Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getDistribution.xml @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
children |
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30:5677346472b5 | 31:0ab839023fe4 |
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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 on a genome.</description> |
3 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | 3 <command interpreter="python"> |
7 ../Java/Python/GetDistribution.py -i $formatType.inputFileName | 4 ../Java/Python/GetDistribution.py -i $formatType.inputFileName |
8 #if $formatType.FormatInputFileName == 'bed': | 5 #if $formatType.FormatInputFileName == 'bed': |
9 -f bed | 6 -f bed |
10 #elif $formatType.FormatInputFileName == 'gff': | 7 #elif $formatType.FormatInputFileName == 'gff': |
11 -f gff | 8 -f gff |
12 #elif $formatType.FormatInputFileName == 'gff2': | 9 #elif $formatType.FormatInputFileName == 'gff2': |
13 -f gff2 | 10 -f gff2 |
14 #elif $formatType.FormatInputFileName == 'gff3': | 11 #elif $formatType.FormatInputFileName == 'gff3': |
15 -f gff3 | 12 -f gff3 |
13 #elif $formatType.FormatInputFileName == 'csv': | |
14 -f csv | |
16 #elif $formatType.FormatInputFileName == 'sam': | 15 #elif $formatType.FormatInputFileName == 'sam': |
17 -f sam | 16 -f sam |
18 #elif $formatType.FormatInputFileName == 'gtf': | 17 #elif $formatType.FormatInputFileName == 'gtf': |
19 -f gtf | 18 -f gtf |
20 #end if | 19 #end if |
58 #end if | 57 #end if |
59 | 58 |
60 $bothStrands | 59 $bothStrands |
61 $average | 60 $average |
62 $normalize | 61 $normalize |
62 $csv $outputCSV | |
63 $gff $outputGFF | |
63 -m | 64 -m |
64 -o $outputFile | 65 -o $outputFile |
65 | 66 |
66 </command> | 67 </command> |
67 | 68 |
70 <param name="FormatInputFileName" type="select" label="Input File Format"> | 71 <param name="FormatInputFileName" type="select" label="Input File Format"> |
71 <option value="bed">bed</option> | 72 <option value="bed">bed</option> |
72 <option value="gff">gff</option> | 73 <option value="gff">gff</option> |
73 <option value="gff2">gff2</option> | 74 <option value="gff2">gff2</option> |
74 <option value="gff3">gff3</option> | 75 <option value="gff3">gff3</option> |
76 <option value="csv">csv</option> | |
75 <option value="sam">sam</option> | 77 <option value="sam">sam</option> |
76 <option value="gtf">gtf</option> | 78 <option value="gtf">gtf</option> |
77 </param> | 79 </param> |
78 <when value="bed"> | 80 <when value="bed"> |
79 <param name="inputFileName" format="bed" type="data" label="Input File"/> | 81 <param name="inputFileName" format="bed" type="data" label="Input File"/> |
85 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | 87 <param name="inputFileName" format="gff2" type="data" label="Input File"/> |
86 </when> | 88 </when> |
87 <when value="gff3"> | 89 <when value="gff3"> |
88 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | 90 <param name="inputFileName" format="gff3" type="data" label="Input File"/> |
89 </when> | 91 </when> |
92 <when value="csv"> | |
93 <param name="inputFileName" format="csv" type="data" label="Input File"/> | |
94 </when> | |
90 <when value="sam"> | 95 <when value="sam"> |
91 <param name="inputFileName" format="sam" type="data" label="Input File"/> | 96 <param name="inputFileName" format="sam" type="data" label="Input File"/> |
92 </when> | 97 </when> |
93 <when value="gtf"> | 98 <when value="gtf"> |
94 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | 99 <param name="inputFileName" format="gtf" type="data" label="Input File"/> |
96 </conditional> | 101 </conditional> |
97 | 102 |
98 <param name="refFile" format="fasta" type="data" label="reference genome file"/> | 103 <param name="refFile" format="fasta" type="data" label="reference genome file"/> |
99 | 104 |
100 <conditional name="optionNbBin"> | 105 <conditional name="optionNbBin"> |
