snpsift: snpSift_filter.xml annotate

annotate snpSift_filter.xml @ 7:2e497a770bca draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"

author	iuc
date	Sun, 29 Nov 2020 21:14:56 +0000
parents	09d6806c609e
children

rev	line source
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	1 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.galaxy1">
0 9e8280e19338 Uploaded iuc parents: diff changeset	2 <description>Filter variants using arbitrary expressions</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 -Xmx6G filter -f '$input' -e '$exprFile' $inverse
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	11 #if str($filter_expression.type) == 'complex':
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	12 #for $set_file in $filter_expression.set:
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	13 --set $set_file
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	14 #end for
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	15 #end if
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	16 #if $filtering.mode == 'set_filter':
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	17 --filterID $filtering.filter_id
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	18 #elif $filtering.mode == 'remove_filter':
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	19 --rmFilter $filtering.rm_filter
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	20 #elif $filtering.mode == 'add_filter':
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	21 --addFilter $filtering.add_filter
3 20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	22 #end if
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	23 > '$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	24 ]]></command>
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	25 <configfiles>
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	26 <configfile name="exprFile">
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	27 $filter_expression.expr#slurp
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	28 </configfile>
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	29 </configfiles>
0 9e8280e19338 Uploaded iuc parents: diff changeset	30 <inputs>
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	31 <param name="input" type="data" format="vcf" label="Input variant list in VCF format"/>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	32 <conditional name="filter_expression">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	33 <param name="type" type="select"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	34 label="Type of filter expression">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	35 <option value="simple">Simple expression</option>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	36 <option value="complex">Expression using value set(s)</option>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	37 </param>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	38 <when value="simple">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	39 <param name="expr" type="text" label="Filter criteria"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	40 help="Need help? See the tool help below for some examples.">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	41 <sanitizer sanitize="False"/>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	42 </param>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	43 </when>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	44 <when value="complex">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	45 <param name="expr" type="text" label="Filter criteria"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	46 help="Need help? See the tool help below for some examples.">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	47 <sanitizer sanitize="False"/>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	48 </param>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	49 <param name="set" type="data" format="txt" multiple="true" optional="False"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	50 label="Set value source"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	51 help="Select one or more datasets for construction of value sets. The datasets are supposed to specify one value per line. See also: the help section on Sets below." />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	52 </when>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	53 </conditional>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	54 <param argument="--inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Invert filter" help="Select variants that do not match the filter expression." />
0 9e8280e19338 Uploaded iuc parents: diff changeset	55 <conditional name="filtering">
9e8280e19338 Uploaded iuc parents: diff changeset	56 <param name="mode" type="select" label="Filter mode">
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	57 <option value="entries" selected="true">Retain selected variants, remove others</option>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	58 <option value="set_filter">Add a value to FILTER field of non-selected variants</option>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	59 <option value="remove_filter">Remove a value from FILTER field of selected variants</option>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	60 <option value="add_filter">Add a value to the FILTER field of selected variants</option>
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	61 </param>
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	62 <when value="entries" />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	63 <when value="set_filter">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	64 <param argument="--filterID" name="filter_id" type="text" optional="false"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	65 label="Value to add to FILTER field of non-selected variants"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	66 help="The value provided here will be added to the FILTER field of variants that are NOT selected by the expression above. Selected variants, in contrast, will have their FILTER field cleared and set to PASS." />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	67 </when>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	68 <when value="remove_filter">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	69 <param argument="--rmFilter" name="rm_filter" type="text" optional="false"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	70 label="Value to remove from FILTER field of selected variants"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	71 help="The FILTER field of variants that are selected by the expression above will be checked for existence of the specified value. When the value is found it will be removed, but other values will be preserved. If the removed value was the only value in a FILTER field, that field will be set to the '.' (missing) value." />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	72 </when>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	73 <when value="add_filter">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	74 <param argument="--addFilter" name="add_filter" type="text" optional="false"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	75 label="Value to add to FILTER field of selected variants"
