Mercurial > repos > takadonet > tabix
changeset 0:75064adad442 draft default tip
Uploaded
| author | takadonet |
|---|---|
| date | Thu, 16 Jan 2014 10:57:12 -0500 |
| parents | |
| children | |
| files | bgzip.xml tabix.sh tabix.xml tool_dependencies.xml |
| diffstat | 4 files changed, 178 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bgzip.xml Thu Jan 16 10:57:12 2014 -0500 @@ -0,0 +1,50 @@ +<tool id="bgzip" name="bgzip" version="0.0.2"> + <description>Block compression/decompression utility. Required for use of tabix.</description> + <requirements> + <requirement type="package" version="0.2.6">tabix</requirement> + </requirements> + <command> + bgzip + + #if str($virtualOffset) != "" + -b $virtualOffset + #end if + + #if str($size) != "" + -s $size + #end if + + $input + -c > $output + </command> + <inputs> + <param name="input" type="data" label="Input file" /> + <param name="virtualOffset" type="text" optional="yes" label="Virtual Offset" /> + <param name="size" type="text" optional="yes" label="Size" /> + </inputs> + + <outputs> + <data format= "gz" name="output"/> + </outputs> + + <help> +**What it does:** + +The input data file is sorted and compressed by bgzip which has a gzip(1) like interface. Tabix requires the file to be compressed using this tool first. + +**Citation:** + +Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching. + +http://samtools.sourceforge.net/tabix.shtml + +**Example:** + +(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz; + +tabix -p gff sorted.gff.gz; + +tabix sorted.gff.gz chr1:10,000,000-20,000,000; + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tabix.sh Thu Jan 16 10:57:12 2014 -0500 @@ -0,0 +1,12 @@ +#!/bin/bash + + +output=$1 +shift +#get working directory so we can find the output files +CUR_DIR=`pwd` + +#run tabix +$CUR_DIR/tabix.sh $@ > $output + +exit 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tabix.xml Thu Jan 16 10:57:12 2014 -0500 @@ -0,0 +1,89 @@ +<tool id="tabix" name="tabix" version="0.0.2"> + <description>Generic indexer for TAB-delimited genome position files.</description> + <requirements> + <requirement type="package" version= "0.2.6">tabix</requirement> + </requirements> + <command> + tabix.sh $output + #if str($optional.extension) == "tabular" + #if str($optional.position) == "no" + -0 + #end if + + #if str($optional.columnseq) != "" + -s $optional.columnseq + #end if + + #if str($optional.columnstart) != "" + -b $optional.columnstart + #end if + + #if str($optional.columnend) != "" + -e $optional.columnend + #end if + + #if str($optional.skiplines) != "" + -S $optional.skiplines + #end if + + #if str($optional.skipchar) != "" + -c $optional.skipchar + #end if + #else + -p + #end if + + $input $region + + </command> + <inputs> + <param name="input" type="data" label="Input file" format="gff,bed,sam,vcf,tabular"> + </param> + <param name="region" type="text" optional="true" label="Regions (seperate with spaces)"> </param> + <conditional name="optional"> + <param name= "extension" type="select" value= "tabular" label= "Input Extension"> + <option value="tabular">tabular</option> + <option value="gff">gff</option> + <option value="bed">bed</option> + <option value="sam">sam</option> + <option value="vcf">vcf</option> + </param> + <when value="tabular"> + <param name="columnseq" type="integer" optional= "true" label="Column of sequence name" /> + <param name="columnstart" type="integer" optional= "true" label="Column of start chromosomal position" /> + <param name="columnend" type="integer" optional= "true" label="Column of end chromosomal position" /> + <param name="skiplines" type="integer" optional= "true" label="Skip first INT lines" /> + <param name="skipchar" type="text" optional= "true" label="Skip lines started with CHAR" /> + <param name="position" type= "select" value= "yes" label="1-based? (if not, 0-based)"> + <option value= "yes">yes</option> + <option value= "no">no</option> + </param> + </when> + </conditional> + </inputs> + + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> +**What it does:** + +Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. + +**Citation:** + +Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching. + +http://samtools.sourceforge.net/tabix.shtml + +**Example:** + +(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz; + +tabix -p gff sorted.gff.gz; + +tabix sorted.gff.gz chr1:10,000,000-20,000,000; + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jan 16 10:57:12 2014 -0500 @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="tabix" version="0.2.6"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>tabix</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bgzip</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Tabix version 0.2.6. Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching. + </readme> + </package> + + +</tool_dependency>