annotate bamsort.xml @ 3:ba685c655e18

Uploaded
author wolma
date Wed, 11 Feb 2015 09:26:43 -0500
parents 72d20758ba2c
children bdd1995c9e66
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
1 <tool id="bamsort" name="Sort BAM file">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
2
72d20758ba2c final upload
wolma
parents: 1
diff changeset
3 <macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
4 <import>toolshed_macros.xml</import>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
5 </macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
6 <expand macro="requirements"/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
7 <version_command>mimodd version -q</version_command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
8 <command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
9 mimodd sort "$inputfile" -o "$output" --oformat $oformat $by_name
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
10 </command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
11
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
12 <inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
13 <param name="inputfile" type="data" format="bam" label="Input file to sort" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
14 <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
15 <param name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
16 </inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
17
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
18 <outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
19 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
20 <change_format>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
21 <when input="oformat" value="sam" format="sam" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
22 </change_format>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
23 </data>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
24 </outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
25
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
26 <help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
27 .. class:: infomark
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
28
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
29 **What it does**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
30
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
31 The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
32
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
33 Coordinate-sorted input files are expected by most downstream MiModD tools, but note that the *SNAP Read Alignment* produces coordinate-sorted output by default and it is only necessary to sort files that come from other sources or from *SNAP Read Alignment* jobs with a custom sort order.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
34
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
35 The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
36
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
37 </help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
38 </tool>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
39