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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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<tool id="cshl_fastx_trimmer" name="Trim"> <description>sequences</description> <command>zcat -f '$input' | fastx_trimmer $GZIPOUT -v -f $first -l $last -o $output</command> <inputs> <param format="fasta,fastqsolexa" name="input" type="data" label="Library to clip" /> <param name="first" size="4" type="integer" value="1"> <label>First base to keep</label> </param> <param name="last" size="4" type="integer" value="21"> <label>Last base to keep</label> </param> <param name="GZIPOUT" type="select" label="Compress output file (using GZIP) "> <option value="-z">yes</option> <option value="">no</option> </param> </inputs> <tests> <test> <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) --> <param name="input" value="fastx_trimmer1.fasta" /> <param name="first" value="5"/> <param name="last" value="36"/> <param name="GZIPOUT" value=""/> <output name="output" file="fastx_trimmer1.out" /> </test> <test> <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) --> <param name="input" value="fastx_trimmer2.fastq" /> <param name="first" value="1"/> <param name="last" value="27"/> <param name="GZIPOUT" value=""/> <output name="output" file="fastx_trimmer2.out" /> </test> </tests> <outputs> <data format="input" name="output" label="$input.tag trimmed" metadata_source="input" /> </outputs> <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 </help> </tool> <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->