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annotate fastq_paired_end_deinterlacer.xml @ 2:f408707593be 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 28c441e8aa66a55d276b0f6325d34086eb715872
author devteam
date Sat, 07 Oct 2017 10:00:17 -0400
parents 64fa25e9b916
children e1f52cc8b54f
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f408707593be planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
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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>
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4 <requirement type="package" version="1.1.2">galaxy_sequence_utils</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 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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8 ]]></command>
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9 <inputs>
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10 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
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11 </inputs>
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12 <outputs>
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13 <data name="output1_pairs_file" format_source="input_file" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
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14 <data name="output2_pairs_file" format_source="input_file" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
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15 <data name="output1_singles_file" format_source="input_file" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
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16 <data name="output2_singles_file" format_source="input_file" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
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21 <output name="output1_pairs_file" file="paired_end_1.fastqsanger" ftype="fastqsanger" />
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22 <output name="output2_pairs_file" file="paired_end_2.fastqsanger" ftype="fastqsanger" />
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23 <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" ftype="fastqsanger" />
64fa25e9b916 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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24 <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" ftype="fastqsanger" />
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25 </test>
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26 <test>
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27 <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
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28 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger" />
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29 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger" />
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30 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger" />
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31 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger" />
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32 </test>
2
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33 <test>
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34 <param name="input_file" value="paired_end_merged_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
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35 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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36 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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37 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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38 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.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="input_file" value="paired_end_merged_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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42 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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43 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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44 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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45 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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46 </test>
1
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47 </tests>
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48 <help><![CDATA[
0
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49 **What it does**
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50
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51 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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52
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53 Sequence identifiers for paired-end reads must follow the /1 and /2 convention.
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54
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55 -----
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56
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57 **Input**
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58
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59 A multiple-fastq file containing paired-end reads, for example::
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60
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61 @1539:931/1
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62 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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63 +1539:931/1
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64 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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65 @1539:931/2
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66 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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67 +1539:931/2
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68 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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69
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70 -----
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71
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72 **Output**
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73
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74 Multi-fastq file with left-hand mate only::
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75
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76 @1539:931/1
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77 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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78 +1539:931/1
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79 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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80
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81 Multi-fastq file with right-hand mate only::
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82
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83 @1539:931/2
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84 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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85 +1539:931/2
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86 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
1
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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>