| Previous changeset 7:e5723e64ea43 (2015-02-27) Next changeset 9:1855edc16e48 (2015-02-27) |
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jvarkit/commons-jexl-2.1.1.jar jvarkit/commons-logging-1.1.1.jar jvarkit/groupbygene.jar jvarkit/groupbygene.xml jvarkit/htsjdk-1.128.jar jvarkit/snappy-java-1.0.3-rc3.jar jvarkit/vcffilterjs.jar jvarkit/vcffilterjs.xml jvarkit/vcffilterso.jar jvarkit/vcffilterso.xml jvarkit/vcfhead.jar jvarkit/vcfhead.xml jvarkit/vcftail.jar jvarkit/vcftail.xml jvarkit/vcftrio.jar jvarkit/vcftrio.xml |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/commons-jexl-2.1.1.jar |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/commons-logging-1.1.1.jar |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/groupbygene.jar |
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| Binary file jvarkit/groupbygene.jar has changed |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/groupbygene.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jvarkit/groupbygene.xml Fri Feb 27 09:52:06 2015 -0500 |
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| @@ -0,0 +1,63 @@ +<?xml version="1.0"?> +<tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.groupbygene.GroupByGene" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="groupbygene"> + <!--Date: 2015-02-27T15:54:07+01:00--> + <description>Group VCF (+ VEP + SnpEff) data by gene/transcript</description> + <requirements> + <requirement type="binary">java</requirement> + </requirements> + <command>(gunzip -c ${input} || cat ${input}) | java -cp $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/groupbygene.jar com.github.lindenb.jvarkit.tools.groupbygene.GroupByGene -o ${output}.tsv && mv ${output}.tsv ${output}</command> + <inputs> + <param format="vcf" name="input" type="data" label="VCF input"/> + </inputs> + <outputs> + <data format="vcf" name="output"/> + </outputs> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + </stdio> + <help> + +**Inputs** + + +- **VCF input** : VCF input + + +**Outputs** + + +- **output** : output + + +**Wiki** + +https://github.com/lindenb/jvarkit/wiki/GroupByGene + +----- + + +**Author** + +Pierre Lindenbaum PhD @yokofakun + +**Citation** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit + +**Contribute** + +- Issue Tracker: http://github.com/lindenb/jvarkit/issues` +- Source Code: http://github.com/lindenb/jvarkit + +**License** + +The project is licensed under the MIT license. + +**Compilation** + +Date: 2015-02-27T15:54:07+01:00 +Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9 +</help> +</tool> |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/htsjdk-1.128.jar |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcffilterjs.jar |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcffilterjs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jvarkit/vcffilterjs.xml Fri Feb 27 09:52:06 2015 -0500 |
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| @@ -0,0 +1,72 @@ +<?xml version="1.0"?> +<tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcffilterjs"> + <!--Date: 2015-02-27T15:54:02+01:00--> + <description>Filters a VCF with Javascript</description> + <requirements> + <requirement type="binary">java</requirement> + </requirements> + <command>(gunzip -c ${input} || cat ${input}) | java -cp $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcffilterjs.jar com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e '${expression}' -o ${output}.vcf.gz && mv ${output}.vcf.gz ${output} </command> + <inputs> + <param format="vcf" name="input" type="data" label="VCF input"/> + <param name="expression" type="text" label="javascript expression"> + <sanitizer> + <valid initial="string.printable"> + <add source="'" target="\'"/> + </valid> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="vcf" name="output"/> + </outputs> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + </stdio> + <help> + +**Inputs** + + +- **VCF input** : VCF input + +- **javascript expression** : javascript expression + + +**Outputs** + + +- **output** : output + + +**Wiki** + +https://github.com/lindenb/jvarkit/wiki/VCFFilterJS + +----- + + +**Author** + +Pierre Lindenbaum PhD @yokofakun + +**Citation** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit + +**Contribute** + +- Issue Tracker: http://github.com/lindenb/jvarkit/issues` +- Source Code: http://github.com/lindenb/jvarkit + +**License** + +The project is licensed under the MIT license. + +**Compilation** + +Date: 2015-02-27T15:54:02+01:00 +Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9 +</help> +</tool> |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcffilterso.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jvarkit/vcffilterso.xml Fri Feb 27 09:52:06 2015 -0500 |
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| @@ -0,0 +1,84 @@ +<?xml version="1.0"?> +<tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.misc.VcfFilterSequenceOntology" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcffilterso"> + <!--Date: 2015-02-27T15:54:06+01:00--> + <description>Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology</description> + <requirements> + <requirement type="binary">java</requirement> + </requirements> + <command>(gunzip -c ${input} || cat ${input}) | java -cp $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcffilterso.jar com.github.lindenb.jvarkit.tools.misc.VcfFilterSequenceOntology +#for s in $accessions + -A '$s' +#end for +$inverse $noreason -o ${output}.vcf.gz && mv ${output}.vcf.gz ${output} </command> + <inputs> + <param format="vcf" name="input" type="data" label="VCF input"/> + <repeat name="accessions" title="accessions"> + <param name="acn" type="text" label="SO Accession Number"> + <validator type="regex" message="must match with SO:(number)">SO\:[0-9]+</validator> + </param> + </repeat> + <param name="inverse" type="boolean" checked="false" label="inverse selection" truevalue="-v" falsevalue=""/> + <param name="noreason" type="boolean" checked="false" label="disable reasoning" truevalue="-d" falsevalue=""/> + </inputs> + <outputs> + <data format="vcf" name="output"/> + </outputs> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + </stdio> + <help> + + +**Examples** + + + + +**Inputs** + + +- **VCF input** : VCF input + +- **inverse selection** : inverse selection + +- **disable reasoning** : disable reasoning + + +**Outputs** + + +- **output** : output + + +**Wiki** + +https://github.com/lindenb/jvarkit/wiki/VcfFilterSequenceOntology + +----- + + +**Author** + +Pierre Lindenbaum PhD @yokofakun + +**Citation** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit + +**Contribute** + +- Issue Tracker: http://github.com/lindenb/jvarkit/issues` +- Source Code: http://github.com/lindenb/jvarkit + +**License** + +The project is licensed under the MIT license. + +**Compilation** + +Date: 2015-02-27T15:54:06+01:00 +Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9 +</help> +</tool> |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcfhead.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jvarkit/vcfhead.xml Fri Feb 27 09:52:06 2015 -0500 |
