Mercurial > repos > devteam > samtools_flagstat
changeset 0:1bbde47ebd2a draft
Uploaded
| author | devteam |
|---|---|
| date | Tue, 20 Aug 2013 12:33:44 -0400 |
| parents | |
| children | f92f13ccee76 |
| files | samtools_flagstat.xml test-data/3unsorted.bam test-data/samtools_flagstat_out1.txt tool_dependencies.xml |
| diffstat | 4 files changed, 54 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_flagstat.xml Tue Aug 20 12:33:44 2013 -0400 @@ -0,0 +1,37 @@ +<tool id="samtools_flagstat" name="flagstat" version="1.0.0"> + <requirements> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <description>provides simple stats on BAM files</description> + <command>samtools flagstat "$input1" > "$output1" + </command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File to Convert" /> + </inputs> + <outputs> + <data name="output1" format="txt" /> + </outputs> + <tests> + <test> + <param name="input1" value="3unsorted.bam" ftype="bam" /> + <output name="output1" file="samtools_flagstat_out1.txt" /> + </test> + </tests> + <help> + +**What it does** + +This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file. + +.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + +------ + +**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_flagstat_out1.txt Tue Aug 20 12:33:44 2013 -0400 @@ -0,0 +1,11 @@ +10 + 0 in total (QC-passed reads + QC-failed reads) +0 + 0 duplicates +10 + 0 mapped (100.00%:nan%) +0 + 0 paired in sequencing +0 + 0 read1 +0 + 0 read2 +0 + 0 properly paired (nan%:nan%) +0 + 0 with itself and mate mapped +0 + 0 singletons (nan%:nan%) +0 + 0 with mate mapped to a different chr +0 + 0 with mate mapped to a different chr (mapQ>=5)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Aug 20 12:33:44 2013 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.18"> + <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>