Mercurial > repos > iuc > snp_sites
annotate snp-sites.xml @ 0:efe8f0e53d3e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
author | iuc |
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date | Fri, 30 Jun 2017 16:43:26 -0400 |
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children | 5804f786060d |
rev | line source |
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0
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'?> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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2 <tool id='snp_sites' name='Finds SNP sites' version='0.1.0'> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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3 <description>from a multi-FASTA alignment file</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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4 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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5 <requirement type='package' version='2.3.2'>snp-sites</requirement> |
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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7 <version_command>snp-sites -V</version_command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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8 <command detect_errors='aggressive'><![CDATA[ |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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9 snp-sites |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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10 -mvp |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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11 -o output |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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12 '$input_fasta' |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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13 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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14 <inputs> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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15 <param name='input_fasta' format='fasta' type='data' label='FASTA file' /> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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16 </inputs> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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17 <outputs> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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18 <data name='output_fasta' format='fasta' label='${tool.name} on ${on_string}: FASTA' from_work_dir='output.snp_sites.aln'/> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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19 <data name='output_vcf' format='vcf' label='${tool.name} on ${on_string}: VCF' from_work_dir='output.vcf'/> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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20 <data name='output_phylip' format='phylip' label='${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
iuc
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21 </outputs> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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22 <tests> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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23 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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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
iuc
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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
iuc
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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
iuc
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27 <output name='output_phylip' value='output.phylip' ftype='phylip' /> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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28 </test> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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29 </tests> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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30 <help> |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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31 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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32 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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33 **SNP-sites** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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34 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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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
iuc
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36 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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37 **Input FASTA format:** |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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38 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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39 The first sequence will be taken as a reference. |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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40 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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41 .. code-block:: |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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42 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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43 >sample1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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44 AGACACAGTCAC |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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45 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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46 >sample1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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47 AGACAC----AC |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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48 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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49 >sample1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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50 AAACGCATTCAN |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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51 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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52 **Output files:** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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53 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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54 The output of the tool are three different files in following format: |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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55 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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56 - a multi fasta alignment, |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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57 - relaxed phylip format and, |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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58 - VCF. |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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59 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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60 The VCF file for the above specified input is |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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61 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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62 The output of the tool are three different files in following format: |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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63 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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64 - a multi fasta alignment, |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
iuc
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65 - relaxed phylip format and, |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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66 - VCF. |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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67 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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68 The VCF file for the above specified input is |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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69 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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70 ===== === == === === ==== ====== ==== ====== ======= ======= ======= |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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71 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample1 sample1 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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72 ----- --- -- --- --- ---- ------ ---- ------ ------- ------- ------- |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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73 1 2 . G A . . . GT 0 0 1 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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74 ----- --- -- --- --- ---- ------ ---- ------ ------- ------- ------- |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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75 1 5 . A G . . . GT 0 0 1 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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76 ----- --- -- --- --- ---- ------ ---- ------ ------- ------- ------- |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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77 1 8 . G .,T . . . GT 0 1 2 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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78 ===== === == === === ==== ====== ==== ====== ======= ======= ======= |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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79 |
efe8f0e53d3e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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82 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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83 ]]> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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87 </citations> |
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88 </tool> |