| Previous changeset 8:edf6d4003fad (2021-02-23) Next changeset 10:9fb055604648 (2021-04-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3" |
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modified:
macros.xml variant.xml |
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added:
test-data/ref.fasta.gz |
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| diff -r edf6d4003fad -r 43815fa60f3a macros.xml --- a/macros.xml Tue Feb 23 20:13:39 2021 +0000 +++ b/macros.xml Mon Mar 29 20:05:39 2021 +0000 |
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| @@ -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> |
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| diff -r edf6d4003fad -r 43815fa60f3a test-data/ref.fasta.gz |
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| Binary file test-data/ref.fasta.gz has changed |
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| diff -r edf6d4003fad -r 43815fa60f3a variant.xml --- a/variant.xml Tue Feb 23 20:13:39 2021 +0000 +++ b/variant.xml Mon Mar 29 20:05:39 2021 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy6" profile="@PROFILE@"> +<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy7" profile="@PROFILE@"> <description>Probability decoding</description> <macros> <import>macros.xml</import> @@ -166,7 +166,7 @@ </conditional> <conditional name="reference_source"> <param name="reference_source_selector" value="history"/> - <param name="ref_file" value="ref.fasta"/> + <param name="ref_file" value="ref.fasta.gz" ftype="fasta.gz"/> </conditional> <conditional name="output_annotated"> <param name="output_annotated_select" value="true"/> |