Mercurial > repos > iuc > snpsift

annotate snpSift_vcfCheck.xml @ 2:bf8c1526871b draft

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/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:11:18 -0500
parents 98708b88af9f
children 20c7d583fec1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.1">
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
2 <description>basic checks for VCF specification compliance</description>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
3 <macros>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
4 <import>snpSift_macros.xml</import>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
5 </macros>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
6 <expand macro="requirements" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
7 <expand macro="stdio" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
8 <expand macro="version_command" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
9 <command><![CDATA[
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
10 @CONDA_SNPSIFT_JAR_PATH@ &&
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
11 java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
12 ]]>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
13 </command>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
14 <inputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
15 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
16 </inputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
17 <outputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
18 <data format="vcf" name="output" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
19 </outputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
20 <tests>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
21 <test>
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
22 <param name="input" ftype="vcf" value="test_bad.vcf"/>
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
23 <assert_stderr>
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
24 <has_text text="Errors" />
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
25 </assert_stderr>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
26 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
27 </tests>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
28 <help><![CDATA[
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
29 Perform some basic check ups on VCF files to spot common problems.
9e8280e19338 Uploaded
iuc
parents:
diff changeset
30
9e8280e19338 Uploaded
iuc
parents:
diff changeset
31 SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool.
9e8280e19338 Uploaded
iuc
parents:
diff changeset
32
9e8280e19338 Uploaded
iuc
parents:
diff changeset
33 @EXTERNAL_DOCUMENTATION@
9e8280e19338 Uploaded
iuc
parents:
diff changeset
34 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
35 ]]>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
36 </help>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
37 <expand macro="citations" />
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
38 </tool>