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comparison vcfcheck.xml @ 4:2b86cb8d0d51 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:54:30 +0000
parents 713575be4f77
children 8628527d2d7f
comparison
equal deleted inserted replaced
3:713575be4f77 4:2b86cb8d0d51
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}" "${reference_fasta_filename}" &amp;&amp; 13 ln -s '${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>