Mercurial > repos > devteam > vcfbedintersect

annotate vcfbedintersect.xml @ 3:67ec5bcc35ec draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:53:46 +0000
parents b886d025cc05
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
b886d025cc05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
1 <tool id="vcfbedintersect" name="VCF-BEDintersect:" version="@WRAPPER_VERSION@+galaxy0">
1
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
2 <description>Intersect VCF and BED datasets</description>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
3 <macros>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
4 <import>macros.xml</import>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
5 </macros>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
6 <expand macro="requirements"/>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
7 <expand macro="stdio" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
8 <command>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
9 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
3
67ec5bcc35ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
10 vcfintersect -b '${bed_vs_interval.bed_input}' ${invert} '${vcf_input}' > '${out_file1}'
1
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
11 #else:
3
67ec5bcc35ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
12 vcfintersect -R '${bed_vs_interval.int_input}' ${invert} '${vcf_input}' > '${out_file1}'
1
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
13 #end if
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
14 </command>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
15 <inputs>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
16 <!-- selecting refernce source -->
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
17 <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
18 <conditional name="bed_vs_interval">
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
19 <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with">
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
20 <option value="bed">BED</option>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
21 <option value="interval">Interval</option>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
22 </param>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
23 <when value="bed">
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
24 <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
25 </when>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
26 <when value="interval">
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
27 <param name="int_input" type="text" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
28 </when>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
29 </conditional>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
30 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
31 </inputs>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
32 <outputs>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
33 <data format="vcf" name="out_file1" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
34 </outputs>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
35 <tests>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
36 <test>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
37 <param name="bed_vs_interval_selector" value="bed" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
38 <param name="bed_input" value="vcfannotate.bed" ftype="bed" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
39 <param name="invert" value="False" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
40 <param name="vcf_input" value="vcflib.vcf"/>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
41 <output name="out_file1" file="vcfbedintersect-test1.vcf"/>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
42 </test>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
43 <test>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
44 <param name="bed_vs_interval_selector" value="interval" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
45 <param name="int_input" value="20:1-30000" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
46 <param name="invert" value="False" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
47 <param name="vcf_input" value="vcflib.vcf"/>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
48 <output name="out_file1" file="vcfbedintersect-test2.vcf"/>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
49 </test>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
50 </tests>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
51 <help>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
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).
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
53
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
54 ----
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
55
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
56 VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
57 </help>
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
58 <expand macro="citations" />
300910e82a2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
59 </tool>