Mercurial > repos > iuc > snp_sites

annotate snp-sites.xml @ 0:efe8f0e53d3e draft

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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
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efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id='snp_sites' name='Finds SNP sites' version='0.1.0'>
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3 <description>from a multi-FASTA alignment file</description>
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4 <requirements>
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5 <requirement type='package' version='2.3.2'>snp-sites</requirement>
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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6 </requirements>
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7 <version_command>snp-sites -V</version_command>
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8 <command detect_errors='aggressive'><![CDATA[
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9 snp-sites
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10 -mvp
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11 -o output
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12 '$input_fasta'
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13 ]]></command>
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14 <inputs>
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15 <param name='input_fasta' format='fasta' type='data' label='FASTA file' />
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16 </inputs>
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17 <outputs>
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18 <data name='output_fasta' format='fasta' label='${tool.name} on ${on_string}: FASTA' from_work_dir='output.snp_sites.aln'/>
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19 <data name='output_vcf' format='vcf' label='${tool.name} on ${on_string}: VCF' from_work_dir='output.vcf'/>
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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20 <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip' from_work_dir='output.phylip'/>
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name='input_fasta' value='input.fasta' ftype='fasta' />
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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25 <output name='output_fasta' value='output.fasta' ftype='fasta' />
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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26 <output name='output_vcf' value='output.vcf' ftype='vcf' />
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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27 <output name='output_phylip' value='output.phylip' ftype='phylip' />
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28 </test>
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29 </tests>
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30 <help>
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31 <![CDATA[
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32
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33 **SNP-sites**
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34
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35 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.
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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36
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37 **Input FASTA format:**
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38
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39 The first sequence will be taken as a reference.
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40
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41 .. code-block::
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42
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43 >sample1
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44 AGACACAGTCAC
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45
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46 >sample1
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47 AGACAC----AC
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48
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49 >sample1
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50 AAACGCATTCAN
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51
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52 **Output files:**
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53
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54 The output of the tool are three different files in following format:
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55
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56 - a multi fasta alignment,
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57 - relaxed phylip format and,
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58 - VCF.
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59
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60 The VCF file for the above specified input is
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61
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62 The output of the tool are three different files in following format:
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63
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64 - a multi fasta alignment,
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65 - relaxed phylip format and,
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66 - VCF.
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67
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68 The VCF file for the above specified input is
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69
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70 ===== === == === === ==== ====== ==== ====== ======= ======= =======
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71 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample1 sample1
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72 ----- --- -- --- --- ---- ------ ---- ------ ------- ------- -------
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73 1 2 . G A . . . GT 0 0 1
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74 ----- --- -- --- --- ---- ------ ---- ------ ------- ------- -------
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75 1 5 . A G . . . GT 0 0 1
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76 ----- --- -- --- --- ---- ------ ---- ------ ------- ------- -------
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77 1 8 . G .,T . . . GT 0 1 2
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78 ===== === == === === ==== ====== ==== ====== ======= ======= =======
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79
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80 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).
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81
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82
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83 ]]>
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84 </help>
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85 <citations>
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86 <citation type="doi">10.1099/mgen.0.000056</citation>
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87 </citations>
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
parents:
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88 </tool>