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	76 help="The value provided here will be added to the FILTER field of variants that are selected by the expression above. USE WITH CARE: The tool will NOT add a corresponding FILTER entry to the VCF header of the output, i.e. will produce output that violates the VCF format specification. To avoid issues with downstream tools it may be necessary to add such a header line using standard text processing tools before proceeding." />
0 9e8280e19338 Uploaded iuc parents: diff changeset	77 </when>
9e8280e19338 Uploaded iuc parents: diff changeset	78 </conditional>
9e8280e19338 Uploaded iuc parents: diff changeset	79 </inputs>
9e8280e19338 Uploaded iuc parents: diff changeset	80 <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	81 <data name="output" format="vcf" />
0 9e8280e19338 Uploaded iuc parents: diff changeset	82 </outputs>
9e8280e19338 Uploaded iuc parents: diff changeset	83 <tests>
9e8280e19338 Uploaded iuc parents: diff changeset	84 <test>
9e8280e19338 Uploaded iuc parents: diff changeset	85 <param name="input" ftype="vcf" value="test01.vcf"/>
9e8280e19338 Uploaded iuc parents: diff changeset	86 <param name="expr" value="QUAL >= 50"/>
9e8280e19338 Uploaded iuc parents: diff changeset	87 <param name="mode" value="entries"/>
9e8280e19338 Uploaded iuc parents: diff changeset	88 <output name="output">
9e8280e19338 Uploaded iuc parents: diff changeset	89 <assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	90 <has_text text="28837706" />
9e8280e19338 Uploaded iuc parents: diff changeset	91 <not_has_text text="NT_166464" />
9e8280e19338 Uploaded iuc parents: diff changeset	92 </assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	93 </output>
9e8280e19338 Uploaded iuc parents: diff changeset	94 </test>
9e8280e19338 Uploaded iuc parents: diff changeset	95 <test>
9e8280e19338 Uploaded iuc parents: diff changeset	96 <param name="input" ftype="vcf" value="test01.vcf"/>
9e8280e19338 Uploaded iuc parents: diff changeset	97 <param name="expr" value="(CHROM = '19')"/>
9e8280e19338 Uploaded iuc parents: diff changeset	98 <param name="mode" value="entries"/>
9e8280e19338 Uploaded iuc parents: diff changeset	99 <output name="output">
9e8280e19338 Uploaded iuc parents: diff changeset	100 <assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	101 <has_text text="3205820" />
9e8280e19338 Uploaded iuc parents: diff changeset	102 <not_has_text text="NT_16" />
9e8280e19338 Uploaded iuc parents: diff changeset	103 </assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	104 </output>
9e8280e19338 Uploaded iuc parents: diff changeset	105 </test>
9e8280e19338 Uploaded iuc parents: diff changeset	106 <test>
9e8280e19338 Uploaded iuc parents: diff changeset	107 <param name="input" ftype="vcf" value="test01.vcf"/>
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	108 <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/>
0 9e8280e19338 Uploaded iuc parents: diff changeset	109 <param name="mode" value="entries"/>
9e8280e19338 Uploaded iuc parents: diff changeset	110 <output name="output">
9e8280e19338 Uploaded iuc parents: diff changeset	111 <assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	112 <has_text text="20175" />
9e8280e19338 Uploaded iuc parents: diff changeset	113 <has_text text="35549" />
9e8280e19338 Uploaded iuc parents: diff changeset	114 <has_text text="22256" />
9e8280e19338 Uploaded iuc parents: diff changeset	115 <not_has_text text="18933" />
9e8280e19338 Uploaded iuc parents: diff changeset	116 <not_has_text text="37567" />
9e8280e19338 Uploaded iuc parents: diff changeset	117 </assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	118 </output>
9e8280e19338 Uploaded iuc parents: diff changeset	119 </test>
9e8280e19338 Uploaded iuc parents: diff changeset	120 <test>
9e8280e19338 Uploaded iuc parents: diff changeset	121 <param name="input" ftype="vcf" value="test01.vcf"/>
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	122 <param name="expr" value="( DP >= 5 )"/>
0 9e8280e19338 Uploaded iuc parents: diff changeset	123 <param name="mode" value="entries"/>
9e8280e19338 Uploaded iuc parents: diff changeset	124 <output name="output">
9e8280e19338 Uploaded iuc parents: diff changeset	125 <assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	126 <has_text text="DP=5;" />
9e8280e19338 Uploaded iuc parents: diff changeset	127 <has_text text="DP=6;" />
9e8280e19338 Uploaded iuc parents: diff changeset	128 <not_has_text text="DP=1;" />
9e8280e19338 Uploaded iuc parents: diff changeset	129 </assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	130 </output>
9e8280e19338 Uploaded iuc parents: diff changeset	131 </test>
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	132 <test>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	133 <param name="input" ftype="vcf" value="test01.vcf"/>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	134 <conditional name="filter_expression">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	135 <param name="type" value="complex" />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	136 <param name="expr" value="( POS in SET[0] ) \| ( POS in SET[1] )" />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	137 <param name="set" ftype="txt" value="test_set1.txt,test_set2.txt" />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	138 </conditional>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	139 <param name="mode" value="entries"/>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	140 <output name="output">
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	141 <assert_contents>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	142 <has_text text="NT_166464 7268 " />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	143 <has_text text="NT_166464 7283 " />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	144 <has_text text="NT_166464 7335 " />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	145 <has_text text="NT_166480 12474 " />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	146 <has_text text="NT_166480 12483 " />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	147 <not_has_text text="NT_166464 7258 " />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	148 <not_has_text text="NT_166452 16693 " />
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	149 </assert_contents>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	150 </output>
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	151 </test>
0 9e8280e19338 Uploaded iuc parents: diff changeset	152 </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	153 <help><![CDATA[
0 9e8280e19338 Uploaded iuc parents: diff changeset	154 SnpSift filter
