Mercurial > repos > devteam > fastq_paired_end_deinterlacer

annotate fastq_paired_end_deinterlacer.xml @ 3:03d57fea6482 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_deinterlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
author devteam
date Fri, 01 Nov 2019 13:24:38 -0400
parents b7ce72b00e62
children f3936d0632cb
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1 <tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1.2">
1
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2 <description>on paired end reads</description>
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3 <requirements>
2
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4 <requirement type="package" version="1.1.2">galaxy_sequence_utils</requirement>
1
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5 </requirements>
3
03d57fea6482 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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6 <edam_topics>
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7 <edam_topic>topic_0622</edam_topic>
03d57fea6482 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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8 </edam_topics>
03d57fea6482 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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9 <edam_operations>
03d57fea6482 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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10 <edam_operation>operation_3359</edam_operation>
03d57fea6482 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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11 </edam_operations>
1
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12 <command><![CDATA[
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13 gx-fastq-paired-end-deinterlacer '$input_file' '${input_file.extension[len('fastq'):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'
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14 ]]></command>
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15 <inputs>
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16 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
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17 </inputs>
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18 <outputs>
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19 <data name="output1_pairs_file" format_source="input_file" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
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20 <data name="output2_pairs_file" format_source="input_file" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
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21 <data name="output1_singles_file" format_source="input_file" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
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22 <data name="output2_singles_file" format_source="input_file" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
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27 <output name="output1_pairs_file" file="paired_end_1.fastqsanger" ftype="fastqsanger" />
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28 <output name="output2_pairs_file" file="paired_end_2.fastqsanger" ftype="fastqsanger" />
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29 <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" ftype="fastqsanger" />
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30 <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" ftype="fastqsanger" />
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31 </test>
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32 <test>
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33 <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
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34 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger" />
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35 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger" />
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36 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger" />
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37 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger" />
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38 </test>
2
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39 <test>
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40 <param name="input_file" value="paired_end_merged_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
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41 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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42 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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43 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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44 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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45 </test>
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46 <test>
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47 <param name="input_file" value="paired_end_merged_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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48 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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49 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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50 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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51 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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52 </test>
1
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53 </tests>
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54 <help><![CDATA[
0
f0949bc49926 Imported from capsule None
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55 **What it does**
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56
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57 De-interlaces a single fastq dataset representing paired-end run into two fastq datasets containing only the first or second mate read. Reads without mate are saved in separate output files.
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58
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59 Sequence identifiers for paired-end reads must follow the /1 and /2 convention.
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60
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61 -----
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62
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63 **Input**
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64
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65 A multiple-fastq file containing paired-end reads, for example::
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66
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67 @1539:931/1
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68 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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69 +1539:931/1
f0949bc49926 Imported from capsule None
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70 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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71 @1539:931/2
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72 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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73 +1539:931/2
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74 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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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 Multi-fastq file with left-hand mate only::
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81
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82 @1539:931/1
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83 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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84 +1539:931/1
f0949bc49926 Imported from capsule None
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85 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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86
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87 Multi-fastq file with right-hand mate only::
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88
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89 @1539:931/2
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90 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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91 +1539:931/2
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92 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
1
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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93 ]]></help>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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94 <citations>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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95 <citation type="doi">10.1093/bioinformatics/btq281</citation>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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96 </citations>
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97 </tool>