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annotate fastq_paired_end_splitter.xml @ 4:eec33cc2e1a4 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_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
author devteam
date Fri, 01 Nov 2019 13:19:34 -0400
parents fec4c8314668
children bac1702fd30b
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fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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1 <tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="1.1.1">
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>on joined paired end reads</description>
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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3 <requirements>
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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5 </requirements>
4
eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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6 <edam_topics>
eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_topic>topic_0622</edam_topic>
eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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8 </edam_topics>
eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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9 <edam_operations>
eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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10 <edam_operation>operation_3359</edam_operation>
eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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11 </edam_operations>
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12 <command><![CDATA[
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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13 gx-fastq-paired-end-splitter '$input1_file' '${input1_file.extension[len('fastq'):]}' '$output1_file' '$output2_file'
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14 ]]></command>
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15 <inputs>
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16 <param name="input1_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_file" format_source="input1_file" />
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20 <data name="output2_file" format_source="input1_file" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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25 <output name="output1_file" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 <output name="output2_file" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
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27 </test>
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28 </tests>
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29 <help><![CDATA[
0
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30 **What it does**
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31
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32 Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length.
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33
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34 Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively.
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35
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36 -----
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37
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38 **Input format**
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39
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40 A multiple-fastq file, for example::
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41
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42 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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43 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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44 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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45 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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46
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47 -----
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48
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49 **Outputs**
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50
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51 Left-hand Read::
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52
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53 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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54 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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55 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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56 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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57
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58 Right-hand Read::
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59
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60 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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61 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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62 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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63 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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64 ]]></help>
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65 <citations>
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66 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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67 </citations>
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68 </tool>