| Previous changeset 0:026d0f104183 (2013-11-24) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7 |
|
modified:
tool_dependencies.xml vcftools_isec.xml |
| b |
| diff -r 026d0f104183 -r aa232e38338f tool_dependencies.xml --- a/tool_dependencies.xml Sun Nov 24 14:03:51 2013 -0500 +++ b/tool_dependencies.xml Wed Nov 11 13:02:25 2015 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="vcftools" version="0.1.11"> - <repository changeset_revision="61f9ddecde82" name="package_vcftools_0_1_11" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="710efaae2ff8" name="package_vcftools_0_1_11" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
| b |
| diff -r 026d0f104183 -r aa232e38338f vcftools_isec.xml --- a/vcftools_isec.xml Sun Nov 24 14:03:51 2013 -0500 +++ b/vcftools_isec.xml Wed Nov 11 13:02:25 2015 -0500 |
| [ |
| @@ -1,17 +1,17 @@ -<tool id="vcftools_isec" name="Intersect" version="0.1"> +<tool id="vcftools_isec" name="Intersect" version="0.1.1"> <description>multiple VCF datasets</description> <requirements> <requirement type="package">tabix</requirement> <requirement type="package" version="0.1.11">vcftools</requirement> </requirements> - + <command> ## Preprocessing for each dataset. #set dataset_names = [] - #for i, $input in enumerate( $inputs ): + #for i, $input in enumerate( $input_files ): ## Sort file. - vcf-sort ${input.file} > ${i}.vcf.sorted ; + vcf-sort ${input} > ${i}.vcf.sorted ; ## Compress. bgzip ${i}.vcf.sorted ; @@ -26,13 +26,11 @@ vcf-isec -f #if $complement: -c - #end if + #end if #echo ' '.join( dataset_names ) # > ${output} </command> <inputs> - <repeat name="inputs" title="Dataset" min="2"> - <param name="file" label="Dataset" type="data" format="vcf"/> - </repeat> + <param name="input_files" label="Datasets" type="data" format="vcf" min="2" multiple="True"/> <param name="complement" type="boolean" label="Complement intersection" help="If checked, output positions present in the first file but missing from the other files"/> </inputs> @@ -47,8 +45,8 @@ <tests> <!-- Cannot specify multiple repeats in test framework right now. <test> - <param name='inputs|1' value='1.vcf' /> - <param name='inputs|2' value='2.vcf' /> + <param name='input_files|1' value='1.vcf' /> + <param name='input_files|2' value='2.vcf' /> <param name='complement' value='False' /> <output name='output' file='out.vcf' /> </test> |