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comparison samtools_idxstats.xml @ 0:87398ae795c7 draft

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author devteam
date Tue, 21 Apr 2015 16:00:31 -0400
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1 <tool id="samtools_idxstats" name="IdxStats" version="2.0">
2 <description>tabulate mapping statistics for BAM dataset</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
9 <command><![CDATA[
10 if [ ! -f "${input}.bai" ] ; then
11 ln -s "${input}" input.bam ;
12 samtools sort -o sorted.bam -O bam -T sts "${input}" ;
13 samtools index sorted.bam ;
14 samtools idxstats sorted.bam > "${output}" ;
15 else
16 samtools idxstats "${input}" > "${output}" ;
17 fi]]>
18 </command>
19 <inputs>
20 <param name="input" type="data" format="bam" label="BAM file" />
21 </inputs>
22 <outputs>
23 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
24 </outputs>
25 <tests>
26 <test>
27 <param name="input" value="phiX.bam" ftype="bam" />
28 <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
29 </test>
30 </tests>
31 <help>
32 <![CDATA[
33 **What it does**
34
35 Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file.
36
37 Input is a sorted and indexed BAM file, the output is tabular with
38 four columns (one row per reference sequence plus a final line for
39 unmapped reads)::
40
41 Column Description
42 ------ -----------------------------
43 1 Reference sequence identifier
44 2 Reference sequence length
45 3 Number of mapped reads
46 4 Number of placed but unmapped reads
47 (typically unmapped partners of mapped reads)
48
49 ------
50
51 **Example** output from a *de novo* assembly::
52
53 contig_1 170035 98397 0
54 contig_2 403835 199564 0
55 contig_3 553102 288189 0
56 ... ... ... ...
57 contig_603 653 50 0
58 contig_604 214 6 0
59 \* 0 0 50320
60
61
62 In this example there were 604 contigs, each with one line in the output table,
63 plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
64 In this BAM file, the final column was otherwise zero.
65
66 ------
67
68 Peter J.A. Cock (2013), `Galaxy wrapper <https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats>`_ for the samtools idxstats command
69 ]]>
70 </help>
71 <expand macro="citations"></expand>
72 </tool>