Mercurial > repos > iuc > jasminesv
changeset 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 | |
| files | jasminesv.xml macros.xml test-data/all_fasta.loc test-data/genome.fa test-data/genome.fa.gz |
| diffstat | 5 files changed, 16 insertions(+), 27 deletions(-) [+] |
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--- a/jasminesv.xml Wed Jan 20 19:49:40 2021 +0000 +++ b/jasminesv.xml Thu Apr 29 12:24:00 2021 +0000 @@ -29,7 +29,7 @@ 'spec_reads=${spec_reads}' 'spec_len=${spec_len}' #if $dup_to_ins.dup_to_ins: - 'genome_file=reference.fa' + 'genome_file=reference' #end if ## Flags: @@ -156,7 +156,7 @@ <param name="dup_to_ins" value="--dup_to_ins"/> <conditional name="reference_source"> <param name="reference_source_selector" value="history"/> - <param name="ref_file" ftype="fasta" value="genome.fa"/> + <param name="ref_file" ftype="fasta.gz" value="genome.fa.gz"/> </conditional> </conditional> <output name="out_vcf" file="out1.vcf"/> @@ -195,3 +195,4 @@ ]]></help> <expand macro="citations"/> </tool> +
--- 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> +
--- a/test-data/all_fasta.loc Wed Jan 20 19:49:40 2021 +0000 +++ b/test-data/all_fasta.loc Thu Apr 29 12:24:00 2021 +0000 @@ -16,4 +16,4 @@ #fasta file. So there will be multiple fasta files for each build, #such as with hg19 above. # -jasmine jasmine jasmine ${__HERE__}/genome.fa \ No newline at end of file +jasmine jasmine jasmine ${__HERE__}/genome.fa.gz
--- a/test-data/genome.fa Wed Jan 20 19:49:40 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ ->1 -TAACCCTAACACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC -TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA -CACGTACGTACGTACGTACGTACGTACTGACGTACGT -AACCCTAACCCAA -CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAAC -CCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCT -CACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCC -TAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCA -ACCCCAACCCCAACCCTAACCCCTAACCCTAACCCTAACCCTACCCTAAC ->2 -TAACCCTAACACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC -TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA -CACGTACGTACGTACGTACGTACGTACTGACGTACGT -AACCCTAACCCAA -CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAAC -CCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCT -CACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCC -TAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCA -ACCCCAACCCCAACCCTAACCCCTAACCCTAACCCTAACCCTACCCTAAC \ No newline at end of file