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comparison vcfleftalign.xml @ 0:4155d2ba5561 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfleftalign commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:33:24 -0500
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children f0982f54fef1
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1 <tool id="vcfleftalign" name="VCFleftAlign:" version="0.0.3">
2 <description>Left-align indels and complex variants in VCF dataset</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <command>
9 #set $reference_fasta_filename = "localref.fa"
10 #if str( $reference_source.reference_source_selector ) == "history":
11 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
12 #else:
13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
14 #end if
15 vcfleftalign -r "${reference_fasta_filename}" -w "${window_size}" "${input_vcf}" > "${out_file1}"</command>
16 <inputs>
17 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" />
18 <conditional name="reference_source">
19 <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="history">History</option>
22 </param>
23 <when value="cached">
24 <param name="ref_file" type="select" label="Select reference genome">
25 <options from_data_table="fasta_indexes">
26 </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 </param>
29 </when>
30 <when value="history"> <!-- FIX ME!!!! -->
31 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
32 </when>
33 </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 </inputs>
36 <outputs>
37 <data format="vcf" name="out_file1" />
38 </outputs>
39 <tests>
40 <test>
41 <param name="reference_source_selector" value="history" />
42 <param name="input_vcf" value="vcflib-phix.vcf"/>
43 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
44 <param name="window_size" value="150" />
45 <output name="out_file1" file="vcfleftalign-test1.vcf"/>
46 </test>
47 </tests>
48 <help>
49
50 Left-aligns variants in VCF dataset. Window size is determined dynamically according to the entropy of the regions flanking the indel. These must have entropy > 1 bit/bp, or be shorter than ~5kb.
51
52 ----
53
54 Vcfleftalign @IS_PART_OF_VCFLIB@
55 </help>
56 <expand macro="citations" />
57 </tool>