Mercurial > repos > iuc > sarscov2formatter

annotate sarscov2formatter.xml @ 2:2e993ff8e7dc draft default tip

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/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
author iuc
date Mon, 22 Nov 2021 10:41:59 +0000
parents e3a7995dce75
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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1 <tool id="sarscov2formatter" name="sarscov2formatter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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2 <macros>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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3 <token name="@TOOL_VERSION@">1.0</token>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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4 <token name="@VERSION_SUFFIX@">0</token>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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5 </macros>
0
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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6 <requirements>
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2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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7 <requirement type="package" version="@TOOL_VERSION@">sarscov2formatter</requirement>
0
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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8 </requirements>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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9 <command><![CDATA[
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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10 sarscov2formatter
1
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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11 -a '$align'
0
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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12 #if $source.source_choice == 'ncbi':
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2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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13 #if $source.meta
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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14 -n '$source.meta'
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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15 #end if
0
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16 #else:
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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17 -m '$source.meta'
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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18 #end if
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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19 ]]></command>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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20 <inputs>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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21 <param name="align" type="data" format="fasta" label="Multiple Sequence Alignment (MSA)" help='MSA to be used in HyPhy analysis' />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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22 <conditional name="source" >
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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23 <param name="source_choice" type="select" label="NCBI datasource or other?" >
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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24 <option value="ncbi">NCBI</option>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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25 <option value="other">Other</option>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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26 </param>
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27 <when value="ncbi">
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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28 <param name="meta" type="data" format="json" optional="true" label="Metadata from NCBI" help="If not given it will be downloaded" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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29 </when>
0
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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30 <when value="other" >
2
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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31 <param name="meta" type="data" format="tabular" label="Metadata" help="Tabular file with metadata with the correct columns (see below)" />
0
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32 </when>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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33 </conditional>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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34 </inputs>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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35 <outputs>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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36 <data name="msa" format="fasta" from_work_dir="msa.fasta" label="${tool.name}: MSA" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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37 <data name="dups" format="json" from_work_dir="duplicates.json" label="${tool.name}: Duplicates" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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38 <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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39 </outputs>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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40 <tests>
2
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41 <!-- note: test with ncbi yields unstable results for meta -> assert contents. -->
0
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42 <test>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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43 <param name="align" ftype="fasta" value="align.fasta" />
2
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44 <conditional name="source" >
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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45 <param name="source_choice" value="ncbi" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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46 </conditional>
0
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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47 <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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48 <output name="dups" ftype="json" compare="diff" value="dups.json" />
1
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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49 <output name="outmeta" ftype="json">
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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50 <assert_contents>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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51 <has_line_matching expression="\{"/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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52 <has_line_matching expression="\}"/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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53 <has_text_matching expression='"LR757995": \{'/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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54 <has_text_matching expression='"collected": '/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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55 <has_text_matching expression='"collected": '/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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56 <has_text_matching expression='"location": '/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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57 <has_text_matching expression='"country": '/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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58 <has_text_matching expression='"locality": '/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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59 <has_text_matching expression='"state": '/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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60 <has_text_matching expression='"subregion": '/>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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61 </assert_contents>
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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62 </output>
0
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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63 </test>
2
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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64 <!-- test with local NCBI data, here a json file containing only the entries relevant for the fasta -->
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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65 <test>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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66 <param name="align" ftype="fasta" value="align.fasta" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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67 <conditional name="source" >
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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68 <param name="source_choice" value="ncbi" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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69 <param name="meta" ftype="json" value="test.json" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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70 </conditional>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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71 <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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72 <output name="dups" ftype="json" compare="diff" value="dups.json" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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73 <output name="outmeta" ftype="json">
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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74 <assert_contents>
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75 <has_line_matching expression="\{"/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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76 <has_line_matching expression="\}"/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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77 <has_text_matching expression='"LR757995": \{'/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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78 <has_text_matching expression='"collected": '/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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79 <has_text_matching expression='"collected": '/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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80 <has_text_matching expression='"location": '/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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81 <has_text_matching expression='"country": '/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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82 <has_text_matching expression='"locality": '/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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83 <has_text_matching expression='"state": '/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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84 <has_text_matching expression='"subregion": '/>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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85 </assert_contents>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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86 </output>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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87 </test>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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88 <!-- TODO test with tabular input -->
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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89 <test>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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90 <param name="align" ftype="fasta" value="align.fasta" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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91 <conditional name="source" >
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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92 <param name="source_choice" value="other" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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93 <param name="meta" ftype="tabular" value="test.tsv" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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94 </conditional>
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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95 <output name="msa" ftype="fasta" compare="diff" value="msa-other.fasta" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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96 <output name="dups" ftype="json" compare="diff" value="dups-other.json" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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97 <output name="outmeta" ftype="json" compare="diff" value="meta-other.json" />
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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98 </test>
0
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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99 </tests>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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100 <help><![CDATA[
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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101
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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102 =================
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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103 sarscov2formatter
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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104 =================
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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105
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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106 Custom sript that performs necessary formatting operations for the SARS-CoV2 Selection Analysis workflow.
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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107
2
2e993ff8e7dc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
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108 If using NCBI as data source the file can be obtained from https://www.ncbi.nlm.nih.gov/projects/genome/sars-cov-2-seqs/ncov-sequences.yaml.
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109 If not given the tool will download it automatically.
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110
0
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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111 If using non-NCBI data, the metadata input file must be tabular with the following columns: ID, collection_date, country, state (optional), and locality (optional). Optional columns should still be created even if they are not used.
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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112
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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113 Dates should be of the format: YYMMDD (example: May 1 2020 = 20200501).
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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114
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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115 ]]></help>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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116 <citations>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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117 <citation type="bibtex">
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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118 @misc{githubsarscov2formatter,
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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119 author = {Nicholas Keener},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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120 year = {2020},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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121 title = {sarscov2formatter},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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122 publisher = {Github},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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123 journal = {Github repository},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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124 url = {https://github.com/nickeener/sarscov2formatter},
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125 }</citation>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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126 </citations>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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127 </tool>