Mercurial > repos > iuc > jasminesv
diff macros.xml @ 1:2b62154e39c8 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit 600a9e3c1d884e5cf106e4477c7b8223ef105cdb"
| author | iuc |
|---|---|
| date | Thu, 29 Apr 2021 12:24:00 +0000 |
| parents | 630e2929a131 |
| children |
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--- a/macros.xml Wed Jan 20 19:49:40 2021 +0000 +++ b/macros.xml Thu Apr 29 12:24:00 2021 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.0.11</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.01</token> <xml name="requirements"> <requirements> @@ -27,9 +27,16 @@ --> <token name="@REF_FASTA@"><![CDATA[ #if $dup_to_ins.reference_source.reference_source_selector == 'history': - ln -f -s '$dup_to_ins.reference_source.ref_file' reference.fa && + #set reference = $dup_to_ins.reference_source.ref_file + #set ext = $reference.ext #else: - ln -f -s '$dup_to_ins.reference_source.ref_file.fields.path' reference.fa && + #set reference = $dup_to_ins.reference_source.ref_file.fields.path + #set ext = $dup_to_ins.reference_source.ref_file.fields.path + #end if + #if $ext.endswith(".gz"): + gunzip -c '$reference' > reference && + #else: + ln -sf '$reference' reference && #end if ]]></token> @@ -49,7 +56,7 @@ </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> @@ -64,3 +71,4 @@ More information is available in the `github <https://github.com/mkirsche/Jasmine>`_. ]]></token> </macros> +