Mercurial > repos > iuc > sarscov2formatter

annotate sarscov2formatter.xml @ 0:1c664ff29354 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
author iuc
date Mon, 04 May 2020 05:39:35 -0400
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children e3a7995dce75
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1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1 <tool id="sarscov2formatter" name="sarscov2formatter" version="0.1" profile="18.01">
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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2 <requirements>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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3 <requirement type="package" version="0.5.2">sarscov2formatter</requirement>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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4 </requirements>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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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
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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7 -a $align
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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8 #if $source.source_choice == 'ncbi':
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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9 -m ncbi
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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10 #else:
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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11 -m '$source.meta'
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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12 #end if
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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13 ]]></command>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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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' />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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16 <conditional name="source" >
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17 <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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18 <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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19 <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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20 </param>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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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)" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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24 </when>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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25 </conditional>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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26 </inputs>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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27 <outputs>
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28 <data name="msa" format="fasta" from_work_dir="msa.fasta" label="${tool.name}: MSA" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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29 <data name="dups" format="json" from_work_dir="duplicates.json" label="${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" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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31 </outputs>
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32 <tests>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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33 <test>
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34 <param name="align" ftype="fasta" value="align.fasta" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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35 <param name="source_choice" value="ncbi" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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36 <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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37 <output name="dups" ftype="json" compare="diff" value="dups.json" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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38 <output name="outmeta" ftype="json" compare="diff" value="meta.json" />
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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39 </test>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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40 </tests>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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41 <help><![CDATA[
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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42
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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43 =================
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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44 sarscov2formatter
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45 =================
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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46
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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47 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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48
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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49 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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50
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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51 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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52
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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53
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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54 ]]></help>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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55 <citations>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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56 <citation type="bibtex">
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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57 @misc{githubsarscov2formatter,
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58 author = {Nicholas Keener},
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59 year = {2020},
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60 title = {sarscov2formatter},
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61 publisher = {Github},
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62 journal = {Github repository},
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63 url = {https://github.com/nickeener/sarscov2formatter},
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64 }</citation>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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65 </citations>
1c664ff29354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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66 </tool>