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comparison tools/samtools_idxstats/samtools_idxstats.xml @ 0:d4412c04d7b1 draft

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Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
author peterjc
date Wed, 20 Nov 2013 12:27:33 -0500
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children 8945bad80f4a
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1 <tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.1">
2 <description>samtools idxstats</description>
3 <requirements>
4 <requirement type="binary">samtools</requirement>
5 <requirement type="package" version="0.1.19">samtools</requirement>
6 </requirements>
7 <version_command interpreter="python">samtools_idxstats.py --version</version_command>
8 <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command>
9 <inputs>
10 <param name="input_bam" type="data" format="bam" label="Input BAM file" />
11 </inputs>
12 <outputs>
13 <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" />
14 </outputs>
15 <stdio>
16 <!-- Assume anything other than zero is an error -->
17 <exit_code range="1:" />
18 <exit_code range=":-1" />
19 </stdio>
20 <tests>
21 <test>
22 <param name="input_bam" value="ex1.bam" ftype="bam" />
23 <output name="out_tabular" file="ex1.idxstats.tabular" ftype="tabular" />
24 </test>
25 </tests>
26 <help>
27 **What it does**
28
29 This tool runs the ``samtools idxstats`` command in the SAMtools toolkit.
30
31 Input is a sorted and indexed BAM file, the output is tabular with
32 four columns (one row per reference sequence plus a final line for
33 unmapped reads):
34
35 ====== =================================================================================
36 Column Description
37 ------ ---------------------------------------------------------------------------------
38 1 Reference sequence identifier
39 2 Reference sequence length
40 3 Number of mapped reads
41 4 Number of placed but unmapped reads (typically unmapped partners of mapped reads)
42 ====== =================================================================================
43
44 Example output from a *de novo* assembly:
45
46 ========== ====== ====== =====
47 contig_1 170035 98397 0
48 contig_2 403835 199564 0
49 contig_3 553102 288189 0
50 ... ... ... ...
51 contig_603 653 50 0
52 contig_604 214 6 0
53 \* 0 0 50320
54 ========== ====== ====== =====
55
56 In this example there were 604 contigs, each with one line in the output table,
57 plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
58 In this BAM file, the final column was otherwise zero.
59
60
61 **Citation**
62
63 If you use this Galaxy tool in work leading to a scientific publication please
64 cite:
65
66 Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools.
67 Bioinformatics 25(16), 2078-9.
68 http://dx.doi.org/10.1093/bioinformatics/btp352
69
70 Peter J.A. Cock (2013), Galaxy wrapper for the samtools idxstats command
71 http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
72
73 This wrapper is available to install into other Galaxy Instances via the Galaxy
74 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
75 </help>
76 </tool>