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annotate fastq_paired_end_deinterlacer.xml @ 1:64fa25e9b916 draft

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author devteam
date Sat, 30 Sep 2017 14:56:49 -0400
parents e6e6498bf63c
children f408707593be
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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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1 <tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1.1">
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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="1.1.1">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'
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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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" />
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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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>
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33 </tests>
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34 <help><![CDATA[
0
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35 **What it does**
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36
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37 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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38
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39 Sequence identifiers for paired-end reads must follow the /1 and /2 convention.
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40
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41 -----
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42
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43 **Input**
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44
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45 A multiple-fastq file containing paired-end reads, for example::
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46
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47 @1539:931/1
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48 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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49 +1539:931/1
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50 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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51 @1539:931/2
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52 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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53 +1539:931/2
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54 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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55
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56 -----
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57
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58 **Output**
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59
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60 Multi-fastq file with left-hand mate only::
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61
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62 @1539:931/1
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63 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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64 +1539:931/1
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65 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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66
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67 Multi-fastq file with right-hand mate only::
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68
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69 @1539:931/2
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70 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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71 +1539:931/2
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72 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
1
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73 ]]></help>
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74 <citations>
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75 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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76 </citations>
0
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77 </tool>