option value="old" selected="true">old</option>
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21 <option value="new">new</option>
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22 </param>
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23 <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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24 </inputs>
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25 <outputs>
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26 <data name="output_file" format_source="input1_file" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
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31 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
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32 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger" />
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33 </test>
5
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34 <test>
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35 <param name="input1_file" value="split_pair_reads_1.fastqsanger.gz" ftype="fastqsanger.gz" />
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36 <param name="input2_file" value="split_pair_reads_2.fastqsanger.gz" ftype="fastqsanger.gz" />
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37 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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38 </test>
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39 <test>
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40 <param name="input1_file" value="split_pair_reads_1.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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41 <param name="input2_file" value="split_pair_reads_2.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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42 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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43 </test>
4
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44 </tests>
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45 <help><![CDATA[
0
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46 **What it does**
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47
1
270a8ed8a300 Uploaded tool version 2.0.0 by Simone Leo.
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48 This tool joins paired end FASTQ reads from two separate files into a
270a8ed8a300 Uploaded tool version 2.0.0 by Simone Leo.
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49 single read in one file. The join is performed using sequence
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50 identifiers, allowing the two files to contain differing ordering. If
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51 a sequence identifier does not appear in both files, it is excluded
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52 from the output.
0
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53
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54 -----
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55
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56 **Input formats**
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57
1
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58 Both old and new (from recent Illumina software) style FASTQ headers
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59 are supported. The following example uses the "old" style.
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60
0
2793d1d765b9 Imported from capsule None
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61 Left-hand Read::
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62
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63 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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64 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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65 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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66 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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67
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68 Right-hand Read::
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69
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70 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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71 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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72 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
2793d1d765b9 Imported from capsule None
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73 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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74
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75 -----
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76
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77 **Output**
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78
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79 A multiple-fastq file, for example::
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80
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81 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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82 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
2793d1d765b9 Imported from capsule None
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83 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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84 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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85
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86 ------
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87
1
270a8ed8a300 Uploaded tool version 2.0.0 by Simone Leo.
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88 **The "new" style**
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89
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90 Recent Illumina FASTQ headers are structured as follows::
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91
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92 @COORDS FLAGS
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93 COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y
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94 FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE
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95
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96 where the whitespace character between COORDS and FLAGS can be either
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97 a space or a tab.
0
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98
1
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99 ------
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100
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101 **Credits**
0
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102
4
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103 New style header support added by Simone Leo <simone.leo@crs4.it> .
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104 ]]></help>
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105 <citations>
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106 <citation type="doi">10.1093/bioinformatics/btq281</citation>
080a058abf1e 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 </citations>
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2793d1d765b9 Imported from capsule None
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108 </tool>