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comparison vcfgeno2haplo.xml @ 0:74d4e986f488 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgeno2haplo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:32:31 -0500
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-1:000000000000 0:74d4e986f488
1 <tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.3">
2 <description>Convert genotype-based phased alleles into haplotype alleles</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 vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
16 <inputs>
17 <conditional name="reference_source">
18 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
19 <option value="cached">Locally cached</option>
20 <option value="history">History</option>
21 </param>
22 <when value="cached">
23 <param name="ref_file" type="select" label="Select reference genome">
24 <options from_data_table="fasta_indexes">
25 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
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 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
30 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
31 <validator type="unspecified_build" />
32 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
33 -->
34 </param>
35 </when>
36 <when value="history"> <!-- FIX ME!!!! -->
37 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
38 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
39 </when>
40 </conditional>
41 <param name="window_size" type="text" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" />
42 <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
43 <!-- <option value=" ">Output entire haplotype</option>
44 <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
45 </param> -->
46 </inputs>
47 <outputs>
48 <data format="vcf" name="out_file1" />
49 </outputs>
50 <tests>
51 <test>
52 <param name="reference_source_selector" value="history" />
53 <param name="output_option" value="true" />
54 <param name="window_size" value="5000" />
55 <param name="input_vcf" value="vcflib-phix.vcf"/>
56 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
57 <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
58 </test>
59 </tests>
60 <help>
61
62 Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.
63
64 The options are::
65
66 -w, --window-size N Merge variants at most this many bp apart (default 30)
67 -o, --only-variants Don't output the entire haplotype, just concatenate
68 REF/ALT strings (delimited by ":")
69
70 ----
71
72 Vcfgeno2haplo @IS_PART_OF_VCFLIB@
73 </help>
74 <expand macro="citations" />
75 </tool>