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comparison SMART/galaxy/getDistribution.xml @ 15:440ceca58672

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author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
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14:c79b9ae3f65f 15:440ceca58672
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 on a genome.</description> 2 <description>Get Distribution: Get the distribution of the genomic coordinates along a genome.</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 ../Java/Python/GetDistribution.py -i $formatType.inputFileName 4 ../Java/Python/GetDistribution.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed': 5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed 6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff': 7 #elif $formatType.FormatInputFileName == 'gff':
56 -l $optionColor.colorValue 56 -l $optionColor.colorValue
57 #end if 57 #end if
58 58
59 $bothStrands 59 $bothStrands
60 $average 60 $average
61 -n $names
62 $normalize 61 $normalize
63 $csv $outputCSV 62 $csv $outputCSV
64 $gff $outputGFF 63 $gff $outputGFF
65 -m 64 -m
66 -o $outputFile 65 -o $outputFile
72 <param name="FormatInputFileName" type="select" label="Input File Format"> 71 <param name="FormatInputFileName" type="select" label="Input File Format">
73 <option value="bed">bed</option> 72 <option value="bed">bed</option>
74 <option value="gff">gff</option> 73 <option value="gff">gff</option>
75 <option value="gff2">gff2</option> 74 <option value="gff2">gff2</option>
76 <option value="gff3">gff3</option> 75 <option value="gff3">gff3</option>
77 <option value="csv">csv</option>
78 <option value="sam">sam</option> 76 <option value="sam">sam</option>
79 <option value="gtf">gtf</option> 77 <option value="gtf">gtf</option>
80 </param> 78 </param>
81 <when value="bed"> 79 <when value="bed">
82 <param name="inputFileName" format="bed" type="data" label="Input File"/> 80 <param name="inputFileName" format="bed" type="data" label="Input File"/>
88 <param name="inputFileName" format="gff2" type="data" label="Input File"/> 86 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
89 </when> 87 </when>
90 <when value="gff3"> 88 <when value="gff3">
91 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 89 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
92 </when> 90 </when>
93 <when value="csv">
94 <param name="inputFileName" format="csv" type="data" label="Input File"/>
95 </when>
96 <when value="sam"> 91 <when value="sam">
97 <param name="inputFileName" format="sam" type="data" label="Input File"/> 92 <param name="inputFileName" format="sam" type="data" label="Input File"/>
98 </when> 93 </when>
99 <when value="gtf"> 94 <when value="gtf">
100 <param name="inputFileName" format="gtf" type="data" label="Input File"/> 95 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
102 </conditional> 97 </conditional>
103 98
104 <param name="refFile" format="fasta" type="data" label="reference genome file"/> 99 <param name="refFile" format="fasta" type="data" label="reference genome file"/>
105 100
106 <conditional name="optionNbBin"> 101 <conditional name="optionNbBin">
107 <param name="Nb" type="select" label="number of bins"> 102 <param name="Nb" type="select" label="number of points">
108 <option value="Yes">Yes</option> 103 <option value="Yes">Yes</option>
109 <option value="No" selected="true">No</option> 104 <option value="No" selected="true">No</option>
110 </param> 105 </param>
111 <when value="Yes"> 106 <when value="Yes">
112 <param name="nbBins" type="integer" value="1000" /> 107 <param name="nbBins" type="integer" value="1000" />
113 </when> 108 </when>
114 <when value="No"> 109 <when value="No">
115 </when> 110 </when>
116 </conditional> 111 </conditional>
117 112
113 <conditional name="optionChrom">
114 <param name="chrom" type="select" label="if you wish to plot only one chromosome, mention the chromosome name">
115 <option value="Yes">Yes</option>
116 <option value="No" selected="true">No</option>
117 </param>
118 <when value="Yes">
119 <param name="chromValue" type="text" value="chromName" />
120 </when>
121 <when value="No">
122 </when>
123 </conditional>
124
118 <conditional name="optionStart"> 125 <conditional name="optionStart">
119 <param name="start" type="select" label="start from a given region"> 126 <param name="start" type="select" label="if you wish to plot only one locus, mention its start position">
120 <option value="Yes">Yes</option> 127 <option value="Yes">Yes</option>
121 <option value="No" selected="true">No</option> 128 <option value="No" selected="true">No</option>
122 </param> 129 </param>
123 <when value="Yes"> 130 <when value="Yes">
124 <param name="startValue" type="integer" value="0" /> 131 <param name="startValue" type="integer" value="0" />
126 <when value="No"> 133 <when value="No">
127 </when> 134 </when>
128 </conditional> 135 </conditional>
129 136
130 <conditional name="optionEnd"> 137 <conditional name="optionEnd">
131 <param name="end" type="select" label="end from a given region"> 138 <param name="end" type="select" label="if you wish to plot only one locus, mention its end position">
