snpeff: snpEff.xml annotate

annotate snpEff.xml @ 7:b26a1aff7f81

Fix issues with snpEff commandline template and add test cases

author	Jim Johnson <jj@umn.edu>
date	Thu, 28 Mar 2013 12:29:45 -0500
parents	3b0c657b852b
children	13b6ad2ddace

rev	line source
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	1 <tool id="snpEff" name="SnpEff" version="3.1">
c07c403fc470 Uploaded jjohnson parents: diff changeset	2 <description>Variant effect and annotation</description>
c07c403fc470 Uploaded jjohnson parents: diff changeset	3 <!--
c07c403fc470 Uploaded jjohnson parents: diff changeset	4 You will need to change the path to wherever your installation is.
c07c403fc470 Uploaded jjohnson parents: diff changeset	5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
c07c403fc470 Uploaded jjohnson parents: diff changeset	6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
c07c403fc470 Uploaded jjohnson parents: diff changeset	7 -->
c07c403fc470 Uploaded jjohnson parents: diff changeset	8 <requirements>
c07c403fc470 Uploaded jjohnson parents: diff changeset	9 <requirement type="package" version="3.1">snpEff</requirement>
c07c403fc470 Uploaded jjohnson parents: diff changeset	10 </requirements>
c07c403fc470 Uploaded jjohnson parents: diff changeset	11 <command>
3 3b0c657b852b Fix command in snpEff.xml Jim Johnson <jj@umn.edu> parents: 0 diff changeset	12 SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config \| sed 's/.data_dir.[=:]//'`;
3b0c657b852b Fix command in snpEff.xml Jim Johnson <jj@umn.edu> parents: 0 diff changeset	13 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	14 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
3 3b0c657b852b Fix command in snpEff.xml Jim Johnson <jj@umn.edu> parents: 0 diff changeset	15 fi";
7 b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	16 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	17 #if $filterIn and $filterIn.__str__ != 'no_filter':
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	18 -$filterIn
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	19 #end if
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	20 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	21 -$filterHomHet
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	22 #end if
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	23 #if $filterOut and $filterOut.__str__ != '':
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	24 #echo ' '.join($filterOut.__str__.split(','))
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	25 #end if
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	26 #if $statsFile:
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	27 -stats $statsFile
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	28 #end if
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	29 #if $offset.__str__ != '':
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	30 -${offset}
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	31 #end if
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	32 $genomeVersion $input > $snpeff_output
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	33 </command>
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	34 <inputs>
c07c403fc470 Uploaded jjohnson parents: diff changeset	35 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
c07c403fc470 Uploaded jjohnson parents: diff changeset	36
c07c403fc470 Uploaded jjohnson parents: diff changeset	37 <param name="inputFormat" type="select" label="Input format">
c07c403fc470 Uploaded jjohnson parents: diff changeset	38 <option value="vcf">VCF</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	39 <option value="txt">Tabular</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	40 <option value="pileup">Pileup</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	41 <option value="bed">BED</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	42 </param>
c07c403fc470 Uploaded jjohnson parents: diff changeset	43
c07c403fc470 Uploaded jjohnson parents: diff changeset	44 <param name="outputFormat" type="select" label="Output format">
c07c403fc470 Uploaded jjohnson parents: diff changeset	45 <option value="txt">Tabular</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	46 <option value="vcf">VCF (only if input is VCF)</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	47 <option value="bed">BED</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	48 <option value="bedAnn">BED Annotations</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	49 </param>
c07c403fc470 Uploaded jjohnson parents: diff changeset	50
c07c403fc470 Uploaded jjohnson parents: diff changeset	51 <param name="genomeVersion" type="select" label="Genome">
c07c403fc470 Uploaded jjohnson parents: diff changeset	52 <options from_file="snpeffect_genomedb.loc">
c07c403fc470 Uploaded jjohnson parents: diff changeset	53 <column name="name" index="1"/>
c07c403fc470 Uploaded jjohnson parents: diff changeset	54 <column name="value" index="0"/>
c07c403fc470 Uploaded jjohnson parents: diff changeset	55 </options>
c07c403fc470 Uploaded jjohnson parents: diff changeset	56 </param>
c07c403fc470 Uploaded jjohnson parents: diff changeset	57
c07c403fc470 Uploaded jjohnson parents: diff changeset	58 <param name="udLength" type="select" label="Upstream / Downstream length">
c07c403fc470 Uploaded jjohnson parents: diff changeset	59 <option value="0">No upstream / downstream intervals (0 bases)</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	60 <option value="200">200 bases</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	61 <option value="500">500 bases</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	62 <option value="1000">1000 bases</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	63 <option value="2000">2000 bases</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	64 <option value="5000" selected="true">5000 bases</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	65 <option value="10000">10000 bases</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	66 <option value="20000">20000 bases</option>
c07c403fc470 Uploaded jjohnson parents: diff changeset	67 </param>
