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comparison SMART/galaxy/getDistribution.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
parents 44d5973c188c
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37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="getDistribution" name="get distribution">
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>
6 <command interpreter="python">
7 ../Java/Python/GetDistribution.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'bed':
9 -f bed
10 #elif $formatType.FormatInputFileName == 'gff':
11 -f gff
12 #elif $formatType.FormatInputFileName == 'gff2':
13 -f gff2
14 #elif $formatType.FormatInputFileName == 'gff3':
15 -f gff3
16 #elif $formatType.FormatInputFileName == 'sam':
17 -f sam
18 #elif $formatType.FormatInputFileName == 'gtf':
19 -f gtf
20 #end if
21
22 -r $refFile
23
24 #if $optionNbBin.Nb == 'Yes':
25 -b $optionNbBin.nbBins
26 #end if
27
28 #if $optionStart.start == 'Yes':
29 -s $optionStart.startValue
30 #end if
31
32 #if $optionEnd.end == 'Yes':
33 -e $optionEnd.endValue
34 #end if
35
36 #if $optionHeight.height == 'Yes':
37 -H $optionHeight.heightValue
38 #end if
39
40 #if $optionWidth.width == 'Yes':
41 -W $optionWidth.widthValue
42 #end if
43
44 #if $optionYMin.YMin == 'Yes':
45 -y $optionYMin.YMinValue
46 #end if
47
48 #if $optionYMax.YMax == 'Yes':
49 -Y $optionYMax.YMaxValue
50 #end if
51
52 #if $optionChrom.chrom == 'Yes':
53 -c $optionChrom.chromValue
54 #end if
55
56 #if $optionColor.color == 'Yes':
57 -l $optionColor.colorValue
58 #end if
59
60 $bothStrands
61 $average
62 $normalize
63 -m
64 -o $outputFile
65
66 </command>
67
68 <inputs>
69 <conditional name="formatType">
70 <param name="FormatInputFileName" type="select" label="Input File Format">
71 <option value="bed">bed</option>
72 <option value="gff">gff</option>
73 <option value="gff2">gff2</option>
74 <option value="gff3">gff3</option>
75 <option value="sam">sam</option>
76 <option value="gtf">gtf</option>
77 </param>
78 <when value="bed">
79 <param name="inputFileName" format="bed" type="data" label="Input File"/>
80 </when>
81 <when value="gff">
82 <param name="inputFileName" format="gff" type="data" label="Input File"/>
83 </when>
84 <when value="gff2">
85 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
86 </when>
87 <when value="gff3">
88 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
89 </when>
90 <when value="sam">
91 <param name="inputFileName" format="sam" type="data" label="Input File"/>
92 </when>
93 <when value="gtf">
94 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
95 </when>
96 </conditional>
97
98 <param name="refFile" format="fasta" type="data" label="reference genome file"/>
99
100 <conditional name="optionNbBin">
101 <param name="Nb" type="select" label="number of points">
102 <option value="Yes">Yes</option>
103 <option value="No" selected="true">No</option>
104 </param>
105 <when value="Yes">
106 <param name="nbBins" type="integer" value="1000" />
107 </when>
108 <when value="No">
109 </when>
110 </conditional>
111
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">
125 <param name="start" type="select" label="if you wish to plot only one locus, mention its start position">
126 <option value="Yes">Yes</option>
127 <option value="No" selected="true">No</option>
128 </param>
129 <when value="Yes">
130 <param name="startValue" type="integer" value="0" />
131 </when>
132 <when value="No">
133 </when>
134 </conditional>
135
136 <conditional name="optionEnd">
137 <param name="end" type="select" label="if you wish to plot only one locus, mention its end position">
138 <option value="Yes">Yes</option>
139 <option value="No" selected="true">No</option>
140 </param>
141 <when value="Yes">
142 <param name="endValue" type="integer" value="0" />
143 </when>
144 <when value="No">
145 </when>
146 </conditional>
147
148 <conditional name="optionHeight">
149 <param name="height" type="select" label="height of the figure">
150 <option value="Yes">Yes</option>
151 <option value="No" selected="true">No</option>
152 </param>
153 <when value="Yes">
154 <param name="heightValue" type="integer" value="300" />
155 </when>
156 <when value="No">
157 </when>
158 </conditional>
159
160 <conditional name="optionWidth">
161 <param name="width" type="select" label="width of the figure">
162 <option value="Yes">Yes</option>
163 <option value="No" selected="true">No</option>
164 </param>
165 <when value="Yes">
166 <param name="widthValue" type="integer" value="1000" />
167 </when>
168 <when value="No">
169 </when>
170 </conditional>
171
172 <conditional name="optionYMin">
173 <param name="YMin" type="select" label="minimum value on the y-axis to plot">
174 <option value="Yes">Yes</option>
175 <option value="No" selected="true">No</option>
176 </param>
177 <when value="Yes">
178 <param name="YMinValue" type="integer" value="1000" />
179 </when>
180 <when value="No">
181 </when>
182 </conditional>
183
184 <conditional name="optionYMax">
185 <param name="YMax" type="select" label="maximum value on the y-axis to plot">
186 <option value="Yes">Yes</option>
187 <option value="No" selected="true">No</option>
188 </param>
189 <when value="Yes">
190 <param name="YMaxValue" type="integer" value="1000" />
191 </when>
192 <when value="No">
193 </when>
194 </conditional>
195
196 <conditional name="optionColor">
197 <param name="color" type="select" label="color of the lines (separated by commas and no space)">
198 <option value="Yes">Yes</option>
199 <option value="No" selected="true">No</option>
200 </param>
201 <when value="Yes">
202 <param name="colorValue" type="text" value="red,blue" />
203 </when>
204 <when value="No">
205 </when>
206 </conditional>
207
208 <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)"/>
210
211 <conditional name="optionNames">
212 <param name="names" type="select" label="name for the tags (separated by commas and no space)">
213 <option value="Yes">Yes</option>
214 <option value="No" selected="true">No</option>
215 </param>
216 <when value="Yes">
217 <param name="namesValue" type="text" value="nbElements" />
218 </when>
219 <when value="No">
220 </when>
221 </conditional>
222
223 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panel sizes are different)"/>
224 </inputs>
225
226 <outputs>
227 <data name="outputFile" format="png" label="[get distribution] output PNG file"/>
228 </outputs>
229
230 <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.
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>
237 </tool>