annotate bamsort.xml @ 18:2742ad4d1608 draft

rebase on package_python_3_4_lean
author wolma
date Tue, 26 Apr 2016 11:21:43 -0400
parents 93db2f9bca12
children c46406466625
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
93db2f9bca12 upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents: 8
diff changeset
1 <tool id="bamsort" name="Sort BAM file" version="0.1.7.2">
0
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>
5
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
9 mimodd sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
10 </command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
11
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
12 <inputs>
5
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
13 <conditional name="input">
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
14 <param name="iformat" type="select" label = "Input data format">
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
15 <option value="bam">bam</option>
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
16 <option value="sam">sam</option>
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
17 </param>
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
18 <when value="bam">
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
19 <param name="ifile" type="data" format="bam" label="BAM input file to sort" />
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
20 </when>
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
21 <when value="sam">
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
22 <param name="ifile" type="data" format="sam" label="SAM input file to sort" />
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
23 </when>
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
24 </conditional>
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
25 <param name="oformat" type="select" label = "Output format for the sorted data">
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
26 <option value="bam">bam</option>
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
27 <option value="sam">sam</option>
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 2
diff changeset
28 </param>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
29 <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
30 </inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
31
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
32 <outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
33 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
34 <change_format>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
35 <when input="oformat" value="sam" format="sam" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
36 </change_format>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
37 </data>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
38 </outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
39
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
40 <help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
41 .. class:: infomark
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
42
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
43 **What it does**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
44
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
45 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
46
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
47 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
48
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
49 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
50
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
51 </help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
52 </tool>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
53