132 <option value="Yes">Yes</option> 139 <option value="Yes">Yes</option>
133 <option value="No" selected="true">No</option> 140 <option value="No" selected="true">No</option>
134 </param> 141 </param>
135 <when value="Yes"> 142 <when value="Yes">
136 <param name="endValue" type="integer" value="0" /> 143 <param name="endValue" type="integer" value="0" />
138 <when value="No"> 145 <when value="No">
139 </when> 146 </when>
140 </conditional> 147 </conditional>
141 148
142 <conditional name="optionHeight"> 149 <conditional name="optionHeight">
143 <param name="height" type="select" label="height of the graphics"> 150 <param name="height" type="select" label="height of the figure">
144 <option value="Yes">Yes</option> 151 <option value="Yes">Yes</option>
145 <option value="No" selected="true">No</option> 152 <option value="No" selected="true">No</option>
146 </param> 153 </param>
147 <when value="Yes"> 154 <when value="Yes">
148 <param name="heightValue" type="integer" value="300" /> 155 <param name="heightValue" type="integer" value="300" />
150 <when value="No"> 157 <when value="No">
151 </when> 158 </when>
152 </conditional> 159 </conditional>
153 160
154 <conditional name="optionWidth"> 161 <conditional name="optionWidth">
155 <param name="width" type="select" label="width of the graphics"> 162 <param name="width" type="select" label="width of the figure">
156 <option value="Yes">Yes</option> 163 <option value="Yes">Yes</option>
157 <option value="No" selected="true">No</option> 164 <option value="No" selected="true">No</option>
158 </param> 165 </param>
159 <when value="Yes"> 166 <when value="Yes">
160 <param name="widthValue" type="integer" value="1000" /> 167 <param name="widthValue" type="integer" value="1000" />
185 </when> 192 </when>
186 <when value="No"> 193 <when value="No">
187 </when> 194 </when>
188 </conditional> 195 </conditional>
189 196
190 <conditional name="optionChrom">
191 <param name="chrom" type="select" label="plot only one given chromosome">
192 <option value="Yes">Yes</option>
193 <option value="No" selected="true">No</option>
194 </param>
195 <when value="Yes">
196 <param name="chromValue" type="text" value="chromName" />
197 </when>
198 <when value="No">
199 </when>
200 </conditional>
201
202 <conditional name="optionColor"> 197 <conditional name="optionColor">
203 <param name="color" type="select" label="color of the lines (separated by commas and no space)"> 198 <param name="color" type="select" label="color of the lines (separated by commas and no space)">
204 <option value="Yes">Yes</option> 199 <option value="Yes">Yes</option>
205 <option value="No" selected="true">No</option> 200 <option value="No" selected="true">No</option>
206 </param> 201 </param>
209 </when> 204 </when>
210 <when value="No"> 205 <when value="No">
211 </when> 206 </when>
212 </conditional> 207 </conditional>
213 208
214
215 <param name="bothStrands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="plot one curve per strand"/> 209 <param name="bothStrands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="plot one curve per strand"/>
216 <param name="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot plot average (instead of sum)"/> 210 <param name="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot the number of element per bin (instead of sum)"/>
217 <param name="names" type="text" value="nbElements" label="name for the tags (separated by commas and no space)"/> 211
218 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panels are different)"/> 212 <conditional name="optionNames">
219 <param name="csv" type="boolean" truevalue="-x" falsevalue="" checked="false" label="write a .csv file."/> 213 <param name="names" type="select" label="name for the tags (separated by commas and no space)">
220 <param name="gff" type="boolean" truevalue="-g" falsevalue="" checked="false" label="write a .gff file."/> 214 <option value="Yes">Yes</option>
215 <option value="No" selected="true">No</option>
216 </param>
217 <when value="Yes">
218 <param name="namesValue" type="text" value="nbElements" />
219 </when>
220 <when value="No">
221 </when>
222 </conditional>
223
224 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panel sizes are different)"/>
221 </inputs> 225 </inputs>
222 226
223 <outputs> 227 <outputs>
224 <data name="outputFile" format="png" label="[getDistribution] out png file"/> 228 <data name="outputFile" format="png" label="[getDistribution] out png file"/>
225 <data name="outputCSV" format="csv" label="[getDistribution] output csv file">
226 <filter>csv</filter>
227 </data>
228
229 <data name="outputGFF" format="gff" label="[getDistribution] output gff file">
230 <filter>gff</filter>
231 </data>
232 </outputs> 229 </outputs>
233 230
234 <help> 231 <help>
235 This script gives a .tar out file, if you want to take look at the results, you have to download it. 232 This script gives a .tar out file, if you want to take look at the results, you have to download it.
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
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).
237
238 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> 239 </help>
237 </tool> 240 </tool>