| Previous changeset 4:6f6bf10618d7 (2018-03-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit 36e9065027cc7bf721e9d203208477ee88906c57" |
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modified:
macros.xml vcfvcfintersect.xml |
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| diff -r 6f6bf10618d7 -r 166c4f50525f macros.xml --- a/macros.xml Mon Mar 26 12:29:13 2018 -0400 +++ b/macros.xml Thu Jan 23 08:11:02 2020 -0500 |
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| @@ -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> |
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| diff -r 6f6bf10618d7 -r 166c4f50525f vcfvcfintersect.xml --- a/vcfvcfintersect.xml Mon Mar 26 12:29:13 2018 -0400 +++ b/vcfvcfintersect.xml Thu Jan 23 08:11:02 2020 -0500 |
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| @@ -5,20 +5,20 @@ </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 #if $adv_options.adv_options_selector == "use_adv_controls": - vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" + vcfintersect '${adv_options.adv_options_input}' ${loci} ${invert} -r '${reference_fasta_filename}' -w "${window_size}" ${isect_union} '${vcf_input1}' '${vcf_input2}' > '${out_file1}' #else: - vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" + vcfintersect ${loci} ${invert} -r '${reference_fasta_filename}' -w "${window_size}" ${isect_union} '${vcf_input1}' '${vcf_input2}' > '${out_file1}' #end if - </command> + ]]></command> <inputs> <!-- selecting refernce source --> <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" /> |