Mercurial > repos > shians > shrnaseq

annotate hairpinTool.xml @ 15:5a917ea5bed2

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
- Fixed read requirement report statistic.
author shian_su <registertonysu@gmail.com>
date Mon, 12 Jan 2015 16:31:48 +1100
parents 44130e484a97
children 438f2733bc27
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
44130e484a97 - Fixed xml file so tool actually functions
shian_su <registertonysu@gmail.com>
parents: 13
diff changeset
1 <tool id="shRNAseq" name="shRNAseq Tool" version="1.2.1">
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
2 <description>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
3 Analyse differential representation for shRNAseq and sgRNA based procedures
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
4 using edgeR package from Bioconductor.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
5 </description>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
6
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
7 <requirements>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
8 <requirement type="R-module" version="3.7.17">edgeR</requirement>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
9 <requirement type="R-module" version="3.21.16">limma</requirement>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
10 <requirement type="package" version="3.1.1">R_3_0_3</requirement>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
11 </requirements>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
12
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
13 <stdio>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
14 <exit_code range="1:" level="fatal" description="Tool exception" />
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
15 </stdio>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
16
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
17 <command interpreter="Rscript">
14
44130e484a97 - Fixed xml file so tool actually functions
shian_su <registertonysu@gmail.com>
parents: 13
diff changeset
18 hairpinTool.R $inputOpt.inputType
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
19 #if $inputOpt.inputType=="fastq":
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
20
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
21 #for $i, $fas in enumerate($inputOpt.fastq):
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
22 fastq::$fas.file
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
23 #end for
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
24
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
25 $inputOpt.hairpin
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
26 $inputOpt.samples
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
27
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
28 #if $inputOpt.positions.posOption=="yes":
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
29 $inputOpt.positions.barstart
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
30 $inputOpt.positions.barend
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
31 0
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
32 0
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
33 $inputOpt.positions.hpstart
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
34 $inputOpt.positions.hpend
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
35 #else:
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
36 1
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
37 5
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
38 0
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
39 0
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
40 37
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
41 57
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
42 #end if
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
43 #elif $inputOpt.inputType=="pairedFastq":
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
44
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
45 #for $i, $fas in enumerate($inputOpt.fastq):
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
46 fastq::$fas.file
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
47 #end for
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
48
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
49 #for $i, $fas in enumerate($inputOpt.fastq):
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
50 fastqRev::$fas.fileRev
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
51 #end for
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
52
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
53 $inputOpt.hairpin
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
54 $inputOpt.samples
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
55
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
56 #if $inputOpt.positions.posOption=="yes":
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
57 $inputOpt.positions.barstart
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
58 $inputOpt.positions.barend
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
59 $inputOpt.positions.barstartRev
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
60 $inputOpt.positions.barendRev
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
61 $inputOpt.positions.hpstart
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
62 $inputOpt.positions.hpend
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
63 #else:
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
64 1
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
65 5
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
66 0
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
67 0
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
68 37
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
69 57
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
70 #end if
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
71
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
72 #elif $inputOpt.inputType=="counts":
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
73 $inputOpt.counts
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
74 $inputOpt.hairpin
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
75 $inputOpt.samples
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
76 0
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
77 0
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
78 0
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
79 0
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
80 0
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
81 #end if
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
82
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
83 #if $inputOpt.secondaryFactor.secFactorOpt=="yes":
15
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
84 "$inputOpt.secondaryFactor.secFactName"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
85 #else:
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
86 "none"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
87 #end if
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
88
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
89 #if $filterCPM.filtOption=="yes":
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
90 $filterCPM.cpmReq
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
91 $filterCPM.sampleReq
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
92 $filterCPM.readReq
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
93 #else:
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
94 -Inf
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
95 -Inf
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
96 -Inf
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
97 #end if
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
98
15
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
99 "$fdr"
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
100 "$lfc"
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
101 "$direction"
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
102 "$workMode.mode"
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
103 "$outFile"
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
104 "$outFile.files_path"
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
105
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
106 #if $workMode.mode=="classic":
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
107 "$workMode.pair1"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
108 "$workMode.pair2"
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
109 #elif $workMode.mode=="glm":
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
110 "$workMode.contrast"
15
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
111 "$workMode.roast.roastOption"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
112
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
113 #if $workMode.roast.roastOption=="yes":
15
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
114 "$workMode.roast.hairpinReq"
5a917ea5bed2 - Fixed read requirement report statistic.
