Mercurial > repos > iuc > irissv
diff macros.xml @ 1:1d4f065fa0ef draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"
author | iuc |
---|---|
date | Mon, 17 May 2021 17:29:39 +0000 |
parents | 30fc9f2bcbe4 |
children | 3242dbeea69c |
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--- a/macros.xml Tue Jan 19 20:30:21 2021 +0000 +++ b/macros.xml Mon May 17 17:29:39 2021 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.0.4</token> - <token name="@PROFILE@">18.01</token> + <token name="@PROFILE@">20.01</token> <xml name="requirements"> <requirements> <requirement type="package" version="1.9">samtools</requirement> @@ -29,9 +29,16 @@ <token name="@REF_FASTA@"><![CDATA[ #if $reference_source.reference_source_selector == 'history': - ln -f -s '$reference_source.ref_file' reference.fa && + #set reference = $reference_source.ref_file + #set ext = $reference.ext #else: - ln -f -s '$reference_source.ref_file.fields.path' reference.fa && + #set reference = $reference_source.ref_file.fields.path + #set ext = $reference_source.ref_file.fields.path + #end if + #if $ext.endswith('.gz'): + gunzip -c '$reference' > reference && + #else: + ln -sf '$reference' reference && #end if ]]></token> @@ -51,7 +58,7 @@ </param> </when> <when value="history"> - <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/> + <param name="ref_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/> </when> </conditional> </xml>