Mercurial > repos > devteam > fastq_paired_end_joiner

annotate fastq_paired_end_joiner.xml @ 5:822cc1e6274e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 28c441e8aa66a55d276b0f6325d34086eb715872
author devteam
date Sat, 07 Oct 2017 09:58:53 -0400
parents 080a058abf1e
children 09a2199cd356
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5
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1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1.1">
4
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2 <description>on paired end reads</description>
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3 <requirements>
5
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4 <requirement type="package" version="1.1.2">galaxy_sequence_utils</requirement>
4
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5 </requirements>
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6 <command><![CDATA[
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7 gx-fastq-paired-end-joiner '$input1_file' '${input1_file.extension[len('fastq'):]}' '$input2_file' '${input2_file.extension[len('fastq'):]}' '$output_file' $style '${paste_sequence}'
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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8 ]]></command>
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9 <inputs>
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10 <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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11 <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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12 <param name="style" type="select" label="FASTQ Header Style">
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13 <option value="old" selected="true">old</option>
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14 <option value="new">new</option>
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15 </param>
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16 <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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17 </inputs>
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18 <outputs>
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19 <data name="output_file" format_source="input1_file" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
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24 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
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25 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger" />
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26 </test>
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27 <test>
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28 <param name="input1_file" value="split_pair_reads_1.fastqsanger.gz" ftype="fastqsanger.gz" />
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29 <param name="input2_file" value="split_pair_reads_2.fastqsanger.gz" ftype="fastqsanger.gz" />
822cc1e6274e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 28c441e8aa66a55d276b0f6325d34086eb715872
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30 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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31 </test>
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32 <test>
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33 <param name="input1_file" value="split_pair_reads_1.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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34 <param name="input2_file" value="split_pair_reads_2.fastqsanger.bz2" ftype="fastqsanger.bz2" />
822cc1e6274e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 28c441e8aa66a55d276b0f6325d34086eb715872
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35 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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36 </test>
4
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37 </tests>
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38 <help><![CDATA[
0
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39 **What it does**
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40
1
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41 This tool joins paired end FASTQ reads from two separate files into a
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42 single read in one file. The join is performed using sequence
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43 identifiers, allowing the two files to contain differing ordering. If
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44 a sequence identifier does not appear in both files, it is excluded
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45 from the output.
0
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46
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47 -----
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48
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49 **Input formats**
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50
1
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51 Both old and new (from recent Illumina software) style FASTQ headers
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52 are supported. The following example uses the "old" style.
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53
0
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54 Left-hand Read::
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55
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56 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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57 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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58 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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59 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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60
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61 Right-hand Read::
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62
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63 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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64 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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65 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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66 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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67
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68 -----
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69
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70 **Output**
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71
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72 A multiple-fastq file, for example::
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73
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74 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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75 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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76 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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77 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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78
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79 ------
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80
1
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81 **The "new" style**
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82
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83 Recent Illumina FASTQ headers are structured as follows::
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84
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85 @COORDS FLAGS
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86 COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y
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87 FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE
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88
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89 where the whitespace character between COORDS and FLAGS can be either
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90 a space or a tab.
0
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91
1
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92 ------
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93
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94 **Credits**
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95
4
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96 New style header support added by Simone Leo <simone.leo@crs4.it> .
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97 ]]></help>
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98 <citations>
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99 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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100 </citations>
0
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101 </tool>