Mercurial > repos > yufei-luo > s_mart

comparison SMART/DiffExpAnal/compareOverlapping_parallel.xml @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 <tool id="CompareOverlapping_parallel" name="CompareOverlapping (for DEA)">
2 <description>Shrink or extend the sets of genomic coordinates to get the information between starts of reads and starts of genes.</description>
3 <command interpreter="python">
4 compareOverlapping_parallel.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 --inputTxt $inputTxt
20
21 -g $format2
22
23 --outTxt $outTxtFile
24
25 #if $optionNFirstFile1.NFirstForFile1 == 'Yes':
26 -S $optionNFirstFile1.firstNtFile1
27 #end if
28 #if $optionNFirstFile2.NFirstForFile2 == 'Yes':
29 -s $optionNFirstFile2.firstNtFile2
30 #end if
31 #if $optionNLastFile1.NLastForFile1 == 'Yes':
32 -U $optionNLastFile1.lastNtFile1
33 #end if
34 #if $optionNLastFile2.NLastForFile2 == 'Yes':
35 -u $optionNLastFile2.lastNtFile2
36 #end if
37
38 #if $optionExtentionCinqFile1.extentionFile1 == 'Yes':
39 -E $optionExtentionCinqFile1.extention51
40 #end if
41 #if $optionExtentionCinqFile2.extentionFile2 == 'Yes':
42 -e $optionExtentionCinqFile2.extention52
43 #end if
44
45 #if $optionExtentionTroisFile1.extentionFile1 == 'Yes':
46 -N $optionExtentionTroisFile1.extention31
47 #end if
48 #if $optionExtentionTroisFile2.extentionFile2 == 'Yes':
49 -n $optionExtentionTroisFile2.extention32
50 #end if
51
52 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
53 -c
54 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
55 -a
56 #end if
57
58 #if $OptionDistance.Dist == 'Yes':
59 -d $OptionDistance.distance
60 #end if
61
62 #if $OptionMinOverlap.MO == 'Yes':
63 -m $OptionMinOverlap.minOverlap
64 #end if
65
66 $InvertMatch
67 $ReportIntron
68 $NotOverlapping
69 $tar $outputTarFile
70 </command>
71
72 <inputs>
73
74 <conditional name="formatType">
75 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
76 <option value="bed">bed</option>
77 <option value="gff">gff</option>
78 <option value="gff2">gff2</option>
79 <option value="gff3">gff3</option>
80 <option value="sam">sam</option>
81 <option value="gtf">gtf</option>
82 </param>
83 <when value="bed">
84 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
85 </when>
86 <when value="gff">
87 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
88 </when>
89 <when value="gff2">
90 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
91 </when>
92 <when value="gff3">
93 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
94 </when>
95 <when value="sam">
96 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
97 </when>
98 <when value="gtf">
99 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
100 </when>
101 </conditional>
102
103 <param name="inputTxt" type="data" format="txt" label="A txt file contains a list of several input transcripts files." />
104
105 <param name="format2" type="text" value="bed" label="format for File 2, you can choose [bed, gff, gff2, gff3, sam, gtf]"/>
106
107 <conditional name="optionNFirstFile1">
108 <param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1">
109 <option value="Yes">Yes</option>
110 <option value="No" selected="true">No</option>
111 </param>
112 <when value="Yes">
113 <param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" />
114 </when>
115 <when value="No">
116 </when>
117 </conditional>
118 <conditional name="optionNFirstFile2">
119 <param name="NFirstForFile2" type="select" label="NFirst for file 2" help="only consider the n first nucleotides of the transcripts in file 2">
120 <option value="Yes">Yes</option>
121 <option value="No" selected="true">No</option>
122 </param>
123 <when value="Yes">
124 <param name="firstNtFile2" type="integer" value="1" label="n first nucleotides for input file 1" />
125 </when>
126 <when value="No">
127 </when>
128 </conditional>
129
130 <conditional name="optionNLastFile1">
131 <param name="NLastForFile1" type="select" label="NLast for file 1">
132 <option value="Yes">Yes</option>
