Mercurial > repos > devteam > fastq_paired_end_splitter
view fastq_paired_end_splitter.xml @ 4:eec33cc2e1a4 draft
"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 |
line wrap: on
line source
<tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="1.1.1"> <description>on joined paired end reads</description> <requirements> <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> </requirements> <edam_topics> <edam_topic>topic_0622</edam_topic> </edam_topics> <edam_operations> <edam_operation>operation_3359</edam_operation> </edam_operations> <command><![CDATA[ gx-fastq-paired-end-splitter '$input1_file' '${input1_file.extension[len('fastq'):]}' '$output1_file' '$output2_file' ]]></command> <inputs> <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" /> </inputs> <outputs> <data name="output1_file" format_source="input1_file" /> <data name="output2_file" format_source="input1_file" /> </outputs> <tests> <test> <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" /> <output name="output1_file" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger" /> <output name="output2_file" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger" /> </test> </tests> <help><![CDATA[ **What it does** 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. Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively. ----- **Input format** A multiple-fastq file, for example:: @HWI-EAS91_1_30788AAXX:7:21:1542:1758 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA +HWI-EAS91_1_30788AAXX:7:21:1542:1758 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR ----- **Outputs** Left-hand Read:: @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Right-hand Read:: @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btq281</citation> </citations> </tool>