annotate snpSift_rmInfo.xml @ 3:20c7d583fec1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:32 -0400
parents bf8c1526871b
children 09d6806c609e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
1 <tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.0">
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
2 <description>remove INFO field annotations</description>
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[
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
10 SnpSift -Xmx2G rmInfo
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
11 '$input'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
12 #echo ' '.join($info_fields.split(','))
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
13 > '$output'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
14 ]]></command>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
15 <inputs>
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
16 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
17 <param name="info_fields" type="text" value="" label="Info fields to remove, e.g. EFF">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
18 <help>Separate multiple INFO fields with a comma, e.g.: EFF,DP</help>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
19 <validator type="empty_field" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
20 </param>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
21 </inputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
22 <outputs>
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
23 <data name="output" format="vcf" />
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
24 </outputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
25 <tests>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
26 <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
27 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
28 <param name="info_fields" value="EFF"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
29 <output name="output">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
30 <assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
31 <has_text text="DP=29" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
32 <not_has_text text="EFF=EXON" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
33 </assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
34 </output>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
35 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
36 </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
37 <help><![CDATA[
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
38 This command removes INFO fields from a VCF file (i.e. removes annotations)
9e8280e19338 Uploaded
iuc
parents:
diff changeset
39
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
40 Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later.
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
41
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
42 SnpEff & SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate.
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
43 The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones.
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
44
9e8280e19338 Uploaded
iuc
parents:
diff changeset
45 @EXTERNAL_DOCUMENTATION@
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
46 - http://snpeff.sourceforge.net/SnpSift.html#rmInfo
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
47 ]]></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
48 <expand macro="citations" />
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
49 </tool>