# HG changeset patch
# User yokofakun
# Date 1425048726 18000
# Node ID 98106098dcd11daf73f559eedb44dee8233c1fad
# Parent e5723e64ea43125f883385b298181e08195f45c6
Uploaded
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/commons-jexl-2.1.1.jar
Binary file jvarkit/commons-jexl-2.1.1.jar has changed
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/commons-logging-1.1.1.jar
Binary file jvarkit/commons-logging-1.1.1.jar has changed
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/groupbygene.jar
Binary file jvarkit/groupbygene.jar has changed
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
@@ -0,0 +1,63 @@
+
+
+
+ Group VCF (+ VEP + SnpEff) data by gene/transcript
+
+ java
+
+ (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}
+
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+**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
+
+
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/htsjdk-1.128.jar
Binary file jvarkit/htsjdk-1.128.jar has changed
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/snappy-java-1.0.3-rc3.jar
Binary file jvarkit/snappy-java-1.0.3-rc3.jar has changed
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcffilterjs.jar
Binary file jvarkit/vcffilterjs.jar has changed
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
@@ -0,0 +1,72 @@
+
+
+
+ Filters a VCF with Javascript
+
+ java
+
+ (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}
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+**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
+
+
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcffilterso.jar
Binary file jvarkit/vcffilterso.jar has changed
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
@@ -0,0 +1,84 @@
+
+
+
+ Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology
+
+ java
+
+ (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}
+
+
+
+
+ SO\:[0-9]+
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+**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
+
+
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcfhead.jar
Binary file jvarkit/vcfhead.jar has changed
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
@@ -0,0 +1,66 @@
+
+
+
+ Print first variants of a VCF
+
+ java
+
+ (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}
+
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+**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
+
+
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcftail.jar
Binary file jvarkit/vcftail.jar has changed
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
@@ -0,0 +1,66 @@
+
+
+
+ Print first variants of a VCF
+
+ java
+
+ (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}
+
+
+
+
+
+
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+
+
+
+
+
+
+**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
+
+
diff -r e5723e64ea43 -r 98106098dcd1 jvarkit/vcftrio.jar
Binary file jvarkit/vcftrio.jar has changed
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
@@ -0,0 +1,69 @@
+
+
+
+ Check for mendelian incompatibilities in a VCF
+
+ java
+
+ (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}
+
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+
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+**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
+
+