Mercurial > repos > iuc > pangolin
changeset 23:77402759b866 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d7751920c666de56e21cf48ffe19191b2d19d534
| author | iuc |
|---|---|
| date | Mon, 18 Jul 2022 14:50:35 +0000 |
| parents | a2099fb98cdb |
| children | 92dd6da871f4 |
| files | pangolin.xml |
| diffstat | 1 files changed, 12 insertions(+), 4 deletions(-) [+] |
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--- a/pangolin.xml Fri Jul 08 08:33:57 2022 +0000 +++ b/pangolin.xml Mon Jul 18 14:50:35 2022 +0000 @@ -1,8 +1,8 @@ <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01"> <description>Phylogenetic Assignment of Outbreak Lineages</description> <macros> - <token name="@TOOL_VERSION@">4.1.1</token> - <token name="@PANGOLIN_DATA_VERSION@">1.11</token> + <token name="@TOOL_VERSION@">4.1.2</token> + <token name="@PANGOLIN_DATA_VERSION@">1.12</token> <token name="@CONSTELLATIONS_VERSION@">0.1.10</token> <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token> <!-- a regex describing the scorpio versions that this wrapper version @@ -153,6 +153,14 @@ echo "Running pangolin with the following possibly updated data packages:" && pangolin --datadir datadir $use_old_datadir --all-versions | grep -E "pangolin-data|assignment|constellations" && #end if +## Since v4.0.6 pangolin can handle compressed fasta as input, +## but recognizes file type by suffix. +#if $input1.is_of_type('fasta.gz'): + #set $query = 'query.fa.gz' +#else: + #set $query = 'query.fa' +#end if +ln -s '$input1' $query && ## Finally run the pangolin analysis pangolin --threads \${GALAXY_SLOTS:-1} @@ -177,7 +185,7 @@ --max-ambig $max_ambig --min-length $min_length $expanded_lineage -'$input1' +$query && csvtk csv2tab report.csv #if not $include_header: | tail -n+2 @@ -185,7 +193,7 @@ > '$output1' ]]></command> <inputs> - <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> + <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" /> <conditional name="engine"> <param argument="--analysis-mode" type="select" label="Analysis mode" help="The analysis engine to use for lineage assignment. UShER is considered more accurate, but pangoLEARN is faster">