snpsift: snpSift_caseControl.xml annotate

annotate snpSift_caseControl.xml @ 5:09d6806c609e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b

author	iuc
date	Wed, 18 Apr 2018 07:28:51 -0400
parents	20c7d583fec1
children

rev	line source
5 09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b iuc parents: 3 diff changeset	1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.galaxy0">
0 9e8280e19338 Uploaded iuc parents: diff changeset	2 <description>Count samples are in 'case' and 'control' groups.</description>
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	3 <!--
0 9e8280e19338 Uploaded iuc parents: diff changeset	4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
9e8280e19338 Uploaded iuc parents: diff changeset	5 -->
9e8280e19338 Uploaded iuc parents: diff changeset	6 <macros>
9e8280e19338 Uploaded iuc parents: diff changeset	7 <import>snpSift_macros.xml</import>
9e8280e19338 Uploaded iuc parents: diff changeset	8 </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	9 <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	10 <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	11 <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	12 <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	13 SnpSift -Xmx1G caseControl -q
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 #if $name.strip():
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	15 -name '$name'
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 #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	17 #if $ctrl.ctrl_src == 'caseString':
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	18 '$ctrl.caseControlStr'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	19 #else
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	20 -tfam '$ctrl.tfam'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	21 #end if
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	22 '$input' > '$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	23 ]]></command>
0 9e8280e19338 Uploaded iuc parents: diff changeset	24 <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	25 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
0 9e8280e19338 Uploaded iuc parents: diff changeset	26 <conditional name="ctrl">
9e8280e19338 Uploaded iuc parents: diff changeset	27 <param name="ctrl_src" type="select" label="Case Control defined in">
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	28 <option value="caseString">Case Control String</option>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	29 <option value="tfam">TFAM file</option>
0 9e8280e19338 Uploaded iuc parents: diff changeset	30 </param>
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	31 <when value="caseString">
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	32 <param name="caseControlStr" type="text" size="50" label="Case / Control column designation">
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	33 <help>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	34 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	35 </help>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	36 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	37 </param>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	38 </when>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	39 <when value="tfam">
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 <param name="tfam" type="data" format="tabular" label="PLINK TFAM file" help="Read more about TFAM at http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr"/>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	41 </when>
0 9e8280e19338 Uploaded iuc parents: diff changeset	42 </conditional>
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	43 <param name="name" type="text" label="Name" help="Name to append to the 'Cases' or 'Controls' tags">
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	44 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]*</validator>
0 9e8280e19338 Uploaded iuc parents: diff changeset	45 </param>
9e8280e19338 Uploaded iuc parents: diff changeset	46 </inputs>
9e8280e19338 Uploaded iuc parents: diff changeset	47 <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	48 <data name="output" format="vcf" />
0 9e8280e19338 Uploaded iuc parents: diff changeset	49 </outputs>
9e8280e19338 Uploaded iuc parents: diff changeset	50 <tests>
9e8280e19338 Uploaded iuc parents: diff changeset	51 <test>
9e8280e19338 Uploaded iuc parents: diff changeset	52 <param name="input" ftype="vcf" value="test.private.01.vcf"/>
9e8280e19338 Uploaded iuc parents: diff changeset	53 <param name="ctrl_src" value="caseString"/>
9e8280e19338 Uploaded iuc parents: diff changeset	54 <param name="caseControlStr" value="--"/>
9e8280e19338 Uploaded iuc parents: diff changeset	55 <output name="output">
9e8280e19338 Uploaded iuc parents: diff changeset	56 <assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	57 <has_text text="Cases=0,0,0;" />
9e8280e19338 Uploaded iuc parents: diff changeset	58 <has_text text="Controls=0,0,0;" />
