Mercurial > repos > iuc > bctools_extract_crosslinked_nucleotides

comparison coords2clnt.xml @ 0:66d1f96c5600 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
author iuc
date Tue, 14 Nov 2017 05:52:26 -0500
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1 <tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@VERSION@">
2 <description>from full alignments</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 coords2clnt.py
9 '$alignment_coordinates'
10 > '$crosslinking_coordinates'
11 ]]></command>
12 <inputs>
13 <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/>
14 </inputs>
15 <outputs>
16 <data name="crosslinking_coordinates" format="bed"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="alignment_coordinates" value="merged_pcr_dupes.bed"/>
21 <output name="crosslinking_coordinates" file="merged_pcr_dupes_clnts.bed"/>
22 </test>
23 </tests>
24 <help><![CDATA[
25
26 bctools - Get crosslinked nucleotides from full alignments
27 ==========================================================
28
29 Given coordinates of aligned reads in BED format, calculate positions of the
30 crosslinked nucleotides. Crosslinked nts are assumed to be one nt upstream of
31 the 5'-end of the read.
32
33 Input
34 -----
35
36 * six column BED file containing coordinates of aligned reads
37
38 Output
39 ------
40
41 * six column BED file containing coordinates of crosslinking events
42
43 ]]></help>
44 <expand macro="citations"/>
45 </tool>