Mercurial > repos > devteam > vcfannotate

annotate vcfannotate.xml @ 3:492d9c83a284 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/vcfannotate commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:53:02 +0000
parents e13203eab380
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
e13203eab380 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
1 <tool id="vcfannotate" name="VCFannotate:" version="@WRAPPER_VERSION@+galaxy0">
1
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
2 <description>Intersect VCF records with BED annotations</description>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
3 <macros>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
4 <import>macros.xml</import>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
5 </macros>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
6 <expand macro="requirements"/>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
7 <expand macro="stdio" />
3
492d9c83a284 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
8 <command>vcfannotate --key '${key_option}' -b '${bed_data}' '${input}' > '${out_file1}'</command>
1
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
9 <inputs>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
10 <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
11 <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
12 <param name="key_option" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
13 </inputs>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
14 <outputs>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
15 <data format="vcf" name="out_file1" />
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
16 </outputs>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
17 <tests>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
18 <test>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
19 <param name="bed_data" value="vcfannotate.bed" ftype="bed"/>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
20 <param name="key_option" value="BED-features"/>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
21 <param name="input" value="vcflib.vcf"/>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
22 <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" />
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
23 </test>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
24 </tests>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
25 <help>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
26
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
27 Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file.
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
28
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
29 -----
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
30
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
31 .. class:: infomark
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
32
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
33
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
34 **Example**:
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
35
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
36 The following VCF line::
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
37
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
38 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
39 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
40
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
41 will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen::
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
42
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
43 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
44 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
45
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
46 ----
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
47
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
48 Vcfannotate @IS_PART_OF_VCFLIB@
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
49 </help>
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
50 <expand macro="citations" />
a5c0a47fd35a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
51 </tool>