Mercurial > repos > sanbi-uwc > vcf_to_alignment
comparison vcf_to_alignment.xml @ 5:4f3f7d390382 draft default tip
planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76-dirty
| author | sanbi-uwc |
|---|---|
| date | Wed, 17 Oct 2018 02:35:51 -0400 |
| parents | f58178c0f00d |
| children |
comparison
equal
deleted
inserted
replaced
| 4:f58178c0f00d | 5:4f3f7d390382 |
|---|---|
| 1 <?xml version="1.0" encoding="utf-8" ?> | 1 <?xml version="1.0" encoding="utf-8" ?> |
| 2 <tool id="vcf_to_alignment" name="Generate FASTA alignment from VCF collection" version="0.4"> | 2 <tool id="vcf_to_alignment" name="Generate FASTA alignment from VCF collection" version="0.5"> |
| 3 <description>Generate a multiple sequence alignment given a collection of variants and a reference sequence</description> | 3 <description>Generate a multiple sequence alignment given a collection of variants and a reference sequence</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="1.67">biopython</requirement> | 5 <requirement type="package" version="1.67">biopython</requirement> |
| 6 <requirement type="package" version="0.6.8">pyvcf</requirement> | 6 <requirement type="package" version="0.6.8">pyvcf</requirement> |
| 7 <requirement type="package" version="2.1.0">intervaltree</requirement> | 7 <requirement type="package" version="2.1.0">intervaltree</requirement> |
| 45 <validator type="no_options" message="No FASTA datasets are available for the selected input dataset" /> | 45 <validator type="no_options" message="No FASTA datasets are available for the selected input dataset" /> |
| 46 </param> | 46 </param> |
| 47 </when> | 47 </when> |
| 48 </conditional> | 48 </conditional> |
| 49 <conditional name="exclude_list"> | 49 <conditional name="exclude_list"> |
| 50 <param name="do_exclude" type="select"> | 50 <param name="do_exclude" type="select" label="Exclude SNPs from specified regions"> |
| 51 <option value="yes">Yes</option> | 51 <option value="yes">Yes</option> |
| 52 <option value="no" selected="true">No</option> | 52 <option value="no" selected="true">No</option> |
| 53 </param> | 53 </param> |
| 54 <when value="yes"> | 54 <when value="yes"> |
| 55 <param name="exclude_file" type="data" format="bed" label="BED file with regions to exclude" /> | 55 <param name="exclude_file" type="data" format="bed" label="BED file with regions to exclude" /> |