101 <param name="Nb" type="select" label="number of points"> | 106 <param name="Nb" type="select" label="number of bins"> |
102 <option value="Yes">Yes</option> | 107 <option value="Yes">Yes</option> |
103 <option value="No" selected="true">No</option> | 108 <option value="No" selected="true">No</option> |
104 </param> | 109 </param> |
105 <when value="Yes"> | 110 <when value="Yes"> |
106 <param name="nbBins" type="integer" value="1000" /> | 111 <param name="nbBins" type="integer" value="1000" /> |
107 </when> | 112 </when> |
108 <when value="No"> | 113 <when value="No"> |
109 </when> | 114 </when> |
110 </conditional> | 115 </conditional> |
111 | 116 |
112 <conditional name="optionChrom"> | |
113 <param name="chrom" type="select" label="if you wish to plot only one chromosome, mention the chromosome name"> | |
114 <option value="Yes">Yes</option> | |
115 <option value="No" selected="true">No</option> | |
116 </param> | |
117 <when value="Yes"> | |
118 <param name="chromValue" type="text" value="chromName" /> | |
119 </when> | |
120 <when value="No"> | |
121 </when> | |
122 </conditional> | |
123 | |
124 <conditional name="optionStart"> | 117 <conditional name="optionStart"> |
125 <param name="start" type="select" label="if you wish to plot only one locus, mention its start position"> | 118 <param name="start" type="select" label="start from a given region"> |
126 <option value="Yes">Yes</option> | 119 <option value="Yes">Yes</option> |
127 <option value="No" selected="true">No</option> | 120 <option value="No" selected="true">No</option> |
128 </param> | 121 </param> |
129 <when value="Yes"> | 122 <when value="Yes"> |
130 <param name="startValue" type="integer" value="0" /> | 123 <param name="startValue" type="integer" value="0" /> |
132 <when value="No"> | 125 <when value="No"> |
133 </when> | 126 </when> |
134 </conditional> | 127 </conditional> |
135 | 128 |
136 <conditional name="optionEnd"> | 129 <conditional name="optionEnd"> |
137 <param name="end" type="select" label="if you wish to plot only one locus, mention its end position"> | 130 <param name="end" type="select" label="end from a given region"> |
138 <option value="Yes">Yes</option> | 131 <option value="Yes">Yes</option> |
139 <option value="No" selected="true">No</option> | 132 <option value="No" selected="true">No</option> |
140 </param> | 133 </param> |
141 <when value="Yes"> | 134 <when value="Yes"> |
142 <param name="endValue" type="integer" value="0" /> | 135 <param name="endValue" type="integer" value="0" /> |
144 <when value="No"> | 137 <when value="No"> |
145 </when> | 138 </when> |
146 </conditional> | 139 </conditional> |
147 | 140 |
148 <conditional name="optionHeight"> | 141 <conditional name="optionHeight"> |
149 <param name="height" type="select" label="height of the figure"> | 142 <param name="height" type="select" label="height of the graphics"> |
150 <option value="Yes">Yes</option> | 143 <option value="Yes">Yes</option> |
151 <option value="No" selected="true">No</option> | 144 <option value="No" selected="true">No</option> |
152 </param> | 145 </param> |
153 <when value="Yes"> | 146 <when value="Yes"> |
154 <param name="heightValue" type="integer" value="300" /> | 147 <param name="heightValue" type="integer" value="300" /> |
156 <when value="No"> | 149 <when value="No"> |
157 </when> | 150 </when> |
158 </conditional> | 151 </conditional> |
159 | 152 |
160 <conditional name="optionWidth"> | 153 <conditional name="optionWidth"> |
161 <param name="width" type="select" label="width of the figure"> | 154 <param name="width" type="select" label="width of the graphics"> |
162 <option value="Yes">Yes</option> | 155 <option value="Yes">Yes</option> |
163 <option value="No" selected="true">No</option> | 156 <option value="No" selected="true">No</option> |
164 </param> | 157 </param> |
165 <when value="Yes"> | 158 <when value="Yes"> |
