Mercurial > repos > devteam > fastq_quality_filter
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author | iuc |
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date | Thu, 10 Aug 2023 06:50:55 +0000 |
parents | b4c9c66a7a4d |
children |
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<?xml version="1.0"?> <macros> <token name="@CATS@"> #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): gunzip -c -f '$input' | #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): bzcat -f '$input' | #else: cat '$input' | #end if </token> <token name="@FQQUAL@"> <![CDATA[ #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'): -Q 33 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'): -Q 64 #end if ]]> </token> <token name="@GZIP@"> <![CDATA[ #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): | gzip -c #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): | bzip2 -c #end if ]]> </token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">fastx_toolkit</requirement> <yield /> </requirements> </xml> <token name="@VERSION@">0.0.14</token> <token name="@VERSION_SUFFIX@">2</token> <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token> <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token> <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token> <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token> <token name="@FASTAS@">fasta,fasta.gz</token> <xml name="citations"> <citations> <citation type="bibtex"> @UNPUBLISHED{agordon, author = "Assaf Gordon", title = "FASTQ/A short-reads pre-processing tools", year = "2010", note = "http://hannonlab.cshl.edu/fastx_toolkit/", url = "http://hannonlab.cshl.edu/fastx_toolkit/"} </citation> </citations> </xml> <xml name="fasta_input"> <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" /> </xml> <xml name="fastq_input"> <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" /> </xml> <xml name="fastx_input"> <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" /> </xml> </macros>