| Previous changeset 3:d2406f98a782 (2018-03-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57" |
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modified:
macros.xml vcfleftalign.xml |
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| diff -r d2406f98a782 -r 29f9b782727e macros.xml --- a/macros.xml Mon Mar 26 12:27:39 2018 -0400 +++ b/macros.xml Thu Jan 23 08:09:46 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 d2406f98a782 -r 29f9b782727e vcfleftalign.xml --- a/vcfleftalign.xml Mon Mar 26 12:27:39 2018 -0400 +++ b/vcfleftalign.xml Thu Jan 23 08:09:46 2020 -0500 |
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| @@ -5,33 +5,34 @@ </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( $reference_source.ref_file.fields.path ) #end if - vcfleftalign -r "${reference_fasta_filename}" -w "${window_size}" "${input_vcf}" > "${out_file1}"</command> + vcfleftalign -r '${reference_fasta_filename}' -w "${window_size}" '${input_vcf}' > '${out_file1}' + ]]></command> <inputs> -<param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" /> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> - <option value="cached">Locally cached</option> - <option value="history">History</option> - </param> - <when value="cached"> - <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"/> - </param> - </when> - <when value="history"> <!-- FIX ME!!!! --> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> - </when> - </conditional> - <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" /> + <param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <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"/> + </param> + </when> + <when value="history"> <!-- FIX ME!!!! --> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" /> </inputs> <outputs> <data format="vcf" name="out_file1" /> |