c07c403fc470 Uploaded jjohnson parents: diff changeset	68
c07c403fc470 Uploaded jjohnson parents: diff changeset	69 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
7 b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	70 <option value="no_filter" selected="true">No filter (analyze everything)</option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	71 <option value="hom">Analyze homozygous sequence changes only </option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	72 <option value="het">Analyze heterozygous sequence changes only </option>
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	73 </param>
c07c403fc470 Uploaded jjohnson parents: diff changeset	74
c07c403fc470 Uploaded jjohnson parents: diff changeset	75 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
7 b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	76 <option value="no_filter" selected="true">No filter (analyze everything)</option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	77 <option value="del">Analyze deletions only </option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	78 <option value="ins">Analyze insertions only </option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	79 <option value="nmp">Only MNPs (multiple nucleotide polymorphisms) </option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	80 <option value="snp">Only SNPs (single nucleotide polymorphisms) </option>
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	81 </param>
c07c403fc470 Uploaded jjohnson parents: diff changeset	82
7 b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	83 <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="true" label="Filter output">
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	84 <option value="-no-downstream">Do not show DOWNSTREAM changes </option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	85 <option value="-no-intergenic">Do not show INTERGENIC changes </option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	86 <option value="-no-intron">Do not show INTRON changes </option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	87 <option value="-no-upstream">Do not show UPSTREAM changes </option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	88 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	89 </param>
c07c403fc470 Uploaded jjohnson parents: diff changeset	90
c07c403fc470 Uploaded jjohnson parents: diff changeset	91 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
7 b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	92 <option value="" selected="true">Use default (based on input type)</option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	93 <option value="0">Force zero-based positions (both input and output)</option>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	94 <option value="1">Force one-based positions (both input and output)</option>
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	95 </param>
7 b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	96 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	97 </inputs>
c07c403fc470 Uploaded jjohnson parents: diff changeset	98 <outputs>
7 b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	99 <data format="tabular" name="snpeff_output" >
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	100 <change_format>
c07c403fc470 Uploaded jjohnson parents: diff changeset	101 <when input="outputFormat" value="txt" format="tabular" />
c07c403fc470 Uploaded jjohnson parents: diff changeset	102 <when input="outputFormat" value="vcf" format="vcf" />
c07c403fc470 Uploaded jjohnson parents: diff changeset	103 <when input="outputFormat" value="bed" format="bed" />
c07c403fc470 Uploaded jjohnson parents: diff changeset	104 <when input="outputFormat" value="bedAnn" format="bed" />
c07c403fc470 Uploaded jjohnson parents: diff changeset	105 </change_format>
c07c403fc470 Uploaded jjohnson parents: diff changeset	106 </data>
7 b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	107
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	108 <data format="html" name="statsFile">
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	109 <filter>generate_stats == True</filter>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	110 </data>
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	111 </outputs>
c07c403fc470 Uploaded jjohnson parents: diff changeset	112 <stdio>
c07c403fc470 Uploaded jjohnson parents: diff changeset	113 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
c07c403fc470 Uploaded jjohnson parents: diff changeset	114 <exit_code range="1:" level="fatal" description="Error" />
c07c403fc470 Uploaded jjohnson parents: diff changeset	115 </stdio>
7 b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	116 <tests>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	117 <test>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	118 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	119 <param name="inputFormat" value="vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	120 <param name="outputFormat" value="vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	121 <param name="genomeVersion" value="testCase"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	122 <param name="udLength" value="0"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	123 <param name="filterHomHet" value="no_filter"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	124 <param name="filterIn" value="no_filter"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	125 <param name="filterOut" value="-no-upstream"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	126 <output name="snpeff_output">
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	127 <assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	128 <!-- Check that an effect was added -->
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	129 <has_text text="EFF=NON_SYNONYMOUS_CODING" />
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	130 </assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	131 </output>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	132 <output name="statsFile">
