Mercurial > repos > devteam > vcf2tsv

annotate vcf2tsv.xml @ 3:483d5234923e 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/vcf2tsv commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:51:57 +0000
parents eee41a27d68a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
eee41a27d68a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 1
diff changeset
1 <tool id="vcf2tsv" name="VCFtoTab-delimited:" version="@WRAPPER_VERSION@+galaxy0">
1
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
2 <description>Convert VCF data into TAB-delimited format</description>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
3 <macros>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
4 <import>macros.xml</import>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
5 </macros>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
6 <expand macro="requirements"/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
7 <expand macro="stdio" />
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
8 <command>vcf2tsv ${g_option} -n '${null_filler}' '${input}' > '${out_file1}'</command>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
9 <inputs>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
10 <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
11 <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
12 <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" >
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
13 <option value="">Nothing</option>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
14 <option value=".">.</option>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
15 <option value="*">*</option>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
16 <option value="NULL">NULL</option>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
17 </param>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
18 </inputs>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
19 <outputs>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
20 <data format="tabular" name="out_file1" />
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
21 </outputs>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
22 <tests>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
23 <test>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
24 <param name="g_option" value="true"/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
25 <param name="null_filler" value="."/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
26 <param name="input" value="vcflib.vcf"/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
27 <output name="out_file1" file="vcf2tsv-test1.tab"/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
28 </test>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
29 <test>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
30 <param name="g_option" value="false"/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
31 <param name="null_filler" value="."/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
32 <param name="input" value="vcflib.vcf"/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
33 <output name="out_file1" file="vcf2tsv-test2.tab"/>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
34 </test>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
35 </tests>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
36 <help>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
37 Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table.
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
38 Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information.
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
39
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
40 ----
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
41
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
42 Vcf2Tsv @IS_PART_OF_VCFLIB@
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
43 </help>
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
44 <expand macro="citations" />
70e8edde1030 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
45 </tool>