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comparison extract_aln_ends.xml @ 2:de4ea3aa1090 draft

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author rnateam
date Thu, 22 Oct 2015 10:26:45 -0400
parents 119fccb59597
children 1bfc5a5de843
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1:ae0f58d3318f 2:de4ea3aa1090
1 <tool id="extract_aln_ends.py" name="extract_aln_ends.py" version="0.1.0">
2 <description>Extract alignment ends from sam file.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <version_command>python extract_aln_ends.py --version</version_command>
9 <command interpreter="python"><![CDATA[
10 extract_aln_ends.py
11 #if $positional_1 and $positional_1 is not None:
12 $positional_1
13 #end if
14
15 > $default]]></command>
16 <inputs>
17 <param area="false" label="Sam input." name="positional_1" type="data" format="sam"/>
18 </inputs>
19 <outputs>
20 <data format="bed" hidden="false" name="default"/>
21 </outputs>
22 <tests>
23 <test>
24 <param name="positional_1" value="twomates.sam"/>
25 <output name="default" file="tworeads_aln_ends.bed"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29 Extract alignment ends from sam file.
30
31 The resulting bed file contains the outer coordinates of the alignments. The
32 bed name field is set to the read id and the score field is set to the edit
33 distance of the alignment. The crosslinked nucleotide is one nt upstream of the
34 5'-end of the bed entries.
35
36 This tool only reports results for alignments that are properly aligned in FR
37 ("forward-reverse") direction.
38
39 Input:
40 * sam file containing alignments (paired-end sequencing)
41
42 Output:
43 * bed6 file containing outer coordinates (sorted by read id)
44
45 Author: Daniel Maticzka
46 Copyright: 2015
47 License: Apache
48 Email: maticzkd@informatik.uni-freiburg.de
49 Status: Development
50 ]]></help>
51 <expand macro="citations" />
52 </tool>