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comparison vcfleftalign.xml @ 4:50cf7cabae50 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:58:13 +0000
parents 9c4a2ef55965
children
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3:9c4a2ef55965 4:50cf7cabae50
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( $reference_source.ref_file.fields.path )
14 #end if 14 #end if
15 vcfleftalign -r "${reference_fasta_filename}" -w "${window_size}" "${input_vcf}" > "${out_file1}"</command> 15 vcfleftalign -r '${reference_fasta_filename}' -w "${window_size}" '${input_vcf}' > '${out_file1}'
16 ]]></command>
16 <inputs> 17 <inputs>
17 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" /> 18 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" />
18 <conditional name="reference_source"> 19 <conditional name="reference_source">
19 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 20 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
20 <option value="cached">Locally cached</option> 21 <option value="cached">Locally cached</option>
21 <option value="history">History</option> 22 <option value="history">History</option>
22 </param> 23 </param>
23 <when value="cached"> 24 <when value="cached">
24 <param name="ref_file" type="select" label="Select reference genome"> 25 <param name="ref_file" type="select" label="Select reference genome">
25 <options from_data_table="fasta_indexes"> 26 <options from_data_table="fasta_indexes">
26 </options> 27 </options>
27 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 28 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
28 </param> 29 </param>
29 </when> 30 </when>
30 <when value="history"> <!-- FIX ME!!!! --> 31 <when value="history"> <!-- FIX ME!!!! -->
31 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> 32 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
32 </when> 33 </when>
33 </conditional> 34 </conditional>
34 <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" /> 35 <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" />
35 </inputs> 36 </inputs>
36 <outputs> 37 <outputs>
37 <data format="vcf" name="out_file1" /> 38 <data format="vcf" name="out_file1" />
38 </outputs> 39 </outputs>
39 <tests> 40 <tests>