Mercurial > repos > iuc > beacon2_vcf2bff

annotate vcf2bff.xml @ 0:7b17ad8f9fc8 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/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
author iuc
date Sun, 01 Oct 2023 16:29:00 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
1 <tool id="beacon2_vcf2bff" name="Beacon2 VCF2BFF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
2 <description>converting annotated VCF files to Beacon v2 format</description>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
3 <macros>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
4 <import>macros.xml</import>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
5 </macros>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
6 <expand macro="xrefs"/>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
8 <expand macro="creators"/>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
10 ln -s '$input' ./sample.vcf.gz &&
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
11 vcf2bff.pl
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
12 --input ./sample.vcf.gz
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
13 --format '$format'
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
14 --project-dir ./
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
15 --dataset-id '$dataset_id'
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
16 --genome '$genome'
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
17 && gunzip ./genomicVariationsVcf.json.gz
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
18 ]]></command>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
19 <inputs>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
20 <param argument="--input" type="data" format="tabular.gz" label="Annotated vcf file" help="The output genomic variations VCF file of bcftools, snpeff, snpsift" />
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
21 <param argument="--format" type="select" label="Output format" help="">
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
22 <option value="bff" selected="True">BFF</option>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
23 <option value="hash">hash</option>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
24 <option value="json">json</option>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
25 </param>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
26 <param argument="--dataset-id" type="text" label="Dataset ID" value="" help="Give an ID for the created genomicVariations dataset" />
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
27 <param argument="--genome" type="text" label="Reference genome" value="" help="Select the reference genome used the annotate the data to create the genomicVariations dataset examples for reference genomes are hs37, hg37 and hg38" />
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
28 </inputs>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
29 <outputs>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
30 <data name="genomicVariationsVcf" format="json" label="${tool.name} on ${on_string}: genomicVariationsVcf file" from_work_dir="genomicVariationsVcf.json" />
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
31 </outputs>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
32 <tests>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
33 <test expect_num_outputs="1">
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
34 <param name="input" ftype="tabular.gz" value="test.vcf.gz" />
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
35 <param name="format" value="bff"/>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
36 <param name="dataset_id" value="beacon"/>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
37 <param name="genome" value="hg19"/>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
38 <output name="genomicVariationsVcf" file="genomicVariationsVcf.json" ftype="json" compare="sim_size">
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
39 <assert_contents><has_size value="730000" delta="90000" /></assert_contents>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
40 </output>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
41 </test>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
42 </tests>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
43 <help><![CDATA[
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
44 The tool Creates genomicVariations file from annotated genomic variations VCF file. The VCF file is annotated by using the
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
45 workflow of those tools bcftools -> snpeff -> snpsift.
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
46 The tool converts the annotated VCF file into genomicVariations entry type and serializes it as a JSON file also called Beacon Friendly Format (BFF).
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
47 The generated file will be ready to be stored on the MongoDB instance as MongoDB works directly with JSON files.
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
48 ]]></help>
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
49 <expand macro="citations" />
7b17ad8f9fc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
parents:
diff changeset
50 </tool>