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| @@ -0,0 +1,66 @@ +<?xml version="1.0"?> +<tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.misc.VcfHead" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcfhead"> + <!--Date: 2015-02-27T15:54:04+01:00--> + <description>Print first variants of a VCF</description> + <requirements> + <requirement type="binary">java</requirement> + </requirements> + <command>(gunzip -c ${input} || cat ${input}) | java -cp $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcfhead.jar com.github.lindenb.jvarkit.tools.misc.VcfHead -n '${num}' -o ${output}.vcf.gz && mv ${output}.vcf.gz ${output}</command> + <inputs> + <param format="vcf" name="input" type="data" label="VCF input"/> + <param name="num" type="integer" label="Number of variants" min="0" value="10"/> + </inputs> + <outputs> + <data format="vcf" name="output"/> + </outputs> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + </stdio> + <help> + +**Inputs** + + +- **VCF input** : VCF input + +- **Number of variants** : Number of variants + + +**Outputs** + + +- **output** : output + + +**Wiki** + +https://github.com/lindenb/jvarkit/wiki/VcfHead + +----- + + +**Author** + +Pierre Lindenbaum PhD @yokofakun + +**Citation** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit + +**Contribute** + +- Issue Tracker: http://github.com/lindenb/jvarkit/issues` +- Source Code: http://github.com/lindenb/jvarkit + +**License** + +The project is licensed under the MIT license. + +**Compilation** + +Date: 2015-02-27T15:54:04+01:00 +Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9 +</help> +</tool> |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcftail.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jvarkit/vcftail.xml Fri Feb 27 09:52:06 2015 -0500 |
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| @@ -0,0 +1,66 @@ +<?xml version="1.0"?> +<tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.misc.VcfTail" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcftail"> + <!--Date: 2015-02-27T15:54:03+01:00--> + <description>Print first variants of a VCF</description> + <requirements> + <requirement type="binary">java</requirement> + </requirements> + <command>(gunzip -c ${input} || cat ${input}) | java -cp $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcftail.jar com.github.lindenb.jvarkit.tools.misc.VcfTail -n '${num}' -o ${output}.vcf.gz && mv ${output}.vcf.gz ${output}</command> + <inputs> + <param format="vcf" name="input" type="data" label="VCF input"/> + <param name="num" type="integer" label="Number of variants" min="0" value="10"/> + </inputs> + <outputs> + <data format="vcf" name="output"/> + </outputs> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + </stdio> + <help> + +**Inputs** + + +- **VCF input** : VCF input + +- **Number of variants** : Number of variants + + +**Outputs** + + +- **output** : output + + +**Wiki** + +https://github.com/lindenb/jvarkit/wiki/VcfHead + +----- + + +**Author** + +Pierre Lindenbaum PhD @yokofakun + +**Citation** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit + +**Contribute** + +- Issue Tracker: http://github.com/lindenb/jvarkit/issues` +- Source Code: http://github.com/lindenb/jvarkit + +**License** + +The project is licensed under the MIT license. + +**Compilation** + +Date: 2015-02-27T15:54:03+01:00 +Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9 +</help> +</tool> |
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| diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcftrio.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jvarkit/vcftrio.xml Fri Feb 27 09:52:06 2015 -0500 |
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| @@ -0,0 +1,69 @@ +<?xml version="1.0"?> +<tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.vcftrios.VCFTrios" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcftrio"> + <!--Date: 2015-02-27T15:54:05+01:00--> + <description>Check for mendelian incompatibilities in a VCF</description> + <requirements> + <requirement type="binary">java</requirement> + </requirements> + <command>(gunzip -c ${input} || cat ${input}) | java -cp $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcftrio.jar com.github.lindenb.jvarkit.tools.vcftrios.VCFTrios $filter -p $ped -o ${output}.vcf.gz && mv ${output}.vcf.gz ${output}</command> + <inputs> + <param format="vcf" name="input" type="data" label="VCF input"/> + <param name="filter" type="boolean" checked="false" label="Create a FILTER in the FILTER column" truevalue="-f" falsevalue=""/> + <param name="ped" type="data" format="tabular" label="Pedigree file (Family/name/father/mother/sex)"/> + </inputs> + <outputs> + <data format="vcf" name="output"/> + </outputs> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + </stdio> + <help> + +**Inputs** + + +- **VCF input** : VCF input + +- **Create a FILTER in the FILTER column** : Create a FILTER in the FILTER column + +- **Pedigree file (Family/name/father/mother/sex)** : Pedigree file (Family/name/father/mother/sex) + + +**Outputs** + + +- **output** : output + + +**Wiki** + +https://github.com/lindenb/jvarkit/wiki/VCFTrio + +----- + + +**Author** + +Pierre Lindenbaum PhD @yokofakun + +**Citation** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit + +**Contribute** + +- Issue Tracker: http://github.com/lindenb/jvarkit/issues` +- Source Code: http://github.com/lindenb/jvarkit + +**License** + +The project is licensed under the MIT license. + +**Compilation** + +Date: 2015-02-27T15:54:05+01:00 +Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9 +</help> +</tool> |