Mercurial > repos > devteam > vcfprimers
diff vcfprimers.xml @ 4:17096387c0e6 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers commit 36e9065027cc7bf721e9d203208477ee88906c57"
| author | iuc |
|---|---|
| date | Thu, 23 Jan 2020 08:10:02 -0500 |
| parents | d226a7327946 |
| children |
line wrap: on
line diff
--- a/vcfprimers.xml Mon Mar 26 12:28:09 2018 -0400 +++ b/vcfprimers.xml Thu Jan 23 08:10:02 2020 -0500 @@ -5,14 +5,15 @@ </macros> <expand macro="requirements"/> <expand macro="stdio" /> - <command> + <command><![CDATA[ #set $reference_fasta_filename = "localref.fa" #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if - vcfprimers -f "${reference_fasta_filename}" -l "${primer_length}" "${input_vcf}" > "${out_file1}"</command> + vcfprimers -f '${reference_fasta_filename}' -l "${primer_length}" '${input_vcf}' > '${out_file1}' + ]]></command> <inputs> <param name="input_vcf" type="data" format="vcf" label="VCF dataset to extract flanks" /> <conditional name="reference_source"> @@ -24,7 +25,7 @@ <param name="ref_file" type="select" label="Select reference genome"> <options from_data_table="fasta_indexes"> </options> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <!-- FIX ME!!!! -->