root/galaxy-central/tools/filters/wig_to_bigwig.xml

リビジョン 2, 2.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="wig_to_bigWig" name="Wig to bigWig" version="1.0.0">
2  <description>converter</description>
3  <command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 -blockSize=$blockSize -itemsPerSlot=$itemsPerSlot $clip $unc 2&gt;&amp;1 || echo "Error running wigToBigWig." >&amp;2</command>
4  <requirements>
5    <requirement type="package">ucsc_tools</requirement>
6  </requirements>
7  <inputs>
8    <param format="wig" name="input1" type="data" label="Convert">
9      <validator type="unspecified_build" />
10    </param>
11    <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" />
12    <param name="itemsPerSlot" size="4" type="integer" value="1024" label="Data points bundled at lowest level" help="Default is 1024 (itemsPerSlot)" />
13    <param name="clip" type="boolean" truevalue="-clip" falsevalue="" checked="False" label="Clip chromosome positions" help="Issue warning messages rather than dying if wig file contains items off end of chromosome. (clip)"/>
14    <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/>
15  </inputs>
16  <outputs>
17    <data format="bigwig" name="out_file1" />
18  </outputs>
19  <tests>
20    <test>
21      <param name="input1" value="2.wig" dbkey="hg17" />
22      <param name="blockSize" value="256" />
23      <param name="itemsPerSlot" value="1024" />
24      <param name="clip" value="False" />
25      <param name="unc" value="False" />
26      <output name="out_file1" file="2.bigwig"/>
27    </test>
28  </tests>
29  <help>
30**Syntax**
31
32This tool converts wiggle data into bigWig type.
33
34- **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line.  Following the track definition line is the track data, which can be entered in three different formats described below.
35
36  - **BED format** with no declaration line and four columns of data::
37
38      chromA  chromStartA  chromEndA  dataValueA
39      chromB  chromStartB  chromEndB  dataValueB
40
41  - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::
42
43      variableStep  chrom=chrN  [span=windowSize]
44      chromStartA  dataValueA
45      chromStartB  dataValueB
46
47  - **fixedStep** single column data; started by a declaration line and followed with data values::
48
49      fixedStep  chrom=chrN  start=position  step=stepInterval  [span=windowSize]
50      dataValue1
51      dataValue2
52
53</help>
54</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。