9e8280e19338 Uploaded iuc parents: diff changeset	59 </assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	60 </output>
9e8280e19338 Uploaded iuc parents: diff changeset	61 </test>
9e8280e19338 Uploaded iuc parents: diff changeset	62
9e8280e19338 Uploaded iuc parents: diff changeset	63 <test>
9e8280e19338 Uploaded iuc parents: diff changeset	64 <param name="input" ftype="vcf" value="test.private.02.vcf"/>
9e8280e19338 Uploaded iuc parents: diff changeset	65 <param name="ctrl_src" value="caseString"/>
9e8280e19338 Uploaded iuc parents: diff changeset	66 <param name="caseControlStr" value="--"/>
9e8280e19338 Uploaded iuc parents: diff changeset	67 <output name="output">
9e8280e19338 Uploaded iuc parents: diff changeset	68 <assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	69 <has_text text="Cases=0,0,0;" />
9e8280e19338 Uploaded iuc parents: diff changeset	70 <has_text text="Controls=2,0,4;" />
9e8280e19338 Uploaded iuc parents: diff changeset	71 </assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	72 </output>
9e8280e19338 Uploaded iuc parents: diff changeset	73 </test>
9e8280e19338 Uploaded iuc parents: diff changeset	74
9e8280e19338 Uploaded iuc parents: diff changeset	75 <test>
9e8280e19338 Uploaded iuc parents: diff changeset	76 <param name="input" ftype="vcf" value="test.private.02.vcf"/>
9e8280e19338 Uploaded iuc parents: diff changeset	77 <param name="name" value=""/>
9e8280e19338 Uploaded iuc parents: diff changeset	78 <param name="ctrl_src" value="caseString"/>
9e8280e19338 Uploaded iuc parents: diff changeset	79 <param name="caseControlStr" value="-+"/>
9e8280e19338 Uploaded iuc parents: diff changeset	80 <output name="output">
9e8280e19338 Uploaded iuc parents: diff changeset	81 <assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	82 <has_text text="Cases=1,0,2;" />
9e8280e19338 Uploaded iuc parents: diff changeset	83 <has_text text="Controls=1,0,2;" />
9e8280e19338 Uploaded iuc parents: diff changeset	84 </assert_contents>
9e8280e19338 Uploaded iuc parents: diff changeset	85 </output>
9e8280e19338 Uploaded iuc parents: diff changeset	86 </test>
9e8280e19338 Uploaded iuc parents: diff changeset	87 </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	88 <help><![CDATA[
0 9e8280e19338 Uploaded iuc parents: diff changeset	89 SnpSift CaseControl
9e8280e19338 Uploaded iuc parents: diff changeset	90
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	91 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
0 9e8280e19338 Uploaded iuc parents: diff changeset	92
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	93 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral.
0 9e8280e19338 Uploaded iuc parents: diff changeset	94
9e8280e19338 Uploaded iuc parents: diff changeset	95 This command adds two annotations to the VCF file:
9e8280e19338 Uploaded iuc parents: diff changeset	96
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	97 - CaseControl: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example::
0 9e8280e19338 Uploaded iuc parents: diff changeset	98
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	99 "CaseControl=3,4" the variant is present in 3 cases and 4 controls.
0 9e8280e19338 Uploaded iuc parents: diff changeset	100
9e8280e19338 Uploaded iuc parents: diff changeset	101
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	102 - CaseControlP: A p-value (Fisher exact test) that the number of cases is N or more. Example::
0 9e8280e19338 Uploaded iuc parents: diff changeset	103
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	104 "CaseControl=4,0;CaseControlP=3.030303e-02" in this case the pValue of having 4 or more cases and zero controls is 0.03
0 9e8280e19338 Uploaded iuc parents: diff changeset	105
9e8280e19338 Uploaded iuc parents: diff changeset	106 For example, if we have ten samples (which means ten genotype columns in the VCF file), the first four are 'case' and the last six are 'control', so the description string would be "++++------". Let's say we want to distinguish genotypes that are homozygous in 'case' and either homozygous or heterozygous in 'control'. We would set:
9e8280e19338 Uploaded iuc parents: diff changeset	107
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	108 - Hom/Het case = "hom"
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	109 - Hom/Het control = "any"
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	110 - Case / Control column designation = ""++++------"
0 9e8280e19338 Uploaded iuc parents: diff changeset	111
9e8280e19338 Uploaded iuc parents: diff changeset	112 @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	113 - http://snpeff.sourceforge.net/SnpSift.html#casecontrol
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	114 ]]></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	115 <expand macro="citations" />
0 9e8280e19338 Uploaded iuc parents: diff changeset	116 </tool>

Mercurial > repos > iuc > snpsift

annotate snpSift_caseControl.xml @ 5:09d6806c609e draft