Mercurial > repos > peterjc > samtools_idxstats
view tools/samtools_idxstats/samtools_idxstats.xml @ 2:71afa65f444a draft default tip
v0.0.5 Internal changes to command line handling
author | peterjc |
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date | Tue, 16 May 2017 09:24:18 -0400 |
parents | 8945bad80f4a |
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<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.5"> <description>samtools idxstats</description> <requirements> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> <version_command> python $__tool_directory__/samtools_idxstats.py --version </version_command> <command detect_errors="aggressive"> python $__tool_directory__/samtools_idxstats.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular' </command> <inputs> <param name="input_bam" type="data" format="bam" label="Input BAM file" /> </inputs> <outputs> <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" /> </outputs> <tests> <test> <param name="input_bam" value="ex1.bam" ftype="bam" /> <output name="out_tabular" file="ex1.idxstats.tabular" ftype="tabular" /> </test> </tests> <help> **What it does** This tool runs the ``samtools idxstats`` command in the SAMtools toolkit. Input is a sorted and indexed BAM file, the output is tabular with four columns (one row per reference sequence plus a final line for unmapped reads): ====== ================================================================================= Column Description ------ --------------------------------------------------------------------------------- 1 Reference sequence identifier 2 Reference sequence length 3 Number of mapped reads 4 Number of placed but unmapped reads (typically unmapped partners of mapped reads) ====== ================================================================================= Example output from a *de novo* assembly: ========== ====== ====== ===== contig_1 170035 98397 0 contig_2 403835 199564 0 contig_3 553102 288189 0 ... ... ... ... contig_603 653 50 0 contig_604 214 6 0 \* 0 0 50320 ========== ====== ====== ===== In this example there were 604 contigs, each with one line in the output table, plus the final row (labelled with an asterisk) representing 50320 unmapped reads. In this BAM file, the final column was otherwise zero. **Citation** If you use this Galaxy tool in work leading to a scientific publication please cite: Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16), 2078-9. http://dx.doi.org/10.1093/bioinformatics/btp352 Peter J.A. Cock (2013), Galaxy wrapper for the samtools idxstats command http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats </help> <citations> <citation type="doi">10.1093/bioinformatics/btp352</citation> </citations> </tool>