Mercurial > repos > iuc > sarscov2formatter
comparison sarscov2formatter.xml @ 0:1c664ff29354 draft
"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 |
| parents | |
| children | e3a7995dce75 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:1c664ff29354 |
|---|---|
| 1 <tool id="sarscov2formatter" name="sarscov2formatter" version="0.1" profile="18.01"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="0.5.2">sarscov2formatter</requirement> | |
| 4 </requirements> | |
| 5 <command><![CDATA[ | |
| 6 sarscov2formatter | |
| 7 -a $align | |
| 8 #if $source.source_choice == 'ncbi': | |
| 9 -m ncbi | |
| 10 #else: | |
| 11 -m '$source.meta' | |
| 12 #end if | |
| 13 ]]></command> | |
| 14 <inputs> | |
| 15 <param name="align" type="data" format="fasta" label="Multiple Sequence Alignment (MSA)" help='MSA to be used in HyPhy analysis' /> | |
| 16 <conditional name="source" > | |
| 17 <param name="source_choice" type="select" label="NCBI datasource or other?" > | |
| 18 <option value="ncbi">NCBI</option> | |
| 19 <option value="other">Other</option> | |
| 20 </param> | |
| 21 <when value="ncbi" /> | |
| 22 <when value="other" > | |
| 23 <param name="meta" type="data" format='tabular' label="Metadata source" help="Tabular file with metadata with the correct columns (see below)" /> | |
| 24 </when> | |
| 25 </conditional> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data name="msa" format="fasta" from_work_dir="msa.fasta" label="${tool.name}: MSA" /> | |
| 29 <data name="dups" format="json" from_work_dir="duplicates.json" label="${tool.name}: Duplicates" /> | |
| 30 <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" /> | |
| 31 </outputs> | |
| 32 <tests> | |
| 33 <test> | |
| 34 <param name="align" ftype="fasta" value="align.fasta" /> | |
| 35 <param name="source_choice" value="ncbi" /> | |
| 36 <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" /> | |
| 37 <output name="dups" ftype="json" compare="diff" value="dups.json" /> | |
| 38 <output name="outmeta" ftype="json" compare="diff" value="meta.json" /> | |
| 39 </test> | |
| 40 </tests> | |
| 41 <help><![CDATA[ | |
| 42 | |
| 43 ================= | |
| 44 sarscov2formatter | |
| 45 ================= | |
| 46 | |
| 47 Custom sript that performs necessary formatting operations for the SARS-CoV2 Selection Analysis workflow. | |
| 48 | |
| 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. | |
| 50 | |
| 51 Dates should be of the format: YYMMDD (example: May 1 2020 = 20200501). | |
| 52 | |
| 53 | |
| 54 ]]></help> | |
| 55 <citations> | |
| 56 <citation type="bibtex"> | |
| 57 @misc{githubsarscov2formatter, | |
| 58 author = {Nicholas Keener}, | |
| 59 year = {2020}, | |
| 60 title = {sarscov2formatter}, | |
| 61 publisher = {Github}, | |
| 62 journal = {Github repository}, | |
| 63 url = {https://github.com/nickeener/sarscov2formatter}, | |
| 64 }</citation> | |
| 65 </citations> | |
| 66 </tool> |