Mercurial > repos > iuc > bctools_extract_alignment_ends
comparison extract_aln_ends.xml @ 0:0e70f9058b02 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
author | iuc |
---|---|
date | Tue, 14 Nov 2017 05:53:02 -0500 |
parents | |
children | 0be29a221b16 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:0e70f9058b02 |
---|---|
1 <tool id="bctools_extract_alignment_ends" name="Extract alignment ends" version="@VERSION@"> | |
2 <description>from SAM or BAM</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 extract_aln_ends.py | |
9 '$alignments' | |
10 > '$alignment_ends' | |
11 ]]></command> | |
12 <inputs> | |
13 <param name="alignments" type="data" format="sam,bam" label="Alignments in SAM or BAM format"/> | |
14 </inputs> | |
15 <outputs> | |
16 <data name="alignment_ends" format="bed"/> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <param name="alignments" value="twomates.sam"/> | |
21 <output name="alignment_ends" file="tworeads_aln_ends.bed"/> | |
22 </test> | |
23 </tests> | |
24 <help><![CDATA[ | |
25 | |
26 bctools - Extract alignment ends from from SAM or BAM alignments | |
27 ================================================================ | |
28 | |
29 The resulting BED file contains the outer coordinates of the alignments. The BED | |
30 name field is set to the read id and the score field is set to the edit distance | |
31 of the alignment. The crosslinked nucleotide is one nt upstream of the 5'-end of | |
32 the BED entries. | |
33 | |
34 This tool only reports results for alignments that are properly aligned in FR | |
35 ("forward-reverse") direction. | |
36 | |
37 Input: | |
38 ------ | |
39 | |
40 * BAM file containing alignments (paired-end sequencing) | |
41 | |
42 Output: | |
43 ------- | |
44 | |
45 * BED file containing outer coordinates (sorted by read id) | |
46 | |
47 ]]></help> | |
48 <expand macro="citations"/> | |
49 </tool> |