Mercurial > repos > iuc > snp_dists

annotate snp-dists.xml @ 0:1959cc43b414 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
author iuc
date Sat, 19 Oct 2019 05:08:45 -0400
parents
children f78492521996
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0
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
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1 <tool id="snp_dists" name="SNP distance matrix" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
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2 <macros>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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3 <token name="@TOOL_VERSION@">0.6.3</token>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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4 </macros>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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5 <description>Compute distance in SNPs between all sequences in a FASTA file</description>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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6 <requirements>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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7 <requirement type="package" version="@TOOL_VERSION@">snp-dists</requirement>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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8 </requirements>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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9 <command detect_errors="exit_code"><![CDATA[
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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10 snp-dists -q
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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11 $a
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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12 $k
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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13 $b
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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14 '$input' > '$output'
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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15 ]]></command>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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16 <inputs>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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17 <param name="input" type="data" format="fasta,fasta.gz" label="FASTA multiple sequence alignment"
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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18 help="Provide a multiple sequence alignment containing sequences of equal length" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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19 <param argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Count all differences, not just ACTG" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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20 <param argument="-k" type="boolean" truevalue="-k" falsevalue="" label="Keep case, don't uppercase all letters" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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21 <param argument="-b" type="boolean" truevalue="-b" falsevalue="" label="Blank top left corner cell" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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22 </inputs>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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23 <outputs>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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24 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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25 </outputs>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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26 <tests>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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27 <test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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28 <param name="input" ftype="fasta" value="input1.fasta" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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29 <output name="output" value="output_default1.tabular" ftype="tabular" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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30 </test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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31 <test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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32 <param name="input" ftype="fasta" value="input1.fasta" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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33 <param name="a" value="True" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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34 <output name="output" value="output_all_diffs1.tabular" ftype="tabular" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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35 </test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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36 <test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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37 <param name="input" ftype="fasta" value="input1.fasta" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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38 <param name="k" value="True" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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39 <output name="output" value="output_keep_case1.tabular" ftype="tabular" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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40 </test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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41 <test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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42 <param name="input" ftype="fasta" value="input1.fasta" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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43 <param name="b" value="True" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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44 <output name="output" value="output_blank_cell1.tabular" ftype="tabular" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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45 </test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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46 </tests>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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47 <help><![CDATA[
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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48 **snp-dists**
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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49
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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50 This tool computes a SNP distance matrix from a multiple sequence alignment (MSA) of
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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51 sequences (all of the same length). Such distance matrices are often used as in
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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52 studies of disease outbreaks.
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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53
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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54 The output is a tabular file, for example this matrix describing four M. tuberculosis isolates
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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55 and their relationship to the inferred ancestral reference sequence:
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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56
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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57 =============== ======= ========= ========= ========= =========
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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58 snp-dists 0.6.3 MTB_anc ERR550641 ERR550671 ERR550691 ERR550703
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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59 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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60 MTB_anc 0 746 726 772 749
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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61 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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62 ERR550641 746 0 26 44 13
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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63 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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64 ERR550671 726 26 0 64 29
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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65 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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66 ERR550691 772 44 64 0 39
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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67 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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68 ERR550703 749 13 29 39 0
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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69 =============== ======= ========= ========= ========= =========
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70
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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71 ]]></help>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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72 <citations>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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73 <citation type="bibtex">
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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74 @misc{githubsnp-dists,
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75 author = {Seemann, Torsten},
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76 year = {2019},
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77 title = {snp-dists},
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78 publisher = {GitHub},
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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79 journal = {GitHub repository},
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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80 url = {https://github.com/tseemann/snp-dists},
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81 }</citation>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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82 </citations>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
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83 </tool>