| Next changeset 1:f627c4b93c55 (2014-06-20) |
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Commit message:
Uploaded |
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samtools_sort.xml test-data/1.bam tool_dependencies.xml |
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| diff -r 000000000000 -r 80fffde691eb samtools_sort.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_sort.xml Fri Jun 20 10:54:37 2014 -0400 |
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| @@ -0,0 +1,45 @@ +<tool id="samtools_rmdup" name="sort" version="1.0.1"> + <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <description>a BAM file</description> + <command> + samtools sort + $sort_mode + "${input1}" "${output1}" + 2>&1 || echo "Error running samtools sort." >&2 + </command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File" /> + <param name="sort_mode" type="select" label="Sort by "> + <option value="" selected="True">chromosomal coordinates </option> + <option value="-n">read names rather than by</option> + </param> + </inputs> + <outputs> + <data name="output1" format="bam" /> + </outputs> + <tests> + <test> + <param name="input1" value="1.bam" ftype="bam" /> + <output name="output1" file="1.bam" ftype="bam" sort="True"/> + </test> + </tests> + <help> + +**What it does** + +This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names. + +.. _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> |
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| diff -r 000000000000 -r 80fffde691eb test-data/1.bam |
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| Binary file test-data/1.bam has changed |
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| diff -r 000000000000 -r 80fffde691eb tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 20 10:54:37 2014 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |