Mercurial > repos > iuc > flair_correct
changeset 1:c784170f3b5e draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
| author | iuc |
|---|---|
| date | Fri, 09 Apr 2021 21:15:31 +0000 |
| parents | 6927379c9ede |
| children | |
| files | flair_correct.xml flair_macros.xml |
| diffstat | 2 files changed, 11 insertions(+), 4 deletions(-) [+] |
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--- a/flair_correct.xml Fri Nov 27 21:55:45 2020 +0000 +++ b/flair_correct.xml Fri Apr 09 21:15:31 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="flair_correct" name="FLAIR correct" version="@TOOL_VERSION@" profile="20.01"> +<tool id="flair_correct" name="FLAIR correct" version="@TOOL_VERSION@+galaxy0" profile="20.01"> <description>corrects misaligned splice sites using genome annotations</description> <macros>
--- a/flair_macros.xml Fri Nov 27 21:55:45 2020 +0000 +++ b/flair_macros.xml Fri Apr 09 21:15:31 2021 +0000 @@ -13,10 +13,17 @@ <token name="@PREPARE_REF@"><![CDATA[ #if str($reference_source_genome.ref_selector_genome) == 'history': - ln -s '$reference_source_genome.reffile' reference.fa && + #set reference = $reference_source_genome.reffile + #set ext = $reference.ext samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 && #else - ln -s '${reference_source_genome.reffile.fields.path}' reference.fa && + #set reference = $reference_source_genome.reffile.fields.path + #set ext = $reference_source_genome.reffile.fields.path + #end if + #if $ext.endswith(".gz"): + gunzip -c '$reference' > reference.fa && + #else: + ln -sf '$reference' reference.fa && #end if ]]></token> @@ -34,7 +41,7 @@ </param> </when> <when value="history"> - <param name="reffile" argument="-g" type="data" format="fasta" label="Reference" help="Reference sequence" /> + <param name="reffile" argument="-g" type="data" format="fasta,fasta.gz" label="Reference" help="Reference sequence" /> </when> </conditional> </xml>