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changeset 8:98106098dcd1 draft

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Uploaded
author yokofakun
date Fri, 27 Feb 2015 09:52:06 -0500
parents e5723e64ea43
children 1855edc16e48
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, 420 insertions(+), 0 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
--- /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 @@
+<?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
--- /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 @@
+<?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
--- /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 @@
+<?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
--- /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 @@
+<?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
--- /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 @@
+<?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
--- /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 @@
+<?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>