Mercurial > repos > iuc > medaka_variant_pipeline
changeset 9:336b3def9b2b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
| author | iuc |
|---|---|
| date | Mon, 29 Mar 2021 20:06:01 +0000 |
| parents | 1040a307be0c |
| children | 7623e5888be9 |
| files | macros.xml medaka_variant.xml test-data/ref.fasta.gz |
| diffstat | 3 files changed, 7 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Tue Feb 23 20:13:07 2021 +0000 +++ b/macros.xml Mon Mar 29 20:06:01 2021 +0000 @@ -29,7 +29,11 @@ <token name="@REF_FASTA@"><![CDATA[ #if $reference_source.reference_source_selector == 'history': - ln -f -s '$reference_source.ref_file' reference.fa && + #if $reference_source.ref_file.ext.endswith(".gz") + gunzip -c '$reference_source.ref_file' > reference.fa && + #else + ln -f -s '$reference_source.ref_file' reference.fa && + #end if #else: ln -f -s '$reference_source.ref_file.fields.path' reference.fa && #end if @@ -85,7 +89,7 @@ </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" 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>
--- a/medaka_variant.xml Tue Feb 23 20:13:07 2021 +0000 +++ b/medaka_variant.xml Mon Mar 29 20:06:01 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>via neural networks</description> <macros> <import>macros.xml</import>