Mercurial > repos > iuc > poretools_extract
view poretools_extract.xml @ 1:7e4f1ed70187 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
author | iuc |
---|---|
date | Sun, 19 Jan 2020 09:08:56 -0500 |
parents | 7593f94691fb |
children |
line wrap: on
line source
<?xml version="1.0"?> <tool id="poretools_extract" name="Extract reads" version="@VERSION@.0"> <description>in FASTA or FASTQ format from nanopore files</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="aggressive"> <![CDATA[ poretools $output_format --type $type --min-length $min_length --max-length $max_length $quality #if $group: --group '$group' #end if #if $start: --start '$start' #end if #if $end: --end '$end' #end if '$input' > '$output' ]]> </command> <inputs> <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" /> <param name="output_format" type="select" label="Output format"> <option value="fastq">FASTQ</option> <option value="fasta">FASTA</option> </param> <expand macro="length_options" /> <param argument="--type" type="select" label="FASTQ Type"> <option value="all">All</option> <option value="fwd">Forward</option> <option value="rev">Reverse</option> <option value="2D">2D</option> <option value="fwd,rev">Forward and reverse</option> <option value="best">Best</option> </param> <param name="quality" type="select" label="Filter by complement events"> <option value="">Do not filter</option> <option value="--high-quality">Only report reads with more</option> <option value="--normal-quality">Only report reads with fewer</option> </param> <param argument="--group" type="integer" optional="True" label="Base calling group serial number to extract" /> <param argument="--start" type="integer" optional="True" label="Start timestamp" /> <param argument="--end" type="integer" optional="True" label="End timestamp" /> </inputs> <outputs> <data name="output" format="fastq"> <change_format> <when input="output_format" value="fasta" format="fasta" /> </change_format> </data> </outputs> <tests> <test> <expand macro="test_input" /> <param name="output_format" value="fastq" /> <output name="output" file="poretools-extract-out1.fastq" ftype="fastq" /> </test> <test> <expand macro="test_input" /> <param name="output_format" value="fasta" /> <output name="output" file="poretools-extract-out1.fasta" ftype="fasta" /> </test> </tests> <help> Extract sequences from fast5 files generated by the Oxford Nanopore sequencing technology. </help> <expand macro="citations" /> </tool>