Mercurial > repos > devteam > samtools_reheader
changeset 0:c50efc142ad0 draft
Uploaded initial tool definition.
| author | devteam |
|---|---|
| date | Fri, 17 Oct 2014 14:03:47 -0400 |
| parents | |
| children | 8546afbbd7f1 |
| files | samtools_reheader.xml test-data/phiX.bam test-data/samtools_reheader_in1.sam test-data/samtools_reheader_in2.sam test-data/samtools_reheader_out1.bam test-data/samtools_reheader_out2.bam tool_dependencies.xml |
| diffstat | 7 files changed, 47 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_reheader.xml Fri Oct 17 14:03:47 2014 -0400 @@ -0,0 +1,35 @@ +<tool id="samtools_reheader" name="Replace header" version="1.0.0"> + <description>on a BAM or SAM file</description> + <requirements> + <requirement type="package" version="1.1">samtools</requirement> + </requirements> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <inputs> + <param name="input_header" type="data" format="sam" label="SAM file or header" /> + <param name="input_file" type="data" format="sam,bam" label="File to reheader" /> + </inputs> + <outputs> + <data format="bam" name="output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + </tests> + <help> +**What it does** + +This tool runs the ``samtools reheader`` command in the SAMtools toolkit. + +Replace the header for a SAM or BAM file with a different header. + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_reheader_in1.sam Fri Oct 17 14:03:47 2014 -0400 @@ -0,0 +1,3 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:phiX174 LN:5386 +@PG ID:bowtie2 PN:bowtie2 VN:2.1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_reheader_in2.sam Fri Oct 17 14:03:47 2014 -0400 @@ -0,0 +1,3 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:phiX174 LN:5386 +@PG ID:manual PN:vim VN:7.4.52
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Oct 17 14:03:47 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>