annotate samtools_idxstats.xml @ 0:87398ae795c7 draft

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<tool id="samtools_idxstats" name="IdxStats" version="2.0">
    <description>tabulate mapping statistics for BAM dataset</description>
    <macros>
      <import>macros.xml</import>
    </macros>
    <expand macro="requirements"></expand>
    <expand macro="stdio"></expand>
    <expand macro="version_command"></expand>
    <command><![CDATA[
if [ ! -f "${input}.bai" ] ; then
    ln -s "${input}" input.bam ;
    samtools sort -o sorted.bam -O bam -T sts "${input}" ;
    samtools index sorted.bam ;
    samtools idxstats sorted.bam > "${output}" ;
else
    samtools idxstats "${input}" > "${output}" ;
fi]]>
    </command>
    <inputs>
        <param name="input" type="data" format="bam" label="BAM file" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="phiX.bam" ftype="bam" />
            <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file.

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.

------

Peter J.A. Cock (2013), `Galaxy wrapper <https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats>`_ for the samtools idxstats command
]]>
    </help>
    <expand macro="citations"></expand>
</tool>