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view fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit/fastq_to_fasta.xml @ 3:997f5136985f draft default tip
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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_fastq_to_fasta" name="FASTQ to FASTA"> <description>converter</description> <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v </command> <inputs> <param format="fastqsolexa" name="input" type="data" label="FASTQ Library to convert" /> <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> <option value="">yes</option> <option value="-n">no</option> </param> <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)"> <option value="-r">yes</option> <option value="">no</option> </param> </inputs> <tests> <test> <!-- FASTQ-To-FASTA, keep N, don't rename --> <param name="input" value="fastq_to_fasta1.fastq" /> <param name="SKIPN" value=""/> <param name="RENAMESEQ" value=""/> <output name="output" file="fastq_to_fasta1a.out" /> </test> <test> <!-- FASTQ-To-FASTA, discard N, rename --> <param name="input" value="fastq_to_fasta1.fastq" /> <param name="SKIPN" value="no"/> <param name="RENAMESEQ" value="yes"/> <output name="output" file="fastq_to_fasta1b.out" /> </test> </tests> <outputs> <data format="fasta" name="output" metadata_source="input" /> </outputs> <help> **What it does** This tool converts data from Solexa format to FASTA format (scroll down for format description). -------- **Example** The following data in Solexa-FASTQ format:: @CSHL_4_FC042GAMMII_2_1_517_596 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +CSHL_4_FC042GAMMII_2_1_517_596 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 Will be converted to FASTA (with 'rename sequence names' = NO):: >CSHL_4_FC042GAMMII_2_1_517_596 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT Will be converted to FASTA (with 'rename sequence names' = YES):: >1 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT </help> </tool> <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->