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author yating-l
date Wed, 17 May 2017 16:28:29 -0400
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1 <?xml version="1.0"?>
2 <tool id="bedgraph_to_bigwig" name="bedGraphToBigWig" version="1.0">
3 <description>Converts a bedGraph file to bigWig format</description>
4
5 <macros>
6 <import>ucsc_macros.xml</import>
7 </macros>
8
9 <requirements>
10 <requirement type="package" version="340">ucsc_bigwig</requirement>
11 <requirement type="package" version="340">ucsc_bigbed</requirement>
12 </requirements>
13
14 <command detect_errors="exit_code">
15 <![CDATA[
16 @OPTIONAL_PARAM_FUNC@
17
18 ## Allow UCSC track and browser lines in input file
19 awk '$0 !~ /^(track|browser) /' "${bedgraph_input}" |
20
21 #if str($bed_clip) == "bedClip":
22 bedClip -verbose=2
23 stdin "${chrominfo_input}" stdout |
24 #end if
25
26 sort -k 1,1 -k 2,2n > "${bedgraph_input}".sorted &&
27
28 bedGraphToBigWig
29 $optional_param("-blockSize", $adv.block_size)
30 $optional_param("-itemsPerSlot", $adv.items_per_slot)
31 ${adv.no_compression}
32 "${bedgraph_input}".sorted "${chrominfo_input}" "${bw_output}"
33 ]]>
34 </command>
35
36 <expand macro="environment_LC_COLLATE" />
37
38 <inputs>
39 <param name="bedgraph_input" type="data" format="bedgraph"
40 label="bedGraph input file" />
41
42 <param name="chrominfo_input" type="data" format="tabular"
43 label="Chromosomes sizes file" />
44
45 <param name="bed_clip" type="boolean" checked="false"
46 truevalue="bedClip" falsevalue=""
47 label="Remove BED items that extend beyond the scaffolds"
48 help="bedClip" />
49
50 <section name="adv" title="Advanced options" expanded="false">
51 <param name="block_size" type="integer" label="Block size"
52 min="1" optional="true"
53 help="Number of items to bundle in r-tree" />
54
55 <param name="items_per_slot" type="integer" label="Items per slot"
56 min="1" optional="true"
57 help="Number of data points bundled at the lowest level" />
58
59 <param name="no_compression" type="boolean" checked="false"
60 truevalue="-unc" falsevalue=""
61 label="Do not use compression"
62 help="-unc" />
63 </section>
64 </inputs>
65 <outputs>
66 <data name="bw_output" format="bigwig" />
67 </outputs>
68 <tests>
69 <test>
70 <!-- Test bedGraphToBigWig with default settings -->
71 <param name="bedgraph_input" value="contigs.bedgraph" ftype="bedgraph" />
72 <param name="chrominfo_input" value="contigs_chromInfo.tab" ftype="tabular" />
73 <output name="bw_output" file="contigs.bedgraph.bw" />
74 </test>
75 <test>
76 <!-- Test bedGraphToBigWig with advanced options -->
77 <param name="bedgraph_input" value="contigs.bedgraph" ftype="bedgraph" />
78 <param name="chrominfo_input" value="contigs_chromInfo.tab" ftype="tabular" />
79 <param name="block_size" value="200" />
80 <param name="items_per_slot" value="500" />
81 <param name="no_compression" value="-unc" />
82 <output name="bw_output" file="contigs.bedgraph_advanced.bw" />
83 </test>
84 <test>
85 <!-- Test bedGraphToBigWig with default settings -->
86 <param name="bedgraph_input" value="contigs.clip.bedGraph" ftype="bedgraph" />
87 <param name="chrominfo_input" value="contigs_chromInfo.tab" ftype="tabular" />
88 <param name="bed_clip" value="bedClip" />
89 <output name="bw_output" file="contigs.bedgraph_clip.bw" />
90 </test>
91 </tests>
92 <help>
93 <![CDATA[
94 **What it does**
95
96 bedGraphToBigWig converts a `bedGraph <https://genome.ucsc.edu/goldenpath/help/bedgraph.html>`_ file
97 to the `bigWig format <https://genome.ucsc.edu/goldenpath/help/bigWig.html>`_.
98
99 ----
100
101 **The bedGraph format**
102
103 The first three columns of the bedGraph file are the same as the
104 `BED format <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_, and it uses
105 a `zero-start, half-open <http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/>`_
106 coordinate system. The fourth column of the bedGraph file contains the data values::
107
108 chromA chromStartA chromEndA dataValueA
109 chromB chromStartB chromEndB dataValueB
110
111 ----
112
113 .. class:: infomark
114
115 **Chromosomes sizes file**
116
117 This tool requires a chromosomes sizes (``chrom.sizes``) file, which lists the size of
118 each scaffold within an assembly. For genome assemblies that are hosted by UCSC,
119 the ``chrom.sizes`` file is available through the
120 `Sequence and Annotation Downloads <http://hgdownload.cse.ucsc.edu/downloads.html>`_ page.
121 The `twoBitInfo <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_ tool
122 can be used to generate the ``chrom.sizes`` for the genome assemblies that are not hosted
123 by UCSC.
124
125 ]]></help>
126
127 <expand macro="citations" />
128 </tool>