# HG changeset patch
# User yokofakun
# Date 1425054621 18000
# Node ID 1855edc16e4847c8b9e06c343965243cbb7268e0
# Parent 98106098dcd11daf73f559eedb44dee8233c1fad
Uploaded
diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/commons-jexl-2.1.1.jar
Binary file jvarkit/commons-jexl-2.1.1.jar has changed
diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/commons-logging-1.1.1.jar
Binary file jvarkit/commons-logging-1.1.1.jar has changed
diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/groupbygene.jar
Binary file jvarkit/groupbygene.jar has changed
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
@@ -1,63 +0,0 @@
-
-
-
- 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}
-
-
-
-
-
-
-
-
-
-
-
-
-**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 98106098dcd1 -r 1855edc16e48 jvarkit/htsjdk-1.128.jar
Binary file jvarkit/htsjdk-1.128.jar has changed
diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/snappy-java-1.0.3-rc3.jar
Binary file jvarkit/snappy-java-1.0.3-rc3.jar has changed
diff -r 98106098dcd1 -r 1855edc16e48 jvarkit/vcffilterjs.jar
Binary file jvarkit/vcffilterjs.jar has changed
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
@@ -1,72 +0,0 @@
-
-
-
- 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}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-**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 98106098dcd1 -r 1855edc16e48 jvarkit/vcffilterso.jar
Binary file jvarkit/vcffilterso.jar has changed
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
@@ -1,84 +0,0 @@
-
-
-
- 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]+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-**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 98106098dcd1 -r 1855edc16e48 jvarkit/vcfhead.jar
Binary file jvarkit/vcfhead.jar has changed
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
@@ -1,66 +0,0 @@
-
-
-
- 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}
-
-
-
-
-
-
-
-
-
-
-
-
-
-**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 98106098dcd1 -r 1855edc16e48 jvarkit/vcftail.jar
Binary file jvarkit/vcftail.jar has changed
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
@@ -1,66 +0,0 @@
-
-
-
- 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}
-
-
-
-
-
-
-
-
-
-
-
-
-
-**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 98106098dcd1 -r 1855edc16e48 jvarkit/vcftrio.jar
Binary file jvarkit/vcftrio.jar has changed
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
@@ -1,69 +0,0 @@
-
-
-
- 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}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-**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
-
-