Mercurial > repos > devteam > vcfcheck
comparison vcfcheck.xml @ 4:2b86cb8d0d51 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck commit 36e9065027cc7bf721e9d203208477ee88906c57"
author | iuc |
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date | Thu, 23 Jan 2020 12:54:30 +0000 |
parents | 713575be4f77 |
children | 8628527d2d7f |
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3:713575be4f77 | 4:2b86cb8d0d51 |
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5 </macros> | 5 </macros> |
6 <expand macro="requirements"></expand> | 6 <expand macro="requirements"></expand> |
7 <stdio> | 7 <stdio> |
8 <regex match="index file" source="stderr" level="warning"/> | 8 <regex match="index file" source="stderr" level="warning"/> |
9 </stdio> | 9 </stdio> |
10 <command> | 10 <command><![CDATA[ |
11 #set $reference_fasta_filename = "localref.fa" | 11 #set $reference_fasta_filename = "localref.fa" |
12 #if str( $reference_source.reference_source_selector ) == "history": | 12 #if str( $reference_source.reference_source_selector ) == "history": |
13 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | 13 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && |
14 #else: | 14 #else: |
15 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | 15 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
16 #end if | 16 #end if |
17 vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command> | 17 vcfcheck $failure_selector -f '${reference_fasta_filename}' '${input_vcf}' > '${out_file1}' |
18 ]]></command> | |
18 <inputs> | 19 <inputs> |
19 <conditional name="reference_source"> | 20 <conditional name="reference_source"> |
20 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | 21 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |
21 <option value="cached">Locally cached</option> | 22 <option value="cached">Locally cached</option> |
22 <option value="history">History</option> | 23 <option value="history">History</option> |