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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
author iuc
date Sun, 23 Nov 2025 17:49:36 +0000
parents c47ce50a06e5
children
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c47ce50a06e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
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1 <tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>on joined paired end reads</description>
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bac1702fd30b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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3 <macros>
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4 <import>macros.xml</import>
bac1702fd30b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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5 </macros>
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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>
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7 <edam_topic>topic_0622</edam_topic>
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8 </edam_topics>
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9 <edam_operations>
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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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c47ce50a06e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
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12 <expand macro="requirements"/>
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13 <command><![CDATA[
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14 gx-fastq-paired-end-splitter '$input1_file' '${input1_file.extension[len('fastq'):]}' '$pairs.forward' '$pairs.reverse'
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15 ]]></command>
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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16 <inputs>
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17 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
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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18 </inputs>
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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19 <outputs>
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20 <collection name="pairs" format_source="input1_file" type="paired" label="${tool.name} on ${on_string}"/>
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21 </outputs>
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22 <tests>
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23 <test>
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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24 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
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25 <output_collection name="pairs">
344ecd827be8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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26 <element name="forward" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger"/>
344ecd827be8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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27 <element name="reverse" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger"/>
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28 </output_collection>
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29 </test>
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30 </tests>
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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31 <help><![CDATA[
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32 **What it does**
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33
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34 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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35
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36 Sequence identifiers will have /1 or /2 appended for the split forward and reverse reads, respectively.
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38 -----
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39
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40 **Input format**
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41
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42 A multiple-fastq file, for example::
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43
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44 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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45 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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46 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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47 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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48
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49 -----
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50
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51 **Outputs**
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52
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53 Forward Read::
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54
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55 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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56 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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57 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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58 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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59
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60 Reverse Read::
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61
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62 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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63 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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64 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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65 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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66 ]]></help>
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67 <citations>
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68 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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69 </citations>
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70 </tool>