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comparison vcfbedintersect.xml @ 2:31a86dbe17c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:08:06 -0400
parents 834e1f313036
children 9edfe5145ba8
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1:834e1f313036 2:31a86dbe17c0
1 <tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.3"> 1 <tool id="vcfbedintersect" name="VCF-BEDintersect:" version="@WRAPPER_VERSION@.0">
2 <description>Intersect VCF and BED datasets</description> 2 <description>Intersect VCF and BED datasets</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed": 9 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
10 vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}" 10 vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}"
11 #else: 11 #else:
12 vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}" 12 vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}"
13 #end if 13 #end if
14 14 </command>
15 </command> 15 <inputs>
16 <inputs> 16 <!-- selecting refernce source -->
17 <!-- selecting refernce source --> 17 <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" />
18 <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" /> 18 <conditional name="bed_vs_interval">
19 <conditional name="bed_vs_interval"> 19 <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with">
20 <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with"> 20 <option value="bed">BED</option>
21 <option value="bed">BED</option> 21 <option value="interval">Interval</option>
22 <option value="interval">Interval</option> 22 </param>
23 </param> 23 <when value="bed">
24 <when value="bed"> 24 <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
25 <param name="bed_input" type="data" format="bed" label="Select BED dataset" /> 25 </when>
26 </when> 26 <when value="interval">
27 <when value="interval"> 27 <param name="int_input" type="text" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" />
28 <param name="int_input" type="text" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" /> 28 </when>
29 </when> 29 </conditional>
30 </conditional> 30 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." />
31 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." /> 31 </inputs>
32 </inputs> 32 <outputs>
33 <outputs> 33 <data format="vcf" name="out_file1" />
34 <data format="vcf" name="out_file1" /> 34 </outputs>
35 </outputs> 35 <tests>
36 <tests> 36 <test>
37 <test> 37 <param name="bed_vs_interval_selector" value="bed" />
38 <param name="bed_vs_interval_selector" value="bed" /> 38 <param name="bed_input" value="vcfannotate.bed" ftype="bed" />
39 <param name="bed_input" value="vcfannotate.bed" /> 39 <param name="invert" value="False" />
40 <param name="invert" value="False" /> 40 <param name="vcf_input" value="vcflib.vcf"/>
41 <param name="vcf_input" value="vcflib.vcf"/> 41 <output name="out_file1" file="vcfbedintersect-test1.vcf"/>
42 <output name="out_file1" file="vcfbedintersect-test1.vcf"/> 42 </test>
43 </test> 43 <test>
44 <test> 44 <param name="bed_vs_interval_selector" value="interval" />
45 <param name="bed_vs_interval_selector" value="interval" /> 45 <param name="int_input" value="20:1-30000" />
46 <param name="int_input" value="20:1-30000" /> 46 <param name="invert" value="False" />
47 <param name="invert" value="False" /> 47 <param name="vcf_input" value="vcflib.vcf"/>
48 <param name="vcf_input" value="vcflib.vcf"/> 48 <output name="out_file1" file="vcfbedintersect-test2.vcf"/>
49 <output name="out_file1" file="vcfbedintersect-test2.vcf"/> 49 </test>
50 </test>
51 </tests> 50 </tests>
52 51 <help>
53 <help>
54
55 Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end). 52 Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end).
56 53
57 ---- 54 ----
58 55
59 VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). 56 VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
60 </help> 57 </help>
61 <expand macro="citations" /> 58 <expand macro="citations" />
62 </tool> 59 </tool>