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annotate fastq_paired_end_joiner.xml @ 4:080a058abf1e 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 f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:59:13 -0400
parents 6a7f5da7c76d
children 822cc1e6274e
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4
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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1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1.0">
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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2 <description>on paired end reads</description>
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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3 <requirements>
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
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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5 </requirements>
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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6 <command><![CDATA[
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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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>
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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9 <inputs>
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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10 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Left-hand Reads" />
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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11 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Right-hand Reads" />
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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12 <param name="style" type="select" label="FASTQ Header Style">
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13 <option value="old" selected="true">old</option>
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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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"/>
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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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" />
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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24 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
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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25 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger" />
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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26 </test>
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27 </tests>
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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28 <help><![CDATA[
0
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29 **What it does**
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30
1
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31 This tool joins paired end FASTQ reads from two separate files into a
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32 single read in one file. The join is performed using sequence
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33 identifiers, allowing the two files to contain differing ordering. If
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34 a sequence identifier does not appear in both files, it is excluded
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35 from the output.
0
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36
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37 -----
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38
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39 **Input formats**
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40
1
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41 Both old and new (from recent Illumina software) style FASTQ headers
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42 are supported. The following example uses the "old" style.
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43
0
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44 Left-hand Read::
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45
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46 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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47 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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48 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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49 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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50
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51 Right-hand Read::
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52
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53 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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54 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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55 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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56 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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57
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58 -----
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59
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60 **Output**
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61
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62 A multiple-fastq file, for example::
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63
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64 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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65 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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66 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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67 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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68
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69 ------
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70
1
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71 **The "new" style**
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72
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73 Recent Illumina FASTQ headers are structured as follows::
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74
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75 @COORDS FLAGS
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76 COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y
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77 FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE
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78
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79 where the whitespace character between COORDS and FLAGS can be either
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80 a space or a tab.
0
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81
1
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82 ------
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83
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84 **Credits**
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85
4
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86 New style header support added by Simone Leo <simone.leo@crs4.it> .
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87 ]]></help>
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88 <citations>
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89 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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90 </citations>
0
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91 </tool>