| Previous changeset 8:98106098dcd1 (2015-02-27) |
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Commit message:
Uploaded |
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removed:
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 98106098dcd1 -r 1855edc16e48 jvarkit/commons-jexl-2.1.1.jar |
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| Binary file jvarkit/commons-jexl-2.1.1.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/commons-logging-1.1.1.jar |
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| Binary file jvarkit/commons-logging-1.1.1.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/groupbygene.jar |
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| Binary file jvarkit/groupbygene.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/groupbygene.xml --- a/jvarkit/groupbygene.xml Fri Feb 27 09:52:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,63 +0,0 @@ -<?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 98106098dcd1 -r 1855edc16e48 jvarkit/htsjdk-1.128.jar |
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| Binary file jvarkit/htsjdk-1.128.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/snappy-java-1.0.3-rc3.jar |
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| Binary file jvarkit/snappy-java-1.0.3-rc3.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/vcffilterjs.jar |
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| Binary file jvarkit/vcffilterjs.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/vcffilterjs.xml --- a/jvarkit/vcffilterjs.xml Fri Feb 27 09:52:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,72 +0,0 @@ -<?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 98106098dcd1 -r 1855edc16e48 jvarkit/vcffilterso.jar |
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| Binary file jvarkit/vcffilterso.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/vcffilterso.xml --- a/jvarkit/vcffilterso.xml Fri Feb 27 09:52:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,84 +0,0 @@ -<?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 98106098dcd1 -r 1855edc16e48 jvarkit/vcfhead.jar |
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| Binary file jvarkit/vcfhead.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/vcfhead.xml --- a/jvarkit/vcfhead.xml Fri Feb 27 09:52:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,66 +0,0 @@ -<?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 98106098dcd1 -r 1855edc16e48 jvarkit/vcftail.jar |
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| Binary file jvarkit/vcftail.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/vcftail.xml --- a/jvarkit/vcftail.xml Fri Feb 27 09:52:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,66 +0,0 @@ -<?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 98106098dcd1 -r 1855edc16e48 jvarkit/vcftrio.jar |
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| Binary file jvarkit/vcftrio.jar has changed |
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| diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/vcftrio.xml --- a/jvarkit/vcftrio.xml Fri Feb 27 09:52:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,69 +0,0 @@ -<?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> |