Mercurial > repos > iuc > sarscov2formatter

annotate sarscov2formatter.xml @ 1:e3a7995dce75 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
author iuc
date Fri, 20 Nov 2020 18:21:33 +0000
parents 1c664ff29354
children 2e993ff8e7dc
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e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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1 <tool id="sarscov2formatter" name="sarscov2formatter" version="0.5.3+galaxy1" profile="18.01">
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2 <requirements>
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3 <requirement type="package" version="0.5.3">sarscov2formatter</requirement>
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4 </requirements>
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5 <command><![CDATA[
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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6 sarscov2formatter
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7 -a '$align'
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8 #if $source.source_choice == 'ncbi':
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9 -m ncbi
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10 #else:
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11 -m '$source.meta'
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12 #end if
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13 ]]></command>
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14 <inputs>
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15 <param name="align" type="data" format="fasta" label="Multiple Sequence Alignment (MSA)" help='MSA to be used in HyPhy analysis' />
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16 <conditional name="source" >
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17 <param name="source_choice" type="select" label="NCBI datasource or other?" >
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18 <option value="ncbi">NCBI</option>
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19 <option value="other">Other</option>
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20 </param>
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21 <when value="ncbi" />
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22 <when value="other" >
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23 <param name="meta" type="data" format="tabular" label="Metadata source" help="Tabular file with metadata with the correct columns (see below)" />
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24 </when>
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25 </conditional>
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26 </inputs>
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27 <outputs>
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28 <data name="msa" format="fasta" from_work_dir="msa.fasta" label="${tool.name}: MSA" />
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29 <data name="dups" format="json" from_work_dir="duplicates.json" label="${tool.name}: Duplicates" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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30 <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" />
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31 </outputs>
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32 <tests>
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33 <!-- note: test with ncbi yields unstable results for meta -> assert contents.
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34 also needs a surprising amount memory (1.7G) which might
e3a7995dce75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
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35 become impractival in the future -->
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36 <test>
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37 <param name="align" ftype="fasta" value="align.fasta" />
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38 <param name="source_choice" value="ncbi" />
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39 <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" />
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40 <output name="dups" ftype="json" compare="diff" value="dups.json" />
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41 <output name="outmeta" ftype="json">
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42 <assert_contents>
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43 <has_line_matching expression="\{"/>
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44 <has_line_matching expression="\}"/>
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45 <has_text_matching expression='"LR757995": \{'/>
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46 <has_text_matching expression='"collected": '/>
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47 <has_text_matching expression='"collected": '/>
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48 <has_text_matching expression='"location": '/>
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49 <has_text_matching expression='"country": '/>
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50 <has_text_matching expression='"locality": '/>
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51 <has_text_matching expression='"state": '/>
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52 <has_text_matching expression='"subregion": '/>
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53 </assert_contents>
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54 </output>
0
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55 </test>
1
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56 <!-- TODO test with tabular input, does not work yet
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57 test.tsv has been generated with test.py
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58 https://github.com/nickeener/sarscov2formatter/issues/2 -->
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59 <!-- <test>-->
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60 <!-- <param name="align" ftype="fasta" value="align.fasta" />-->
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61 <!-- <conditional name="source" >-->
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62 <!-- <param name="source_choice" value="other" />-->
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63 <!-- <param name="meta" ftype="tabular" value="test.tsv" />-->
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64 <!-- </conditional>-->
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65 <!-- <output name="msa" ftype="fasta" compare="diff" value="msa-other.fasta" />-->
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66 <!-- <output name="dups" ftype="json" compare="diff" value="dups-other.json" />-->
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67 <!-- <output name="outmeta" ftype="json" compare="diff" value="meta-other.json" />-->
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68 <!-- </test>-->
0
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69 </tests>
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70 <help><![CDATA[
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71
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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72 =================
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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73 sarscov2formatter
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74 =================
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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75
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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76 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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77
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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78 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.
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79
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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80 Dates should be of the format: YYMMDD (example: May 1 2020 = 20200501).
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81
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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82
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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83 ]]></help>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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84 <citations>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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85 <citation type="bibtex">
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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86 @misc{githubsarscov2formatter,
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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87 author = {Nicholas Keener},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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88 year = {2020},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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89 title = {sarscov2formatter},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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90 publisher = {Github},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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91 journal = {Github repository},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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92 url = {https://github.com/nickeener/sarscov2formatter},
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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93 }</citation>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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94 </citations>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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95 </tool>