Mercurial > repos > iuc > snpsift
changeset 11:b884686a80dc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:37:06 -0400 |
| parents | 93577c5e76ec |
| children | 6bf58286d795 |
| files | snpSift_annotate.xml snpSift_caseControl.xml snpSift_filter.xml snpSift_int.xml snpSift_rmInfo.xml snpSift_vartype.xml snpSift_vcfCheck.xml |
| diffstat | 7 files changed, 50 insertions(+), 50 deletions(-) [+] |
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--- a/snpSift_annotate.xml Wed Apr 29 11:55:50 2015 -0400 +++ b/snpSift_annotate.xml Mon May 04 22:37:06 2015 -0400 @@ -1,43 +1,43 @@ <tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0"> <description>SNPs from dbSnp</description> - <!-- + <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <command> - java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd + java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd #if $annotate.id : -id #elif $annotate.info_ids.__str__.strip() != '' : -info "$annotate.info_ids" - #end if - -q $dbSnp $input > $output + #end if + -q $dbSnp $input > $output </command> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> - <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" + <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/> <conditional name="annotate"> <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> <when value="id"/> <when value="info"> <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" - help="list is a comma separated list of fields. When blank, all INFO fields are included"> + help="list is a comma separated list of fields. When blank, all INFO fields are included"> <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> </param> </when> </conditional> - <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> + <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> <help> This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). - Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). + Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). </help> </param> </inputs> - <expand macro="stdio" /> <outputs> <data format="vcf" name="output" /> </outputs>
--- a/snpSift_caseControl.xml Wed Apr 29 11:55:50 2015 -0400 +++ b/snpSift_caseControl.xml Mon May 04 22:37:06 2015 -0400 @@ -1,19 +1,20 @@ <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="4.0.0"> <description>Count samples are in 'case' and 'control' groups.</description> - <!-- + <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <command> - java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q + java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q #if $name.__str__.strip() != '': -name $name #end if #if $ctrl.ctrl_src == 'caseString': - '$ctrl.caseControlStr' + '$ctrl.caseControlStr' #else -tfam "$ctrl.tfam" #end if @@ -45,7 +46,6 @@ <outputs> <data format="vcf" name="output" /> </outputs> - <expand macro="stdio" /> <tests> <test> <param name="input" ftype="vcf" value="test.private.01.vcf"/> @@ -88,13 +88,13 @@ **SnpSift CaseControl** -Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. +Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. -Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. +Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. This command adds two annotations to the VCF file: - - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: + - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.* @@ -108,7 +108,7 @@ - Hom/Het case = "hom" - - Hom/Het control = "any" + - Hom/Het control = "any" - Case / Control column designation = ""++++------"
--- a/snpSift_filter.xml Wed Apr 29 11:55:50 2015 -0400 +++ b/snpSift_filter.xml Mon May 04 22:37:06 2015 -0400 @@ -1,12 +1,13 @@ <tool id="snpSift_filter" name="SnpSift Filter" version="4.0.0"> <options sanitize="False" /> <description>Filter variants using arbitrary expressions</description> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <command> - java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse + java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse #if $filtering.mode == 'field': #if $filtering.replace.pass: --pass @@ -23,6 +24,11 @@ #end if > $output </command> + <configfiles> + <configfile name="exprFile"> +$expr#slurp + </configfile> + </configfiles> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> <param name="expr" type="text" label="Filter criteria" size="160" help="Need help? See below a few examples." /> @@ -31,11 +37,11 @@ <param name="mode" type="select" label="Filter mode"> <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option> <option value="field">Change the FILTER field, but retain all entries</option> - </param> + </param> <when value="entries"/> <when value="field"> <conditional name="replace"> - <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" + <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" help="appends an ID tag to non-matching entry FILTER "/> <when value="no"/> <when value="yes"> @@ -48,16 +54,10 @@ </when> </conditional> </inputs> - <configfiles> - <configfile name="exprFile"> -$expr#slurp - </configfile> - </configfiles> <outputs> <data format="vcf" name="output" /> </outputs> - <expand macro="stdio" /> <tests> <test> <param name="input" ftype="vcf" value="test01.vcf"/> @@ -129,18 +129,18 @@ :: - (FILTER = 'PASS') | ( na FILTER ) + (FILTER = 'PASS') | ( na FILTER ) - *I want to filter lines with an EFF of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*: :: - + ( EFF[*].EFFECT = 'frameshift_variant' ) - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*: :: - + ( EFF[*].EFFECT = 'FRAME_SHIFT' ) - *I want to filter out samples with quality less than 30*: @@ -154,23 +154,23 @@ :: (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 ) - + - *...or any homozygous variant present in more than 3 samples*: :: (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 ) - + - *...or any heterozygous sample with coverage 25 or more*: :: ((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 ) - + - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*: :: - + (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
--- a/snpSift_int.xml Wed Apr 29 11:55:50 2015 -0400 +++ b/snpSift_int.xml Mon May 04 22:37:06 2015 -0400 @@ -1,25 +1,25 @@ <tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0"> <description>Filter variants using intervals</description> - <!-- + <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <command> java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output </command> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> - <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" + <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" help="Filter out (exclude) VCF entries that match any interval in the BED files"/> </inputs> <outputs> <data format="vcf" name="output" /> </outputs> - <expand macro="stdio" /> <tests> <test> <param name="input" ftype="vcf" value="annotate_5.vcf"/>
--- a/snpSift_rmInfo.xml Wed Apr 29 11:55:50 2015 -0400 +++ b/snpSift_rmInfo.xml Mon May 04 22:37:06 2015 -0400 @@ -1,9 +1,10 @@ <tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="4.0.0"> <description>remove INFO field annotations</description> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <command> java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar rmInfo $input ' '.join($info_fields.split(',')) > $output </command> @@ -17,7 +18,6 @@ <outputs> <data format="vcf" name="output" /> </outputs> - <expand macro="stdio" /> <tests> <test> <param name="input" ftype="vcf" value="test-data/test_rmInfo.vcf"/> @@ -42,10 +42,10 @@ <help> This command removes INFO fields from a VCF file (i.e. removes annotations) -Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later. +Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later. -SnpEff & SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate. -The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones. +SnpEff & SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate. +The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones. @EXTERNAL_DOCUMENTATION@ http://snpeff.sourceforge.net/SnpSift.html#rmInfo
--- a/snpSift_vartype.xml Wed Apr 29 11:55:50 2015 -0400 +++ b/snpSift_vartype.xml Mon May 04 22:37:06 2015 -0400 @@ -1,9 +1,10 @@ <tool id="snpsift_vartype" name="SnpSift Variant Type" version="4.0.0"> <description>Annotate with variant type</description> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <command> java -jar \$SNPEFF_JAR_PATH/SnpSift.jar varType $input 2> $log > $output </command> @@ -14,7 +15,6 @@ <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> </outputs> - <expand macro="stdio" /> <tests> </tests> <help>
--- a/snpSift_vcfCheck.xml Wed Apr 29 11:55:50 2015 -0400 +++ b/snpSift_vcfCheck.xml Mon May 04 22:37:06 2015 -0400 @@ -1,9 +1,10 @@ <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0"> <description>basic checks for Vcf specification compliance</description> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <command> java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output </command> @@ -13,7 +14,6 @@ <outputs> <data format="vcf" name="output" /> </outputs> - <expand macro="stdio" /> <tests> <test> <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/> @@ -28,7 +28,7 @@ Perform some basic check ups on VCF files to spot common problems. -SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool. +SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool. @EXTERNAL_DOCUMENTATION@ http://snpeff.sourceforge.net/SnpSift.html#vcfCheck