166 <param name="widthValue" type="integer" value="1000" /> | 159 <param name="widthValue" type="integer" value="1000" /> |
191 </when> | 184 </when> |
192 <when value="No"> | 185 <when value="No"> |
193 </when> | 186 </when> |
194 </conditional> | 187 </conditional> |
195 | 188 |
189 <conditional name="optionChrom"> | |
190 <param name="chrom" type="select" label="plot only one given chromosome"> | |
191 <option value="Yes">Yes</option> | |
192 <option value="No" selected="true">No</option> | |
193 </param> | |
194 <when value="Yes"> | |
195 <param name="chromValue" type="text" value="chromName" /> | |
196 </when> | |
197 <when value="No"> | |
198 </when> | |
199 </conditional> | |
200 | |
196 <conditional name="optionColor"> | 201 <conditional name="optionColor"> |
197 <param name="color" type="select" label="color of the lines (separated by commas and no space)"> | 202 <param name="color" type="select" label="color of the lines (separated by commas and no space)"> |
198 <option value="Yes">Yes</option> | 203 <option value="Yes">Yes</option> |
199 <option value="No" selected="true">No</option> | 204 <option value="No" selected="true">No</option> |
200 </param> | 205 </param> |
203 </when> | 208 </when> |
204 <when value="No"> | 209 <when value="No"> |
205 </when> | 210 </when> |
206 </conditional> | 211 </conditional> |
207 | 212 |
213 | |
208 <param name="bothStrands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="plot one curve per strand"/> | 214 <param name="bothStrands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="plot one curve per strand"/> |
209 <param name="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot the number of element per bin (instead of sum)"/> | 215 <param name="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot plot average (instead of sum)"/> |
210 | 216 |
211 <conditional name="optionNames"> | 217 <conditional name="optionNames"> |
212 <param name="names" type="select" label="name for the tags (separated by commas and no space)"> | 218 <param name="names" type="select" label="name for the tags (separated by commas and no space)"> |
213 <option value="Yes">Yes</option> | 219 <option value="Yes">Yes</option> |
214 <option value="No" selected="true">No</option> | 220 <option value="No" selected="true">No</option> |
218 </when> | 224 </when> |
219 <when value="No"> | 225 <when value="No"> |
220 </when> | 226 </when> |
221 </conditional> | 227 </conditional> |
222 | 228 |
223 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panel sizes are different)"/> | 229 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panels are different)"/> |
230 <param name="csv" type="boolean" truevalue="-x" falsevalue="" checked="false" label="write a .csv file."/> | |
231 <param name="gff" type="boolean" truevalue="-g" falsevalue="" checked="false" label="write a .gff file."/> | |
224 </inputs> | 232 </inputs> |
225 | 233 |
226 <outputs> | 234 <outputs> |
227 <data name="outputFile" format="png" label="[get distribution] output PNG file"/> | 235 <data name="outputFile" format="png" label="[getDistribution] out png file"/> |
236 <data name="outputCSV" format="csv" label="[getDistribution] output csv file"> | |
237 <filter>csv</filter> | |
238 </data> | |
239 | |
240 <data name="outputGFF" format="gff" label="[getDistribution] output gff file"> | |
241 <filter>gff</filter> | |
242 </data> | |
228 </outputs> | 243 </outputs> |
229 | 244 |
230 <help> | 245 <help> |
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. | 246 This script gives a .tar out file, if you want to take look at the results, you have to download it. |
232 | |
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). | |
234 | |
235 If you want, you can also plot a specific region, by mentionning the chromosome, the start and the end positions of the region. | |
236 </help> | 247 </help> |
237 </tool> | 248 </tool> |