/tools/filters/bed_to_bigbed.xml
XML | 55 lines | 52 code | 3 blank | 0 comment | 0 complexity | 6598cddad457cdade66754607293ead6 MD5 | raw file
1<tool id="bed_to_bigBed" name="BED-to-bigBed" version="1.0.0">
2 <description>converter</description>
3 <command>bedToBigBed $input1 $chromInfo $out_file1
4 #if $settings.settingsType == "full":
5 -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.unc}
6 #end if
7 2>&1 || echo "Error running bedToBigBed." >&2
8 </command>
9 <requirements>
10 <requirement type="package">ucsc_tools</requirement>
11 </requirements>
12 <inputs>
13 <param format="bed" name="input1" type="data" label="Convert">
14 <validator type="unspecified_build" />
15 </param>
16 <conditional name="settings">
17 <param name="settingsType" type="select" label="Converter settings to use" help="Default settings should usually be used.">
18 <option value="preset">Default</option>
19 <option value="full">Full parameter list</option>
20 </param>
21 <when value="preset" />
22 <when value="full">
23 <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" />
24 <param name="itemsPerSlot" size="4" type="integer" value="512" label="Data points bundled at lowest level" help="Default is 512 (itemsPerSlot)" />
25 <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/>
26 </when>
27 </conditional>
28 </inputs>
29 <outputs>
30 <data format="bigbed" name="out_file1" />
31 </outputs>
32 <tests>
33 <test>
34 <param name="input1" value="7.bed" dbkey="hg17" />
35 <param name="settingsType" value="full" />
36 <param name="blockSize" value="256" />
37 <param name="itemsPerSlot" value="512" />
38 <param name="unc" value="False" />
39 <output name="out_file1" file="7.bigbed"/>
40 </test>
41 <test>
42 <param name="input1" value="7.bed" dbkey="hg17" />
43 <param name="settingsType" value="preset" />
44 <output name="out_file1" file="7.bigbed"/>
45 </test>
46 </tests>
47 <help>
48
49This tool converts a **sorted** BED file into a bigBed file.
50
51Currently, the bedFields option to specify the number of non-standard fields is not supported as an AutoSQL file must be provided, which is a format
52currently not supported by Galaxy.
53
54</help>
55</tool>