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comparison SMART/galaxy/getDistribution.xml @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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children 440ceca58672
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5:ea3082881bf8 6:769e306b7933
1 <tool id="getDistribution" name="get distribution">
2 <description>Get Distribution: Get the distribution of the genomic coordinates on a genome.</description>
3 <command interpreter="python">
4 ../Java/Python/GetDistribution.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName == 'gff3':
12 -f gff3
13 #elif $formatType.FormatInputFileName == 'csv':
14 -f csv
15 #elif $formatType.FormatInputFileName == 'sam':
16 -f sam
17 #elif $formatType.FormatInputFileName == 'gtf':
18 -f gtf
19 #end if
20
21 -r $refFile
22
23 #if $optionNbBin.Nb == 'Yes':
24 -b $optionNbBin.nbBins
25 #end if
26
27 #if $optionStart.start == 'Yes':
28 -s $optionStart.startValue
29 #end if
30
31 #if $optionEnd.end == 'Yes':
32 -e $optionEnd.endValue
33 #end if
34
35 #if $optionHeight.height == 'Yes':
36 -H $optionHeight.heightValue
37 #end if
38
39 #if $optionWidth.width == 'Yes':
40 -W $optionWidth.widthValue
41 #end if
42
43 #if $optionYMin.YMin == 'Yes':
44 -y $optionYMin.YMinValue
45 #end if
46
47 #if $optionYMax.YMax == 'Yes':
48 -Y $optionYMax.YMaxValue
49 #end if
50
51 #if $optionChrom.chrom == 'Yes':
52 -c $optionChrom.chromValue
53 #end if
54
55 #if $optionColor.color == 'Yes':
56 -l $optionColor.colorValue
57 #end if
58
59 $bothStrands
60 $average
61 -n $names
62 $normalize
63 $csv $outputCSV
64 $gff $outputGFF
65 -m
66 -o $outputFile
67
68 </command>
69
70 <inputs>
71 <conditional name="formatType">
72 <param name="FormatInputFileName" type="select" label="Input File Format">
73 <option value="bed">bed</option>
74 <option value="gff">gff</option>
75 <option value="gff2">gff2</option>
76 <option value="gff3">gff3</option>
77 <option value="csv">csv</option>
78 <option value="sam">sam</option>
79 <option value="gtf">gtf</option>
80 </param>
81 <when value="bed">
82 <param name="inputFileName" format="bed" type="data" label="Input File"/>
83 </when>
84 <when value="gff">
85 <param name="inputFileName" format="gff" type="data" label="Input File"/>
86 </when>
87 <when value="gff2">
88 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
89 </when>
90 <when value="gff3">
91 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
92 </when>
93 <when value="csv">
94 <param name="inputFileName" format="csv" type="data" label="Input File"/>
95 </when>
96 <when value="sam">
97 <param name="inputFileName" format="sam" type="data" label="Input File"/>
98 </when>
99 <when value="gtf">
100 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
101 </when>
102 </conditional>
103
104 <param name="refFile" format="fasta" type="data" label="reference genome file"/>
105
106 <conditional name="optionNbBin">
107 <param name="Nb" type="select" label="number of bins">
108 <option value="Yes">Yes</option>
109 <option value="No" selected="true">No</option>
110 </param>
111 <when value="Yes">
112 <param name="nbBins" type="integer" value="1000" />
113 </when>
114 <when value="No">
115 </when>
116 </conditional>
117
118 <conditional name="optionStart">
119 <param name="start" type="select" label="start from a given region">
120 <option value="Yes">Yes</option>
121 <option value="No" selected="true">No</option>
122 </param>
123 <when value="Yes">
124 <param name="startValue" type="integer" value="0" />
125 </when>
126 <when value="No">
127 </when>
128 </conditional>
129
130 <conditional name="optionEnd">
131 <param name="end" type="select" label="end from a given region">
132 <option value="Yes">Yes</option>
133 <option value="No" selected="true">No</option>
134 </param>
135 <when value="Yes">
136 <param name="endValue" type="integer" value="0" />
137 </when>
138 <when value="No">
139 </when>
140 </conditional>
141
142 <conditional name="optionHeight">
143 <param name="height" type="select" label="height of the graphics">
144 <option value="Yes">Yes</option>
145 <option value="No" selected="true">No</option>
146 </param>
147 <when value="Yes">
148 <param name="heightValue" type="integer" value="300" />
149 </when>
150 <when value="No">
151 </when>
152 </conditional>
153
154 <conditional name="optionWidth">
155 <param name="width" type="select" label="width of the graphics">
156 <option value="Yes">Yes</option>
157 <option value="No" selected="true">No</option>
158 </param>
159 <when value="Yes">
160 <param name="widthValue" type="integer" value="1000" />
161 </when>
162 <when value="No">
163 </when>
164 </conditional>
165
166 <conditional name="optionYMin">
167 <param name="YMin" type="select" label="minimum value on the y-axis to plot">
168 <option value="Yes">Yes</option>
169 <option value="No" selected="true">No</option>
170 </param>
171 <when value="Yes">
172 <param name="YMinValue" type="integer" value="1000" />
173 </when>
174 <when value="No">
175 </when>
176 </conditional>
177
178 <conditional name="optionYMax">
179 <param name="YMax" type="select" label="maximum value on the y-axis to plot">
180 <option value="Yes">Yes</option>
181 <option value="No" selected="true">No</option>
182 </param>
183 <when value="Yes">
184 <param name="YMaxValue" type="integer" value="1000" />
185 </when>
186 <when value="No">
187 </when>
188 </conditional>
189
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">
203 <param name="color" type="select" label="color of the lines (separated by commas and no space)">
204 <option value="Yes">Yes</option>
205 <option value="No" selected="true">No</option>
206 </param>
207 <when value="Yes">
208 <param name="colorValue" type="text" value="red,blue" />
209 </when>
210 <when value="No">
211 </when>
212 </conditional>
213
214
215 <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)"/>
217 <param name="names" type="text" value="nbElements" label="name for the tags (separated by commas and no space)"/>
218 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panels are different)"/>
219 <param name="csv" type="boolean" truevalue="-x" falsevalue="" checked="false" label="write a .csv file."/>
220 <param name="gff" type="boolean" truevalue="-g" falsevalue="" checked="false" label="write a .gff file."/>
221 </inputs>
222
223 <outputs>
224 <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>
233
234 <help>
235 This script gives a .tar out file, if you want to take look at the results, you have to download it.
236 </help>
237 </tool>