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comparison extract_aln_ends.xml @ 14:570a7de9f151 draft

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read from bam; fix header issue
author rnateam
date Mon, 30 Nov 2015 07:53:36 -0500
parents 1bfc5a5de843
children 11ef9c403c72
comparison
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13:258b6f9e19ab 14:570a7de9f151
12 $positional_1 12 $positional_1
13 #end if 13 #end if
14 14
15 > $default]]></command> 15 > $default]]></command>
16 <inputs> 16 <inputs>
17 <param area="false" label="Sam input." name="positional_1" type="data" format="sam"/> 17 <param area="false" label="Alignments in SAM or BAM format." name="positional_1" type="data" format="sam,bam"/>
18 </inputs> 18 </inputs>
19 <outputs> 19 <outputs>
20 <data format="bed" hidden="false" name="default"/> 20 <data format="bed" hidden="false" name="default"/>
21 </outputs> 21 </outputs>
22 <tests> 22 <tests>
24 <param name="positional_1" value="twomates.sam"/> 24 <param name="positional_1" value="twomates.sam"/>
25 <output name="default" file="tworeads_aln_ends.bed"/> 25 <output name="default" file="tworeads_aln_ends.bed"/>
26 </test> 26 </test>
27 </tests> 27 </tests>
28 <help><![CDATA[ 28 <help><![CDATA[
29 Extract alignment ends from sam file. 29 Extract alignment ends from bam file.
30 30
31 The resulting bed file contains the outer coordinates of the alignments. The 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 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 33 distance of the alignment. The crosslinked nucleotide is one nt upstream of the
34 5'-end of the bed entries. 34 5'-end of the bed entries.
36 This tool only reports results for alignments that are properly aligned in FR 36 This tool only reports results for alignments that are properly aligned in FR
37 ("forward-reverse") direction. 37 ("forward-reverse") direction.
38 38
39 Input: 39 Input:
40 40
41 * sam file containing alignments (paired-end sequencing) 41 * bam file containing alignments (paired-end sequencing)
42 42
43 Output: 43 Output:
44 44
45 * bed6 file containing outer coordinates (sorted by read id) 45 * bed6 file containing outer coordinates (sorted by read id)
46 46