Mercurial > repos > geert-vandeweyer > bamtools_wrappers
changeset 0:afa51021226c draft
Uploaded
| author | geert-vandeweyer |
|---|---|
| date | Tue, 18 Feb 2014 04:18:08 -0500 |
| parents | |
| children | 76aff7bca1b2 |
| files | SplitOnRg.pl SplitOnRg.xml bamToFastX.xml tool_dependencies.xml |
| diffstat | 4 files changed, 87 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SplitOnRg.pl Tue Feb 18 04:18:08 2014 -0500 @@ -0,0 +1,37 @@ +#!/usr/bin/perl + +use Getopt::Std; +getopts('i:o:O:k:p:', \%opts) ; + + +# split +$prefix = "primary_$opts{'O'}"."_"; +$command = "cd $opts{'p'} && bamtools split -in $opts{'i'} -tag RG -tagPrefix '$prefix' -stub $opts{'p'}/data" ; +#print $command ."\n"; +system($command); +chdir($opts{'p'}); +# rename to correct format. +my @ls = `ls data.primary_$opts{'O'}_RG_*`; +open OUT, ">$opts{'o'}"; +$idx = 0; +foreach(@ls) { + chomp(); + my $from = $_; + $from =~ m/(.*_RG_)(.*)(\.bam)/; + my $rg = $2; + # remove data_ + my $to = substr($from,5,-4); + $to .= "_visible_bam_$opts{'k'}"; + $to =~ s/RG_//; + $to =~ m/primary_(\d+)_(.*)_visible.*/; + $rgreplace = $2; + $rgreplace =~ s/\.|-|_//g; + $to =~ s/(primary_\d+_)(.*)(_visible.*)/$1$rgreplace$3/; + system("mv $from $to"); + $idx++; + print OUT "File $idx : $to : ReadGroup: $rg\n"; +} +close OUT; +exit; + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SplitOnRg.xml Tue Feb 18 04:18:08 2014 -0500 @@ -0,0 +1,18 @@ +<tool id="bamtools_SplitOnRG" name="Split BAM on ReadGroups" force_history_refresh="True"> +<description/> +<requirements> + <requirement type="package" version="2.3.0">bamtools</requirement> +</requirements> +<command interpreter="perl"> +SplitOnRG.pl -i '$input1' -o $output1 -O $output1.id -k $dbkey -p $__new_file_path__ +</command> +<inputs> +<param format="bam" name="input1" type="data" label="BAM file"/> +</inputs> +<outputs> +<data format="txt" name="output1" metadata_source="input1" /> +</outputs> +<help> +**What it does** This tools splits a bam file by RG-ids. ------- *bamtools split* is part of the `BAMTools package` by Derek Barnett. : https://github.com/pezmaster31/bamtools +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamToFastX.xml Tue Feb 18 04:18:08 2014 -0500 @@ -0,0 +1,26 @@ +<tool id="BAMTools_bamToFastX" name="convert BAM to FASTA/Q"> +<description/> +<requirements> + <requirement type="package" version="2.3.0">bamtools</requirement> +</requirements> +<command> +bamtools convert -in '$input1' -out '$output' -format $format +</command> +<inputs> +<param format="bam" name="input1" type="data" label="BAM file"/> +<param name="format" type="select" label="Output Format"> +<option value="fastq">FASTQ</option> +<option value="fasta">FASTA</option> +</param> +</inputs> +<outputs> +<data format="fastqsanger" name="output" metadata_source="input1" label="$input1.tag (FASTQ/A)"> +<change_format> +<when input="format" value="fasta" format="fasta"/> +</change_format> +</data> +</outputs> +<help> +**What it does** This tools converts a BAM file to a FASTQ or FASTA file. ------- *bamtools convert* is part of the `BAMTools package`__ by Derek Barnett. .. __: https://github.com/pezmaster31/bamtools ------- This wrapper was originally created by A. Gordon. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Feb 18 04:18:08 2014 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bamtools" version="2.3.0"> + <repository changeset_revision="def41213572b" name="package_bamtools_2_3_0" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>