snpsift: snpSift_caseControl.xml annotate

annotate snpSift_caseControl.xml @ 14:80da7fae14b8 draft

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 12:10:54 -0500
parents	ed810da439cc
children	8bd645802765

rev	line source
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.1">
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	2 <description>Count samples are in 'case' and 'control' groups.</description>
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	3 <!--
0 f0faaa4d6ee5 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)
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	5 -->
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	6 <macros>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	7 <import>snpSift_macros.xml</import>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	8 </macros>
11 b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 0 diff changeset	9 <expand macro="requirements" />
b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 0 diff changeset	10 <expand macro="stdio" />
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	11 <expand macro="version_command" />
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	12 <command><![CDATA[
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	13 @CONDA_SNPSIFT_JAR_PATH@ &&
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	14 java -Xmx1G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" caseControl -q
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	15 #if str($name).strip() != '':
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	16 -name "$name"
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	17 #end if
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	18 #if $ctrl.ctrl_src == 'caseString':
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	19 '$ctrl.caseControlStr'
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	20 #else
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	21 -tfam "$ctrl.tfam"
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	22 #end if
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	23 "$input" > "$output"
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	24 ]]>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	25 </command>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	26 <inputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	27 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	28 <conditional name="ctrl">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	29 <param name="ctrl_src" type="select" label="Case Control defined in">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	30 <option value="caseString">Case Control String</option>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	31 <option value="tfam">TFAM file</option>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	32 </param>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	33 <when value="caseString">
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	34 <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	35 <help>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	36 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	37 </help>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	38 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	39 </param>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	40 </when>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	41 <when value="tfam">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	42 <param format="tabular" name="tfam" type="data" label="PLINK TFAM file" help="Read more about TFAM at http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	43 </when>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	44 </conditional>
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	45 <param name="name" type="text" label="name" help="name to append to the 'Cases' or 'Controls' tags">
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	46 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]*</validator>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	47 </param>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	48 </inputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	49 <outputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	50 <data format="vcf" name="output" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	51 </outputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	52 <tests>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	53 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	54 <param name="input" ftype="vcf" value="test.private.01.vcf"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	55 <param name="ctrl_src" value="caseString"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	56 <param name="caseControlStr" value="--"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	57 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	58 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	59 <has_text text="Cases=0,0,0;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	60 <has_text text="Controls=0,0,0;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	61 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	62 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	63 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	64
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	65 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	66 <param name="input" ftype="vcf" value="test.private.02.vcf"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	67 <param name="ctrl_src" value="caseString"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	68 <param name="caseControlStr" value="--"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	69 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	70 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	71 <has_text text="Cases=0,0,0;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	72 <has_text text="Controls=2,0,4;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	73 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	74 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	75 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	76
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	77 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	78 <param name="input" ftype="vcf" value="test.private.02.vcf"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	79 <param name="name" value=""/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	80 <param name="ctrl_src" value="caseString"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	81 <param name="caseControlStr" value="-+"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	82 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	83 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	84 <has_text text="Cases=1,0,2;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	85 <has_text text="Controls=1,0,2;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	86 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	87 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	88 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	89 </tests>
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	90 <help><![CDATA[
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	91
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	92 SnpSift CaseControl
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	93
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	94 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	95
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	96 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral.
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	97
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	98 This command adds two annotations to the VCF file:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	99
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	100 - CaseControl: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example:
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	101
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	102 "CaseControl=3,4" the variant is present in 3 cases and 4 controls.
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	103
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	104
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	105 - CaseControlP: A p-value (Fisher exact test) that the number of cases is N or more. Example:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	106
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	107 "CaseControl=4,0;CaseControlP=3.030303e-02" in this case the pValue of having 4 or more cases and zero controls is 0.03
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	108
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	109
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	110 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:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	111
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	112 - Hom/Het case = "hom"
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	113
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	114 - Hom/Het control = "any"
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	115
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	116 - Case / Control column designation = ""++++------"
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	117
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	118
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	119 @EXTERNAL_DOCUMENTATION@
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	120 http://snpeff.sourceforge.net/SnpSift.html#casecontrol
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	121
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	122 ]]>
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	123 </help>
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	124 <expand macro="citations" />
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	125 </tool>

Mercurial > repos > iuc > snpsift

annotate snpSift_caseControl.xml @ 14:80da7fae14b8 draft