9e8280e19338 Uploaded iuc parents: diff changeset	155
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	156 This tool provides a flexible solution for filtering the variants in a VCF input dataset through the use of arbitrary, possibly rather complex expressions.
0 9e8280e19338 Uploaded iuc parents: diff changeset	157
9e8280e19338 Uploaded iuc parents: diff changeset	158 Some examples:
9e8280e19338 Uploaded iuc parents: diff changeset	159
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	160 - I want just the variants from the second million bases of chr1::
0 9e8280e19338 Uploaded iuc parents: diff changeset	161
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	162 ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 )
0 9e8280e19338 Uploaded iuc parents: diff changeset	163
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	164 - Filter value is either 'PASS' or it is missing::
0 9e8280e19338 Uploaded iuc parents: diff changeset	165
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	166 (FILTER = 'PASS') \| ( na FILTER )
0 9e8280e19338 Uploaded iuc parents: diff changeset	167
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	168 - Variants that have either a QUAL score above 30, or are indel variants, or for which at least two samples have a heterozygous genotype called::
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	169
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	170 (QUAL > 30) \| (exists INDEL) \| ( countHet() > 2 )
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	171
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	172 - Variants that are supported by at least 10 reads (as calculated from the DP4 attribute in the INFO field through zero-based index-access to the multiple values)::
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	173
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	174 (DP4[2] + DP4[3] >= 10)
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	175
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	176 ----
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	177
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	178 Sets:
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	179
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	180 The tool can construct sets of values for use in expressions from text files listing one value per line. Variants can then be filtered based on whether a given field in the variant record has a value that's contained in a set. For example, the expression::
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	181
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	182 ( ID in SET[2] )
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	183
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	184 would filter variants based on whether their ID field value appears in the set parsed from the third dataset used for set construction (the first set can be addressed with index ``[0]``, the second with index ``[1]``, and so on).
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	185
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	186 ----
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	187
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	188 Genotype-based filtering:
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	189
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	190 Genotypes of specific samples can be accessed via zero-based indexing or via sample names.
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	191
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	192 - I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference::
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	193
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	194 (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	195
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	196 ----
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	197
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	198 Filtering based on SnpEff annotations (``ANN`` or ``EFF`` fields):
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	199
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	200 - I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )::
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	201
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	202 ( ANN[*].EFFECT has 'frameshift_variant' )
0 9e8280e19338 Uploaded iuc parents: diff changeset	203
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	204 .. class:: infomark
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	205
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	206 According to the specification, there can be more than one EFFECT separated by ``&`` (e.g. ``'missense_variant&splice_region_variant'``), thus using the ``has`` operator is better than using the equality operator (``=``). For instance, ``'missense_variant&splice_region_variant' = 'missense_variant'`` is false, whereas ``'missense_variant&splice_region_variant' has 'missense_variant'`` is true.
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	207
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	208 - I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )::
0 9e8280e19338 Uploaded iuc parents: diff changeset	209
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	210 ( EFF[*].EFFECT = 'FRAME_SHIFT' )
0 9e8280e19338 Uploaded iuc parents: diff changeset	211
9e8280e19338 Uploaded iuc parents: diff changeset	212
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	213 .. class:: infomark
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	214
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	215 For information regarding HGVS and Sequence Ontology terms versus classic names:
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	216
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	217 - https://pcingola.github.io/SnpEff/se_commandline/ for the options: ``-classic``, ``-hgvs``, and ``-sequenceOntology``
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	218 - https://pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details for the table containing the classic name and sequence onology term for each effect
0 9e8280e19338 Uploaded iuc parents: diff changeset	219
9e8280e19338 Uploaded iuc parents: diff changeset	220 @EXTERNAL_DOCUMENTATION@
7 2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	221 - https://pcingola.github.io/SnpEff/ss_filter/
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	222
2e497a770bca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309" iuc parents: 5 diff changeset	223 The second link in particular has further details and more examples about the tool's expression syntax.
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	224 ]]></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	225 <expand macro="citations" />
0 9e8280e19338 Uploaded iuc parents: diff changeset	226 </tool>

Mercurial > repos > iuc > snpsift

annotate snpSift_filter.xml @ 7:2e497a770bca draft