133 <option value="No" selected="true">No</option>
134 </param>
135 <when value="Yes">
136 <param name="lastNtFile1" type="integer" value="1" label="n last nucleotides for input file 1" help="only consider the n last nucleotides of the transcripts in file 1"/>
137 </when>
138 <when value="No">
139 </when>
140 </conditional>
141 <conditional name="optionNLastFile2">
142 <param name="NLastForFile2" type="select" label="NLast for file 2">
143 <option value="Yes">Yes</option>
144 <option value="No" selected="true">No</option>
145 </param>
146 <when value="Yes">
147 <param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/>
148 </when>
149 <when value="No">
150 </when>
151 </conditional>
152
153 <conditional name="optionExtentionCinqFile1">
154 <param name="extentionFile1" type="select" label="Extension towards 5 for file 1">
155 <option value="Yes">Yes</option>
156 <option value="No" selected="true">No</option>
157 </param>
158 <when value="Yes">
159 <param name="extention51" type="integer" value="1" label="in file 1" />
160 </when>
161 <when value="No">
162 </when>
163 </conditional>
164
165 <conditional name="optionExtentionCinqFile2">
166 <param name="extentionFile2" type="select" label="Extension towards 5 for file 2">
167 <option value="Yes">Yes</option>
168 <option value="No" selected="true">No</option>
169 </param>
170 <when value="Yes">
171 <param name="extention52" type="integer" value="1" label="in file 2"/>
172 </when>
173 <when value="No">
174 </when>
175 </conditional>
176
177 <conditional name="optionExtentionTroisFile1">
178 <param name="extentionFile1" type="select" label="Extension towards 3 for file 1">
179 <option value="Yes">Yes</option>
180 <option value="No" selected="true">No</option>
181 </param>
182 <when value="Yes">
183 <param name="extention31" type="integer" value="1" label="in file 1" />
184 </when>
185 <when value="No">
186 </when>
187 </conditional>
188
189 <conditional name="optionExtentionTroisFile2">
190 <param name="extentionFile2" type="select" label="Extension towards 3 for file 2">
191 <option value="Yes">Yes</option>
192 <option value="No" selected="true">No</option>
193 </param>
194 <when value="Yes">
195 <param name="extention32" type="integer" value="1" label="in file 2" />
196 </when>
197 <when value="No">
198 </when>
199 </conditional>
200
201 <conditional name="OptionColinearOrAntiSens">
202 <param name="OptionCA" type="select" label="Colinear or anti-sens">
203 <option value="Colinear">Colinear</option>
204 <option value="AntiSens">AntiSens</option>
205 <option value="NONE" selected="true">NONE</option>
206 </param>
207 <when value="Colinear">
208 </when>
209 <when value="AntiSens">
210 </when>
211 <when value="NONE">
212 </when>
213 </conditional>
214
215 <conditional name="OptionDistance">
216 <param name="Dist" type="select" label="Maximum Distance between two reads">
217 <option value="Yes">Yes</option>
218 <option value="No" selected="true">No</option>
219 </param>
220 <when value="Yes">
221 <param name="distance" type="integer" value="0"/>
222 </when>
223 <when value="No">
224 </when>
225 </conditional>
226
227 <conditional name="OptionMinOverlap">
228 <param name="MO" type="select" label="Minimum number of overlapping between two reads">
229 <option value="Yes">Yes</option>
230 <option value="No" selected="true">No</option>
231 </param>
232 <when value="Yes">
233 <param name="minOverlap" type="integer" value="1"/>
234 </when>
235 <when value="No">
236 </when>
237 </conditional>
238 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
239 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/>
240 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
241 <param name="tar" type="boolean" truevalue="--tar" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." />
242 </inputs>
243
244 <outputs>
245 <data name="outTxtFile" format="txt" label="overlapping output files "/>
246 <data name="outputTarFile" format="tar">
247 <filter>tar</filter>
248 </data>
249 </outputs>
250
251 </tool>