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/tools/filters/bed_to_bigbed.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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&gt;&amp;1 || echo "Error running bedToBigBed." >&amp;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>