Mercurial > repos > idot > fastx_toolkit2
diff fastq_to_fasta.xml @ 0:78a7d28f2a15 draft
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author | idot |
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date | Wed, 10 Jul 2013 06:13:48 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_to_fasta.xml Wed Jul 10 06:13:48 2013 -0400 @@ -0,0 +1,84 @@ +<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA"> + <description>converter</description> + <command> +cat '$input' | +fastq_to_fasta +#if $input.ext == "fastqsanger": + -Q 33 +#elif $input.ext == "fastq": + -Q 64 +#end if + $SKIPN $RENAMESEQ -o '$output' -v +</command> + <inputs> + <param format="fastq,fastqsanger" 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 + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ +</help> +</tool> +<!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->