|
6
|
1 <tool id="GetDifferentialExpression" name="get differential expression">
|
|
|
2 <description>Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file.</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 ../Java/Python/GetDifferentialExpression.py -i $formatType.inputFileName1
|
|
|
5 #if $formatType.FormatInputFileName1 == 'bed':
|
|
|
6 -f bed
|
|
|
7 #elif $formatType.FormatInputFileName1 == 'gff':
|
|
|
8 -f gff
|
|
|
9 #elif $formatType.FormatInputFileName1 == 'gff2':
|
|
|
10 -f gff2
|
|
|
11 #elif $formatType.FormatInputFileName1 == 'gff3':
|
|
|
12 -f gff3
|
|
|
13 #elif $formatType.FormatInputFileName1 == 'sam':
|
|
|
14 -f sam
|
|
|
15 #elif $formatType.FormatInputFileName1 == 'gtf':
|
|
|
16 -f gtf
|
|
|
17 #end if
|
|
|
18
|
|
|
19 -j $formatType2.inputFileName2
|
|
|
20 #if $formatType2.FormatInputFileName2 == 'bed':
|
|
|
21 -g bed
|
|
|
22 #elif $formatType2.FormatInputFileName2 == 'gff':
|
|
|
23 -g gff
|
|
|
24 #elif $formatType2.FormatInputFileName2 == 'gff2':
|
|
|
25 -g gff2
|
|
|
26 #elif $formatType2.FormatInputFileName2 == 'gff3':
|
|
|
27 -g gff3
|
|
|
28 #elif $formatType2.FormatInputFileName2 == 'sam':
|
|
|
29 -g sam
|
|
|
30 #elif $formatType2.FormatInputFileName2 == 'gtf':
|
|
|
31 -g gtf
|
|
|
32 #end if
|
|
|
33
|
|
|
34 -k $formatTypeRef.inputFileNameRef
|
|
|
35 #if $formatTypeRef.FormatInputFileNameRef == 'bed':
|
|
|
36 -l bed
|
|
|
37 #elif $formatTypeRef.FormatInputFileNameRef == 'gff':
|
|
|
38 -l gff
|
|
|
39 #elif $formatTypeRef.FormatInputFileNameRef == 'gff2':
|
|
|
40 -l gff2
|
|
|
41 #elif $formatTypeRef.FormatInputFileNameRef == 'gff3':
|
|
|
42 -l gff3
|
|
|
43 #elif $formatTypeRef.FormatInputFileNameRef == 'sam':
|
|
|
44 -l sam
|
|
|
45 #elif $formatTypeRef.FormatInputFileNameRef == 'gtf':
|
|
|
46 -l gtf
|
|
|
47 #end if
|
|
|
48
|
|
|
49 -o $outputFileGff
|
|
|
50
|
|
|
51 $simple
|
|
|
52 $adjusted
|
|
|
53
|
|
|
54
|
|
|
55 #if $optionSimplePara.simplePara == 'Yes':
|
|
|
56 -S $optionSimplePara.paraValue
|
|
|
57 #end if
|
|
|
58
|
|
|
59 #if $optionFixedSizeFactor.FSF == 'Yes':
|
|
|
60 -x $optionFixedSizeFactor.FSFValue
|
|
|
61 #end if
|
|
|
62
|
|
|
63 #if $optionFDR.FDR == 'Yes':
|
|
|
64 -d $optionFDR.FDRValue
|
|
|
65 #end if
|
|
|
66 $plot $outputFilePNG
|
|
|
67 </command>
|
|
|
68
|
|
|
69 <inputs>
|
|
|
70 <conditional name="formatType">
|
|
|
71 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
|
|
|
72 <option value="bed">bed</option>
|
|
|
73 <option value="gff">gff</option>
|
|
|
74 <option value="gff2">gff2</option>
|
|
|
75 <option value="gff3">gff3</option>
|
|
|
76 <option value="sam">sam</option>
|
|
|
77 <option value="gtf">gtf</option>
|
|
|
78 </param>
|
|
|
79 <when value="bed">
|
|
|
80 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
|
|
|
81 </when>
|
|
|
82 <when value="gff">
|
|
|
83 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
|
|
|
84 </when>
|
|
|
85 <when value="gff2">
|
|
|
86 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
|
|
|
87 </when>
|
|
|
88 <when value="gff3">
|
|
|
89 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
|
|
|
90 </when>
|
|
|
91 <when value="sam">
|
|
|
92 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
|
|
|
93 </when>
|
|
|
94 <when value="gtf">
|
|
|
95 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
|
|
|
96 </when>
|
|
|
97 </conditional>
|
|
|
98
|
|
|
99 <conditional name="formatType2">
|
|
|
100 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
|
|
|
101 <option value="bed">bed</option>
|
|
|
102 <option value="gff">gff</option>
|
|
|
103 <option value="gff2">gff2</option>
|
|
|
104 <option value="gff3">gff3</option>
|
|
|
105 <option value="sam">sam</option>
|
|
|
106 <option value="gtf">gtf</option>
|
|
|
107 </param>
|
|
|
108 <when value="bed">
|
|
|
109 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
|
|
|
110 </when>
|
|
|
111 <when value="gff">
|
|
|
112 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
|
|
|
113 </when>
|
|
|
114 <when value="gff2">
|
|
|
115 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
