Mercurial > repos > devteam > fastq_to_fasta
view macros.xml @ 2:44ed3f74ea7a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
---|---|
date | Tue, 08 May 2018 12:50:22 -0400 |
parents | |
children | 4498e994e31b |
line wrap: on
line source
<?xml version="1.0"?> <macros> <token name="@CATS@"> #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): zcat -f '$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> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">fastx_toolkit</requirement> <yield /> </requirements> </xml> <token name="@VERSION@">0.0.14</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 @UNPUBLISHED{agordon, author = "Assaf Gordon", title = "FASTQ/A short-reads pre-processing tools", year = "2010", note = "http://hannonlab.cshl.edu/fastx_toolkit/", url =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>