Mercurial > repos > devteam > fastq_paired_end_splitter
view fastq_paired_end_splitter.xml @ 5:bac1702fd30b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author | iuc |
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date | Wed, 19 Feb 2020 16:57:47 +0000 |
parents | eec33cc2e1a4 |
children | b3a603b3fad1 |
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<tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="@TOOL_VERSION@"> <description>on joined paired end reads</description> <macros> <import>macros.xml</import> </macros> <expand macro="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>