| Previous changeset 3:5e850c85ba32 (2018-03-26) Next changeset 5:aa8e8c96ca06 (2021-11-23) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck commit 36e9065027cc7bf721e9d203208477ee88906c57" |
|
modified:
macros.xml vcfcheck.xml |
| b |
| diff -r 5e850c85ba32 -r 2968c6916579 macros.xml --- a/macros.xml Mon Mar 26 12:22:22 2018 -0400 +++ b/macros.xml Thu Jan 23 08:05:52 2020 -0500 |
| b |
| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.0.0_rc1">vcflib</requirement> + <requirement type="package" version="1.0.0_rc3">vcflib</requirement> <yield/> </requirements> </xml> @@ -10,10 +10,10 @@ <exit_code range="1:" level="fatal" /> </stdio> </xml> - <token name="@WRAPPER_VERSION@">1.0.0_rc1</token> - <xml name="citations"> - <citations> - <citation type="bibtex"> + <token name="@WRAPPER_VERSION@">1.0.0_rc3</token> + <xml name="citations"> + <citations> + <citation type="bibtex"> @misc{Garrison2015, author = {Garrison, Erik}, year = {2015}, @@ -22,8 +22,8 @@ journal = {GitHub repository}, url = {https://github.com/ekg/vcflib}, } - </citation> - </citations> - </xml> + </citation> + </citations> + </xml> <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token> </macros> |
| b |
| diff -r 5e850c85ba32 -r 2968c6916579 vcfcheck.xml --- a/vcfcheck.xml Mon Mar 26 12:22:22 2018 -0400 +++ b/vcfcheck.xml Thu Jan 23 08:05:52 2020 -0500 |
| [ |
| @@ -7,14 +7,15 @@ <stdio> <regex match="index file" source="stderr" level="warning"/> </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 - vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command> + vcfcheck $failure_selector -f '${reference_fasta_filename}' '${input_vcf}' > '${out_file1}' + ]]></command> <inputs> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |