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planemo upload commit 7624082bc86d63e7a63cc72a75287b7b7408678d-dirty
author yating-l
date Mon, 10 Jul 2017 12:43:51 -0400
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1 <?xml version="1.0"?>
2 <tool id="hg_gc_percent" name="hgGcPercent" version="1.0">
3 <description>Calculates GC percentages of a twoBit file</description>
4
5 <macros>
6 <import>ucsc_macros.xml</import>
7 </macros>
8
9 <expand macro="requirements_twobit">
10 <requirement type="package" version="340">ucsc_gcpercent</requirement>
11 <requirement type="package" version="340">ucsc_bigwig</requirement>
12 </expand>
13
14 <command detect_errors="exit_code">
15 <![CDATA[
16 ## This tool generates a bigWig file instead of a gzip wiggle file in order
17 ## to facilitate testing. Support for comparing gzip files will be added to
18 ## Galaxy in 17.05: https://github.com/galaxyproject/galaxy/pull/3550
19
20 twoBitInfo "${twobit_input}" "${twobit_input}.chromInfo" &&
21
22 hgGcPercent -doGaps -noDots -verbose=0 -wigOut
23 -win=${window_size}
24 -overlap=${overlap}
25 -file=stdout
26
27 #if str($region_type.region_type_selector) == "chrom":
28 -chr="${region_type.chrom_name}"
29 #end if
30
31 db_placeholder "${twobit_input}" |
32
33 wigToBigWig stdin "${twobit_input}.chromInfo" "${bw_output}"
34 ]]>
35 </command>
36 <inputs>
37 <param name="twobit_input" type="data" format="twobit" label="twoBit input file" />
38
39 <param name="window_size" type="integer" min="1" value="5"
40 label="Window size"
41 help="Size of the sliding window for calculating GC percentages (-win)" />
42
43 <param name="overlap" type="integer" min="0" value="0"
44 label="Overlap size"
45 help="Size of overlap for the sliding window (-overlap)" />
46
47 <conditional name="region_type">
48 <param name="region_type_selector" type="select"
49 label="Choose the analysis region">
50 <option value="all" selected="true">All scaffolds</option>
51 <option value="chrom">Chromosome</option>
52 </param>
53
54 <when value="all"></when>
55
56 <when value="chrom">
57 <param name="chrom_name" type="text" label="Sequence name"
58 help="Process only this sequence in the twoBit file" />
59 </when>
60 </conditional>
61 </inputs>
62 <outputs>
63 <data name="bw_output" format="bigwig" />
64 </outputs>
65 <tests>
66 <test>
67 <!-- Test hgGcPercent with default settings -->
68 <param name="twobit_input" value="contigs.unmasked.2bit" ftype="twobit" />
69 <output name="bw_output" file="contigs_gc5Base.bw" />
70 </test>
71 <test>
72 <!-- Test hgGcPercent with custom window and overlap -->
73 <param name="twobit_input" value="contigs.unmasked.2bit" ftype="twobit" />
74 <param name="window_size" value="100" />
75 <param name="overlap" value="10" />
76 <output name="bw_output" file="contigs_gc100Base_10overlap.bw" />
77 </test>
78 <test>
79 <!-- Test hgGcPercent with only one chromosome -->
80 <param name="twobit_input" value="contigs.unmasked.2bit" ftype="twobit" />
81 <param name="region_type_selector" value="chrom" />
82 <param name="chrom_name" value="contig12" />
83 <output name="bw_output" file="contig12_gc5Base.bw" />
84 </test>
85 </tests>
86 <help>
87 <![CDATA[
88 **What it does**
89
90 hgGcPercent uses a sliding window to calculate the GC percentages
91 of a genome assembly.
92
93 ]]></help>
94
95 <expand macro="citations" />
96 </tool>