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	133 <assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	134 <!-- Check for a HTML header indicating that this was successful -->
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	135 <has_text text="SnpEff: Variant analysis" />
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	136 </assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	137 </output>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	138 </test>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	139 <test>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	140 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	141 <param name="inputFormat" value="vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	142 <param name="outputFormat" value="vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	143 <param name="genomeVersion" value="testCase"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	144 <param name="udLength" value="0"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	145 <param name="filterHomHet" value="het"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	146 <param name="filterIn" value="no_filter"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	147 <!--
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	148 <param name="filterOut" value=""/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	149 -->
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	150 <param name="generate_stats" value="False"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	151 <output name="snpeff_output">
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	152 <assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	153 <!-- Check that NO effects were added since -het is set -->
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	154 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	155 </assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	156 </output>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	157 </test>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	158 <test>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	159 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	160 <param name="inputFormat" value="vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	161 <param name="outputFormat" value="vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	162 <param name="genomeVersion" value="testCase"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	163 <param name="udLength" value="0"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	164 <param name="filterHomHet" value="no_filter"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	165 <param name="filterIn" value="del"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	166 <!--
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	167 <param name="filterOut" value=""/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	168 -->
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	169 <param name="generate_stats" value="False"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	170 <output name="snpeff_output">
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	171 <assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	172 <!-- Check that deleletions were evaluated -->
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	173 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	174 <!-- Check that insertion on last line was NOT evaluated -->
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	175 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	176 </assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	177 </output>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	178 </test>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	179 <test>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	180 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	181 <param name="inputFormat" value="vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	182 <param name="outputFormat" value="vcf"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	183 <param name="genomeVersion" value="testCase"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	184 <param name="udLength" value="0"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	185 <param name="filterHomHet" value="no_filter"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	186 <param name="filterIn" value="no_filter"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	187 <param name="filterOut" value="-no-upstream"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	188 <param name="generate_stats" value="False"/>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	189 <output name="snpeff_output">
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	190 <assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	191 <!-- Check that NO UPSTREAM effect was added -->
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	192 <not_has_text text="UPSTREAM" />
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	193 </assert_contents>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	194 </output>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	195 </test>
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	196
b26a1aff7f81 Fix issues with snpEff commandline template and add test cases Jim Johnson <jj@umn.edu> parents: 3 diff changeset	197 </tests>
0 c07c403fc470 Uploaded jjohnson parents: diff changeset	198 <help>
c07c403fc470 Uploaded jjohnson parents: diff changeset	199
c07c403fc470 Uploaded jjohnson parents: diff changeset	200 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
c07c403fc470 Uploaded jjohnson parents: diff changeset	201
c07c403fc470 Uploaded jjohnson parents: diff changeset	202 For details about this tool, please go to http://snpEff.sourceforge.net
c07c403fc470 Uploaded jjohnson parents: diff changeset	203
c07c403fc470 Uploaded jjohnson parents: diff changeset	204 </help>
c07c403fc470 Uploaded jjohnson parents: diff changeset	205 </tool>
c07c403fc470 Uploaded jjohnson parents: diff changeset	206

Mercurial > repos > jjohnson > snpeff

annotate snpEff.xml @ 7:b26a1aff7f81