Mercurial > repos > vipints > fml_wig2bed

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author vipints
date Tue, 07 Jun 2011 18:08:31 -0400
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45f3fa82369f Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="fml_wig2bed" name="Wig_to_bedGraph" version="1.0.0">
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2 <description>converter</description>
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3 <command interpreter="perl">wig2bedGraph_converter.pl $inf_wig > $bed_format
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4 </command>
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5 <inputs>
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6 <param format="wig" name="inf_wig" type="data" label="Convert this file" help="Data in fixedStep or variableStep wiggle format."/>
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7 </inputs>
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8 <outputs>
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9 <data format="bed" name="bed_format" />
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10 </outputs>
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11 <tests>
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12 <test>
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13 <param name="inf_wig" value="hg17_chrY_pos.wig" />
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14 <output name="bed_format" file="hg17_chrY_pos.bed" />
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15 </test>
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16 </tests>
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17 <help>
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18
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19 **What it does**
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20
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21 This tool converts data in wiggle fixedStep_ or variableStep_ format to four column bedGraph_ format.
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22
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23 .. _fixedStep: http://genome.ucsc.edu/goldenPath/help/wiggle.html
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24 .. _variableStep: http://genome.ucsc.edu/goldenPath/help/wiggle.html
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25 .. _bedGraph: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
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26
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27 --------
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28
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29 **Example**
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30
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31 - The following data in wiggle fixedStep format::
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32
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33 track type=wiggle_0 name="ARTS+ chrY" description="ARTS - TSS Finder - chrY - positive strand" visibility=full autoScale=on color=0,200,100 maxHeightPixels=300:150:50 graphType=bar yLineMark=0 yLineOnOff=on smoothingWindow=2
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34 fixedStep chrom=chrY start=1151 step=50
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35 -1.17966
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36 -0.56397
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37 -0.79706
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38 -0.99435
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39 -1.11338
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40 -1.23153
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41
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42 - Will be converted to bedGraph format::
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43
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44 chrY 1150 1151 -1.17966
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45 chrY 1200 1201 -0.56397
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46 chrY 1250 1251 -0.79706
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47 chrY 1300 1301 -0.99435
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48 chrY 1350 1351 -1.11338
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49 chrY 1400 1401 -1.23153
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50
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51 --------
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52
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53 **About formats**
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54
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55 **Wiggle (variableStep)** The data is introduced by a line beginning with the keyword "variableStep", and the arguments "chrom" and "span", which indicate the chromosome on which the features are located, and the width of each feature, in base pairs. This is followed by a series of two-element lines indicating the start position of each feature, and its quantitative value. Values can be any sort of numeric data, including integers, negative numbers and floating point.
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56
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57 **Wiggle (fixedStep)** The data is introduced by a line beginning with the keyword "fixedStep", and the arguments "chrom", "span", "start" and "step". The first two arguments are the same as wiggle variableStep, while "start" and "step" indicate the starting position of the first feature, and the spacing between each feature. This is followed by a numeric value for each step.
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58
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59 **bedGraph** There are four required fields: ref_sequence,start,end and score. Note that here the coordinates are "zero-indexed", half open, which means the start coordinate is zero-indexed and the end coordinate is 1-indexed.
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61 --------
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62
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63 This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010-2011 Max Planck Society
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64 </help>
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65 </tool>