Mercurial > repos > devteam > fastx_trimmer
view fastx_trimmer.xml @ 2:377ac2829eac draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:40:14 -0500 |
parents | d77c9c6ecf68 |
children | bbb007a39ac2 |
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<tool id="cshl_fastx_trimmer" version="1.0.0" name="Trim sequences"> <description></description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> <command> <![CDATA[ zcat -f < '$input' | fastx_trimmer -v -f $first -l $last -o '$output' #if $input.ext == "fastqsanger": -Q 33 #end if ]]> </command> <inputs> <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" /> <param name="first" type="integer" value="1"> <label>First base to keep</label> </param> <param name="last" type="integer" value="21"> <label>Last base to keep</label> </param> </inputs> <outputs> <data format_source="input" name="output" metadata_source="input" /> </outputs> <tests> <test> <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) --> <param name="input" value="fastx_trimmer1.fasta" /> <param name="first" value="5"/> <param name="last" value="36"/> <output name="output" ftype="fasta" file="fastx_trimmer1.out" /> </test> <test> <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) --> <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/> <param name="first" value="1"/> <param name="last" value="27"/> <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" /> </test> </tests> <help> **What it does** This tool trims (cut bases from) sequences in a FASTA/Q file. -------- **Example** Input Fasta file (with 36 bases in each sequences):: >1-1 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC >2-1 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base):: >1-1 TATGGTCAGAAACCATATGCA >2-1 CAGCGAGGCTTTAATGCCATT Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences:: >1-1 TCAGA >2-1 AGGCT ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>