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comparison vcfvcfintersect.xml @ 0:b29dbe1270b5 draft

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author devteam
date Thu, 19 Mar 2015 14:47:59 -0400
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1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.3">
2 <description>Intersect two VCF datasets</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <command>
9
10 #set $reference_fasta_filename = "localref.fa"
11 #if str( $reference_source.reference_source_selector ) == "history":
12 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
13 #else:
14 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
15 #end if
16
17 #if $adv_options.adv_options_selector == True:
18
19 vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"
20
21 #else:
22
23 vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"
24
25 #end if
26
27 </command>
28 <inputs>
29 <!-- selecting refernce source -->
30 <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" />
31 <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset" help="The second dataset will be instersected with the first"/>
32 <conditional name="reference_source">
33 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome" help="This tools needs to access reference genomes sequence specified by this option.">
34 <option value="cached">Locally cached</option>
35 <option value="history">History</option>
36 </param>
37 <when value="cached">
38 <param name="ref_file" type="select" label="Select reference genome">
39 <options from_data_table="fasta_indexes">
40 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
41 </options>
42 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
43 </param>
44 </when>
45 <when value="history"> <!-- FIX ME!!!! -->
46 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
47 </when>
48 </conditional>
49 <param name="isect_union" type="select" label="Union or intersection" help="-i or -u">
50 <option value="-i">Intersect</option>
51 <option value="-u">Union</option>
52 </param>
53 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" />
54 <param name="window_size" type="integer" value="30" label="compare records up to this many bp away (window size)" help="-w, --window-size" />
55 <param name="loci" type="boolean" truevalue="-l" falsevalue="" label="output whole loci when one alternate allele matches" help="-l, --loci" />
56 <conditional name="adv_options">
57 <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/>
58 <when value="use_adv_controls">
59 <param name="adv_options_input" type="text" value="-t &quot;vcfvcf-intersect-result&quot;" label="Enter additional command line options described in the help section below" help="such as -m, -t, -V, -M, and -T" />
60 <sanitizer>
61 <valid initial="string.printable">
62 <remove value="&apos;"/>
63 </valid>
64 <mapping initial="none">
65 <add source="&apos;" target="__sq__"/>
66 </mapping>
67 </sanitizer>
68 </when>
69 </conditional>
70 </inputs>
71 <outputs>
72 <data format="vcf" name="out_file1" />
73 </outputs>
74 <tests>
75 <test>
76 <param name="reference_source_selector" value="history" />
77 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
78 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
79 <param name="isect_union" value="-i" />
80 <param name="invert" value="False" />
81 <param name="loci" value="False" />
82 <patam name="adv_options" value="False" />
83 <param name="window_size" value="30" />
84 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
85 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/>
86 </test>
87 <test>
88 <param name="reference_source_selector" value="history" />
89 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
90 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
91 <param name="isect_union" value="-u" />
92 <param name="invert" value="False" />
93 <param name="loci" value="False" />
94 <patam name="adv_options" value="False" />
95 <param name="window_size" value="30" />
96 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
97 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/>
98 </test>
99 </tests>
100 <help>
101
102 Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp.
103
104 The options are::
105
106 -v, --invert invert the selection, printing only records which would
107 -i, --intersect-vcf FILE use this VCF for set intersection generation
108 -u, --union-vcf FILE use this VCF for set union generation
109 -w, --window-size N compare records up to this many bp away (default 30)
110 -l, --loci output whole loci when one alternate allele matches
111 -m, --ref-match intersect on the basis of record REF string
112 -t, --tag TAG attach TAG to each record's info field if it would intersect
113 -V, --tag-value VAL use this value to indicate that the allele is passing
114 '.' will be used otherwise. default: 'PASS'
115 -M, --merge-from FROM-TAG
116 -T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG
117 in the current file.
118
119 ----
120
121 VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
122 </help>
123 <expand macro="citations" />
124 </tool>