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comparison SMART/galaxy/getDistribution.xml @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
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17:b0e8584489e6 18:94ab73e8a190
1 <tool id="getDistribution" name="get distribution"> 1 <tool id="getDistribution" name="get distribution">
2 <description>Get Distribution: Get the distribution of the genomic coordinates along a genome.</description> 2 <description>Get Distribution: Get the distribution of the genomic coordinates along a genome.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
3 <command interpreter="python"> 6 <command interpreter="python">
4 ../Java/Python/GetDistribution.py -i $formatType.inputFileName 7 ../Java/Python/GetDistribution.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed': 8 #if $formatType.FormatInputFileName == 'bed':
6 -f bed 9 -f bed
7 #elif $formatType.FormatInputFileName == 'gff': 10 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff 11 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2': 12 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2 13 -f gff2
11 #elif $formatType.FormatInputFileName == 'gff3': 14 #elif $formatType.FormatInputFileName == 'gff3':
12 -f gff3 15 -f gff3
13 #elif $formatType.FormatInputFileName == 'csv':
14 -f csv
15 #elif $formatType.FormatInputFileName == 'sam': 16 #elif $formatType.FormatInputFileName == 'sam':
16 -f sam 17 -f sam
17 #elif $formatType.FormatInputFileName == 'gtf': 18 #elif $formatType.FormatInputFileName == 'gtf':
18 -f gtf 19 -f gtf
19 #end if 20 #end if
57 #end if 58 #end if
58 59
59 $bothStrands 60 $bothStrands
60 $average 61 $average
61 $normalize 62 $normalize
62 $csv $outputCSV
63 $gff $outputGFF
64 -m 63 -m
65 -o $outputFile 64 -o $outputFile
66 65
67 </command> 66 </command>
68 67
223 222
224 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panel sizes are different)"/> 223 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panel sizes are different)"/>
225 </inputs> 224 </inputs>
226 225
227 <outputs> 226 <outputs>
228 <data name="outputFile" format="png" label="[getDistribution] out png file"/> 227 <data name="outputFile" format="png" label="[get distribution] output PNG file"/>
229 </outputs> 228 </outputs>
230 229
231 <help> 230 <help>
232 This script gives a .tar out file, if you want to take look at the results, you have to download it. 231 Print a density profile of the data for each chromosome. You have to provide the reference genome, to know the sizes of the chromosomes. You can also provide the number of points (called *bins*) you want per chromosome.
233
234 Print a density profile of the data for each chromosome, see Figure~\ref{fig:getDistribution}. You have to provide the reference genome, to know the sizes of the chromosomes. You can also provide the number of points (called *bins*) you want per chromosome.
235 232
236 By default, only one curve is plotted per chromosome, but you can plot one curve per strand and per chromosome (the minus strand will be plotted with non-positive values on the *y*-axis). 233 By default, only one curve is plotted per chromosome, but you can plot one curve per strand and per chromosome (the minus strand will be plotted with non-positive values on the *y*-axis).
237 234
238 If you want, you can also plot a specific region, by mentionning the chromosome, the start and the end positions of the region. 235 If you want, you can also plot a specific region, by mentionning the chromosome, the start and the end positions of the region.
239 </help> 236 </help>