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comparison smart_toolShed/SMART/galaxy/GetDifferentialExpression.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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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>