Mercurial > repos > yokofakun > jvarkit

changeset 9:1855edc16e48 draft default tip

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Uploaded
author yokofakun
date Fri, 27 Feb 2015 11:30:21 -0500
parents 98106098dcd1
children
files 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
diffstat 16 files changed, 0 insertions(+), 420 deletions(-) [+]
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Binary file jvarkit/commons-jexl-2.1.1.jar has changed
Binary file jvarkit/commons-logging-1.1.1.jar has changed
Binary file jvarkit/groupbygene.jar has changed
--- 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 @@
-<?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 &amp;&amp; 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>
Binary file jvarkit/htsjdk-1.128.jar has changed
Binary file jvarkit/snappy-java-1.0.3-rc3.jar has changed
Binary file jvarkit/vcffilterjs.jar has changed
--- 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 @@
-<?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 &amp;&amp; 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>
Binary file jvarkit/vcffilterso.jar has changed
--- 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 @@
-<?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  &amp;&amp; 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>
Binary file jvarkit/vcfhead.jar has changed
--- 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 @@
-<?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 &amp;&amp; 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>
Binary file jvarkit/vcftail.jar has changed
--- 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 @@
-<?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  &amp;&amp; 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>
Binary file jvarkit/vcftrio.jar has changed
--- 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 @@
-<?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 &amp;&amp; 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>