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comparison vcfvcfintersect.xml @ 5:166c4f50525f draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 08:11:02 -0500
parents 6f6bf10618d7
children
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4:6f6bf10618d7 5:166c4f50525f
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 #set $reference_fasta_filename = "localref.fa" 9 #set $reference_fasta_filename = "localref.fa"
10 #if str( $reference_source.reference_source_selector ) == "history": 10 #if str( $reference_source.reference_source_selector ) == "history":
11 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 11 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
12 #else: 12 #else:
13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
14 #end if 14 #end if
15 15
16 #if $adv_options.adv_options_selector == "use_adv_controls": 16 #if $adv_options.adv_options_selector == "use_adv_controls":
17 vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" 17 vcfintersect '${adv_options.adv_options_input}' ${loci} ${invert} -r '${reference_fasta_filename}' -w "${window_size}" ${isect_union} '${vcf_input1}' '${vcf_input2}' > '${out_file1}'
18 #else: 18 #else:
19 vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" 19 vcfintersect ${loci} ${invert} -r '${reference_fasta_filename}' -w "${window_size}" ${isect_union} '${vcf_input1}' '${vcf_input2}' > '${out_file1}'
20 #end if 20 #end if
21 </command> 21 ]]></command>
22 <inputs> 22 <inputs>
23 <!-- selecting refernce source --> 23 <!-- selecting refernce source -->
24 <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" /> 24 <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" />
25 <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset" 25 <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset"
26 help="The second dataset will be instersected with the first"/> 26 help="The second dataset will be instersected with the first"/>