Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/plotCoverage.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="plotCoverage" name="plot coverage"> | 1 <tool id="plotCoverage" name="plot coverage"> |
2 <description>Plot the coverage of the first data with respect to the second one.</description> | 2 <description>Plot the coverage of the first data with respect to the second one.</description> |
3 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
3 <command interpreter="python"> | 6 <command interpreter="python"> |
4 ../Java/Python/WrappPlotCoverage.py -i $formatType.inputFileName1 | 7 ../Java/Python/WrappPlotCoverage.py -i $formatType.inputFileName1 |
5 #if $formatType.FormatInputFileName1 == 'bed': | 8 #if $formatType.FormatInputFileName1 == 'bed': |
6 -f bed | 9 -f bed |
7 #elif $formatType.FormatInputFileName1 == 'gff': | 10 #elif $formatType.FormatInputFileName1 == 'gff': |
104 <param name="FormatInputFileName2" type="select" label="Input File Format 2"> | 107 <param name="FormatInputFileName2" type="select" label="Input File Format 2"> |
105 <option value="bed">bed</option> | 108 <option value="bed">bed</option> |
106 <option value="gff">gff</option> | 109 <option value="gff">gff</option> |
107 <option value="gff2">gff2</option> | 110 <option value="gff2">gff2</option> |
108 <option value="gff3">gff3</option> | 111 <option value="gff3">gff3</option> |
109 <option value="gff2">sam</option> | 112 <option value="sam">sam</option> |
110 <option value="gff3">gtf</option> | 113 <option value="gtf">gtf</option> |
111 </param> | 114 </param> |
112 <when value="bed"> | 115 <when value="bed"> |
113 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/> | 116 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/> |
114 </when> | 117 </when> |
115 <when value="gff"> | 118 <when value="gff"> |
254 | 257 |
255 <param name="merge" type="boolean" truevalue="-1" falsevalue="" checked="false" label="merge the 2 plots in 1"/> | 258 <param name="merge" type="boolean" truevalue="-1" falsevalue="" checked="false" label="merge the 2 plots in 1"/> |
256 </inputs> | 259 </inputs> |
257 | 260 |
258 <outputs> | 261 <outputs> |
259 <data name="outputFile" format="tar" label="[plotCoverage] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/> | 262 <data name="outputFile" format="tar" label="[plot coverage] tar output file" help="You can not see the results directly from galaxy, but you can download this tar output file."/> |
260 </outputs> | 263 </outputs> |
261 | 264 |
262 <help> | 265 <help> |
263 Plot the coverage of the first set of genomic coordinates with respect to the second set of genomic coordinates. For each element of the second set (we will suppose that they are annotated genes), it computes the number of elements of the first set (reads, for instance) which overlap it. | 266 Plot the coverage of the first set of genomic coordinates with respect to the second set of genomic coordinates. For each element of the second set (we will suppose that they are annotated genes), it computes the number of elements of the first set (reads, for instance) which overlap it. |
264 | 267 |
265 Alternatively, if the first file is in GFF format, and contains the **Target** file, you can omit the second file. However, a fasta file corresponding to the second file should be given (to compute the size of the reference elements). | 268 Alternatively, if the first file is in GFF format, and contains the **Target** file, you can omit the second file. However, a fasta file corresponding to the second file should be given (to compute the size of the reference elements). |
266 | 269 |
267 The tool produces two plots per gene. The first plot gives the coverage: a point (*x*, *y*) $ means that *y* reads cover the *x*th nucleotide of the gene. The second figure displays the (possibly spliced) gene in black, and the overlapping reads (blue is colinear, red is anti-sense). | 270 The tool produces two plots per gene. The first plot gives the coverage: a point (*x*, *y*) means that *y* reads cover the *x* th nucleotide of the gene. The second figure displays the (possibly spliced) gene in black, and the overlapping reads (blue is colinear, red is anti-sense). |
268 | 271 |
269 This script gives a .tar out file, if you want to take look at the results, you have to download it. | 272 This script gives a .tar out file, if you want to take look at the results, you have to download it. |
270 </help> | 273 </help> |
271 </tool> | 274 </tool> |