Mercurial > repos > devteam > vcfbedintersect
comparison vcfbedintersect.xml @ 3:67ec5bcc35ec draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"
| author | iuc |
|---|---|
| date | Thu, 23 Jan 2020 12:53:46 +0000 |
| parents | b886d025cc05 |
| children |
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| 2:b886d025cc05 | 3:67ec5bcc35ec |
|---|---|
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
| 8 <command> | 8 <command> |
| 9 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed": | 9 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed": |
| 10 vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}" | 10 vcfintersect -b '${bed_vs_interval.bed_input}' ${invert} '${vcf_input}' > '${out_file1}' |
| 11 #else: | 11 #else: |
| 12 vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}" | 12 vcfintersect -R '${bed_vs_interval.int_input}' ${invert} '${vcf_input}' > '${out_file1}' |
| 13 #end if | 13 #end if |
| 14 </command> | 14 </command> |
| 15 <inputs> | 15 <inputs> |
| 16 <!-- selecting refernce source --> | 16 <!-- selecting refernce source --> |
| 17 <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" /> | 17 <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" /> |