Mercurial > repos > peterjc > samtools_idxstats

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
author peterjc
date Wed, 20 Nov 2013 12:27:33 -0500
parents
children 8945bad80f4a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
1 <tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.1">
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
2 <description>samtools idxstats</description>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
3 <requirements>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
4 <requirement type="binary">samtools</requirement>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
5 <requirement type="package" version="0.1.19">samtools</requirement>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
6 </requirements>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
7 <version_command interpreter="python">samtools_idxstats.py --version</version_command>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
8 <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
9 <inputs>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
10 <param name="input_bam" type="data" format="bam" label="Input BAM file" />
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
11 </inputs>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
12 <outputs>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
13 <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" />
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
14 </outputs>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
15 <stdio>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
16 <!-- Assume anything other than zero is an error -->
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
17 <exit_code range="1:" />
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
18 <exit_code range=":-1" />
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
19 </stdio>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
20 <tests>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
21 <test>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
22 <param name="input_bam" value="ex1.bam" ftype="bam" />
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
23 <output name="out_tabular" file="ex1.idxstats.tabular" ftype="tabular" />
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
24 </test>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
25 </tests>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
26 <help>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
27 **What it does**
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
28
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
29 This tool runs the ``samtools idxstats`` command in the SAMtools toolkit.
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
30
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
31 Input is a sorted and indexed BAM file, the output is tabular with
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
32 four columns (one row per reference sequence plus a final line for
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
33 unmapped reads):
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
34
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
35 ====== =================================================================================
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
36 Column Description
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
37 ------ ---------------------------------------------------------------------------------
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
38 1 Reference sequence identifier
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
39 2 Reference sequence length
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
40 3 Number of mapped reads
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
41 4 Number of placed but unmapped reads (typically unmapped partners of mapped reads)
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
42 ====== =================================================================================
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
43
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
44 Example output from a *de novo* assembly:
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
45
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
46 ========== ====== ====== =====
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
47 contig_1 170035 98397 0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
48 contig_2 403835 199564 0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
49 contig_3 553102 288189 0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
50 ... ... ... ...
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
51 contig_603 653 50 0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
52 contig_604 214 6 0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
53 \* 0 0 50320
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
54 ========== ====== ====== =====
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
55
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
56 In this example there were 604 contigs, each with one line in the output table,
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
57 plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
58 In this BAM file, the final column was otherwise zero.
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
59
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
60
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
61 **Citation**
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
62
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
63 If you use this Galaxy tool in work leading to a scientific publication please
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
64 cite:
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
65
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
66 Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools.
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
67 Bioinformatics 25(16), 2078-9.
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
68 http://dx.doi.org/10.1093/bioinformatics/btp352
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
69
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
70 Peter J.A. Cock (2013), Galaxy wrapper for the samtools idxstats command
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
71 http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
72
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
73 This wrapper is available to install into other Galaxy Instances via the Galaxy
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
74 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
75 </help>
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
76 </tool>