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comparison SMART/galaxy/getDistribution.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
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>