Mercurial > repos > iuc > snp_sites
changeset 0:efe8f0e53d3e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
| author | iuc |
|---|---|
| date | Fri, 30 Jun 2017 16:43:26 -0400 |
| parents | |
| children | 5804f786060d |
| files | snp-sites.xml test-data/input.fasta test-data/output.fasta test-data/output.phylip test-data/output.vcf |
| diffstat | 5 files changed, 111 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snp-sites.xml Fri Jun 30 16:43:26 2017 -0400 @@ -0,0 +1,88 @@ +<?xml version='1.0' encoding='UTF-8'?> +<tool id='snp_sites' name='Finds SNP sites' version='0.1.0'> + <description>from a multi-FASTA alignment file</description> + <requirements> + <requirement type='package' version='2.3.2'>snp-sites</requirement> + </requirements> + <version_command>snp-sites -V</version_command> + <command detect_errors='aggressive'><![CDATA[ +snp-sites +-mvp +-o output +'$input_fasta' +]]></command> + <inputs> + <param name='input_fasta' format='fasta' type='data' label='FASTA file' /> + </inputs> + <outputs> + <data name='output_fasta' format='fasta' label='${tool.name} on ${on_string}: FASTA' from_work_dir='output.snp_sites.aln'/> + <data name='output_vcf' format='vcf' label='${tool.name} on ${on_string}: VCF' from_work_dir='output.vcf'/> + <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip' from_work_dir='output.phylip'/> + </outputs> + <tests> + <test> + <param name='input_fasta' value='input.fasta' ftype='fasta' /> + <output name='output_fasta' value='output.fasta' ftype='fasta' /> + <output name='output_vcf' value='output.vcf' ftype='vcf' /> + <output name='output_phylip' value='output.phylip' ftype='phylip' /> + </test> + </tests> + <help> + <![CDATA[ + +**SNP-sites** + +This tool can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3. + +**Input FASTA format:** + +The first sequence will be taken as a reference. + +.. code-block:: + + >sample1 + AGACACAGTCAC + + >sample1 + AGACAC----AC + + >sample1 + AAACGCATTCAN + +**Output files:** + +The output of the tool are three different files in following format: + +- a multi fasta alignment, +- relaxed phylip format and, +- VCF. + +The VCF file for the above specified input is + +The output of the tool are three different files in following format: + +- a multi fasta alignment, +- relaxed phylip format and, +- VCF. + +The VCF file for the above specified input is + +===== === == === === ==== ====== ==== ====== ======= ======= ======= +CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample1 sample1 +----- --- -- --- --- ---- ------ ---- ------ ------- ------- ------- +1 2 . G A . . . GT 0 0 1 +----- --- -- --- --- ---- ------ ---- ------ ------- ------- ------- +1 5 . A G . . . GT 0 0 1 +----- --- -- --- --- ---- ------ ---- ------ ------- ------- ------- +1 8 . G .,T . . . GT 0 1 2 +===== === == === === ==== ====== ==== ====== ======= ======= ======= + +Thus the tool identified three variations (SNPs): in 2nd, 5th, and 8th positions (A instead of G, G instead of A, and unknown nucleotide or T instead of G, respectively). + + + ]]> + </help> + <citations> + <citation type="doi">10.1099/mgen.0.000056</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta Fri Jun 30 16:43:26 2017 -0400 @@ -0,0 +1,6 @@ +>sample1 +AGACACAGTCAC +>sample1 +AGACAC----AC +>sample1 +AAACGCATTCAN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fasta Fri Jun 30 16:43:26 2017 -0400 @@ -0,0 +1,6 @@ +>sample1 +GAG +>sample1 +GA- +>sample1 +AGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.phylip Fri Jun 30 16:43:26 2017 -0400 @@ -0,0 +1,4 @@ +3 3 +sample1 GAG +sample1 GA- +sample1 AGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.vcf Fri Jun 30 16:43:26 2017 -0400 @@ -0,0 +1,7 @@ +##fileformat=VCFv4.1 +##contig=<ID=1,length=12> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample1 sample1 +1 2 . G A . . . GT 0 0 1 +1 5 . A G . . . GT 0 0 1 +1 8 . G *,T . . . GT 0 1 2