Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getDistribution.xml @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | 440ceca58672 |
children | 0ab839023fe4 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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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> |