|
|
|
116 </when>
|
|
|
117 <when value="gff3">
|
|
|
118 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
|
|
|
119 </when>
|
|
|
120 <when value="sam">
|
|
|
121 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
|
|
|
122 </when>
|
|
|
123 <when value="gtf">
|
|
|
124 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
|
|
|
125 </when>
|
|
|
126 </conditional>
|
|
|
127
|
|
|
128 <conditional name="formatTypeRef">
|
|
|
129 <param name="FormatInputFileNameRef" type="select" label="Input Ref File Format ">
|
|
|
130 <option value="bed">bed</option>
|
|
|
131 <option value="gff">gff</option>
|
|
|
132 <option value="gff2">gff2</option>
|
|
|
133 <option value="gff3">gff3</option>
|
|
|
134 <option value="sam">sam</option>
|
|
|
135 <option value="gtf">gtf</option>
|
|
|
136 </param>
|
|
|
137 <when value="bed">
|
|
|
138 <param name="inputFileNameRef" format="bed" type="data" label="Input Ref File"/>
|
|
|
139 </when>
|
|
|
140 <when value="gff">
|
|
|
141 <param name="inputFileNameRef" format="gff" type="data" label="Input Ref File"/>
|
|
|
142 </when>
|
|
|
143 <when value="gff2">
|
|
|
144 <param name="inputFileNameRef" format="gff2" type="data" label="Input Ref File"/>
|
|
|
145 </when>
|
|
|
146 <when value="gff3">
|
|
|
147 <param name="inputFileNameRef" format="gff3" type="data" label="Input Ref File"/>
|
|
|
148 </when>
|
|
|
149 <when value="sam">
|
|
|
150 <param name="inputFileNameRef" format="sam" type="data" label="Input Ref File"/>
|
|
|
151 </when>
|
|
|
152 <when value="gtf">
|
|
|
153 <param name="inputFileNameRef" format="gtf" type="data" label="Input Ref File"/>
|
|
|
154 </when>
|
|
|
155 </conditional>
|
|
|
156
|
|
|
157 <param name="simple" type="boolean" truevalue="-s" falsevalue="" checked="false" label="normalize using the number of reads in each condition"/>
|
|
|
158 <param name="adjusted" type="boolean" truevalue="-a" falsevalue="" checked="false" label="normalize using the number of reads of 'mean' regions"/>
|
|
|
159
|
|
|
160 <conditional name="optionSimplePara">
|
|
|
161 <param name="simplePara" type="select" label="provide the number of reads" >
|
|
|
162 <option value="Yes">Yes</option>
|
|
|
163 <option value="No" selected="true">No</option>
|
|
|
164 </param>
|
|
|
165 <when value="Yes">
|
|
|
166 <param name="paraValue" type="text" value="None" label="provide the number of reads" />
|
|
|
167 </when>
|
|
|
168 <when value="No">
|
|
|
169 </when>
|
|
|
170 </conditional>
|
|
|
171
|
|
|
172 <conditional name="optionFixedSizeFactor">
|
|
|
173 <param name="FSF" type="select" label="give the magnification factor for the normalization using fixed size sliding windows in reference regions (leave empty for no such normalization)">
|
|
|
174 <option value="Yes">Yes</option>
|
|
|
175 <option value="No" selected="true">No</option>
|
|
|
176 </param>
|
|
|
177 <when value="Yes">
|
|
|
178 <param name="FSFValue" type="integer" value="0" />
|
|
|
179 </when>
|
|
|
180 <when value="No">
|
|
|
181 </when>
|
|
|
182 </conditional>
|
|
|
183
|
|
|
184 <conditional name="optionFDR">
|
|
|
185 <param name="FDR" type="select" label="use FDR">
|
|
|
186 <option value="Yes">Yes</option>
|
|
|
187 <option value="No" selected="true">No</option>
|
|
|
188 </param>
|
|
|
189 <when value="Yes">
|
|
|
190 <param name="FDRValue" type="float" value="0.0"/>
|
|
|
191 </when>
|
|
|
192 <when value="No">
|
|
|
193 </when>
|
|
|
194 </conditional>
|
|
|
195
|
|
|
196 <param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="plot cloud plot"/>
|
|
|
197
|
|
|
198 </inputs>
|
|
|
199
|
|
|
200 <outputs>
|
|
|
201 <data name="outputFileGff" format="gff3" label="[GetDifferentialExpression]out file"/>
|
|
|
202 <data name="outputFilePNG" format="PNG" label="[GetDifferentialExpression]PNG file">
|
|
|
203 <filter>plot</filter>
|
|
|
204 </data>
|
|
|
205 </outputs>
|
|
|
206
|
|
|
207 <help>
|
|
|
208 example: python GetDifferentialExpression.py -i input1 -f gff3 -j input2 -g gff3 -k ref -l gff3 -o output.gff3
|
|
|
209 </help>
|
|
|
210 </tool>
|