shian_su <registertonysu@gmail.com>
parents: 14
diff changeset
115 "$workMode.roast.select.selOption"
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
116 "$workMode.roast.select.selection"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
117 #else:
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
118 0
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
119 0
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
120 0
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
121 #end if
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
122
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
123 #end if
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
124 </command>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
125
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
126 <inputs>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
127 <conditional name="inputOpt">
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
128
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
129 <param name="inputType" type="select" label="Input File Type">
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
130 <option value="fastq">FastQ File</option>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
131 <option value="pairedFastq">Paired FastQ File</option>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
132 <option value="counts">Table of Counts</option>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
133 </param>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
134
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
135 <when value="fastq">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
136 <param name="hairpin" type="data" format="tabular"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
137 label="Target Annotation"/>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
138
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
139 <param name="samples" type="data" format="tabular"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
140 label="Sample Annotation"/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
141
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
142 <repeat name="fastq" title="FastQ Files">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
143 <param name="file" type="data" format="fastq"/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
144 </repeat>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
145
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
146 <conditional name="secondaryFactor">
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
147
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
148 <param name="secFactorOpt" type="select"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
149 label="Include Secondary Factor">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
150
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
151 <option value="no" selected="True">No</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
152
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
153 <option value="yes">Yes</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
154
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
155 </param>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
156
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
157 <when value="yes">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
158
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
159 <param name="secFactName" type="text" label="Secondary Factor Name"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
160 size="80"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
161
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
162 </when>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
163
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
164 <when value="no">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
165 </when>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
166 </conditional>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
167
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
168 <conditional name="positions">
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
169 <param name="posOption" type="select"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
170 label="Specify Sample Index and Target Sequence Locations?"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
171 help="Default Positions: Index: 1 to 5, Target: 37 to 57.">
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
172 <option value="no" selected="True">No</option>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
173 <option value="yes">Yes</option>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
174 </param>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
175
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
176 <when value="yes">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
177 <param name="barstart" type="integer" value="1"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
178 label="Index Starting Position"/>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
179 <param name="barend" type="integer" value="5"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
180 label="Index Ending Position"/>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
181
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
182 <param name="hpstart" type="integer" value="37"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
183 label="Target Starting Position"/>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
184
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
185 <param name="hpend" type="integer" value="57"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
186 label="Target Ending Position"/>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
187 </when>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
188
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
189 <when value="no"/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
190 </conditional>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
191 </when>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
192
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
193 <when value="pairedFastq">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
194 <param name="hairpin" type="data" format="tabular"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
195 label="Target Sequence Annotation"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
196
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
197 <param name="samples" type="data" format="tabular"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
198 label="Sample Annotation"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
199
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
200 <repeat name="fastq" title="FastQ Files">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
201 <param name="file" type="data" format="fastq"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
202 <param name="fileRev" type="data" format="fastq"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
203 </repeat>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
204
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
205 <conditional name="secondaryFactor">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
206
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
207 <param name="secFactorOpt" type="select"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
208 label="Include Secondary Factor">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
209
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
210 <option value="no" selected="True">No</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
211
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
212 <option value="yes">Yes</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
213
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
214 </param>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
215
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
216 <when value="yes">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
217
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
218 <param name="secFactName" type="text" label="Secondary Factor Name"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
219 size="80"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
220
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
221 </when>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
222
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
223 <when value="no">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
224 </when>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
225 </conditional>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
226
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
227 <conditional name="positions">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
228
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
229 <param name="posOption" type="select"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
230 label="Specify Sample Index and Target Sequence Locations?"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
231 help="Default Positions: Index: 1 to 5, Input required for
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
232 reverse end, Target: 37 to 57.">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
233
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
234 <option value="no" selected="True">No</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
235
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
236 <option value="yes">Yes</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
237
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
238 </param>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
239
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
240 <when value="yes">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
241 <param name="barstart" type="integer" value="1"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
242 label="Index Starting Position"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
243
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
244 <param name="barend" type="integer" value="5"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
245 label="Index Ending Position"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
246
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
247 <param name="barstartRev" type="integer" value="0"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
248 label="Reverse Index Starting Position"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
249
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
250 <param name="barendRev" type="integer" value="0"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
251 label="Reverse Index Ending Position"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
252
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
253 <param name="hpstart" type="integer" value="37"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
254 label="Target Starting Position"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
255
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
256 <param name="hpend" type="integer" value="57"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
257 label="Target Ending Position"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
258 </when>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
259
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
260 <when value="no">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
261 </when>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
262
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
263 </conditional>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
264
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
265 </when>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
266
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
267 <when value="counts">
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
268
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
269 <param name="counts" type="data" format="tabular" label="Counts Table"/>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
270
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
271 <param name="hairpin" type="data" format="tabular"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
272 label="Target Sequence Annotation"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
273
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
274 <param name="samples" type="data" format="tabular"
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
275 label="Sample Annotation"/>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
276
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
277 <conditional name="secondaryFactor">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
278
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
279 <param name="secFactorOpt" type="select"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
280 label="Include Secondary Factor">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
281
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
282 <option value="no" selected="True">No</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
283
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
284 <option value="yes">Yes</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
285
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
286 </param>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
287
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
288 <when value="yes">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
289
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
290 <param name="secFactName" type="text" label="Secondary Factor Name"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
291 size="80"/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
292
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
293 </when>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
294
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
295 <when value="no">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
296 </when>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
297
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
298 </conditional>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
299
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
300 </when>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
301
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
302 </conditional>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
303
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
304 <conditional name="filterCPM">
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
305 <param name="filtOption" type="select" label="Filter Low CPM?"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
306 help="Ignore target sequences with very low representation when
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
307 performing analysis.">
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
308 <option value="yes">Yes</option>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
309 <option value="no">No</option>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
310 </param>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
311
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
312 <when value="yes">
11
c0a76e30d61b - Removed max on cpm filtering. Really shouldn't have been there in the first
shian_su <registertonysu@gmail.com>
parents: 10
diff changeset
313 <param name="cpmReq" type="float" value="0.5" min="0"
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
314 label="Minimum CPM"/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
315
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
316 <param name="sampleReq" type="integer" value="1" min="0"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
317 label="Minimum Samples"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
318 help="Filter out all the genes that do not meet the minimum
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
319 CPM in at least this many samples."/>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
320
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
321 <param name="readReq" type="integer" value="1000" min="0"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
322 label="Minimum Reads"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
323 help="Filter out all samples that do not have the minimum
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
324 number of reads."/>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
325
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
326 </when>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
327
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
328 <when value="no"/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
329
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
330 </conditional>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
331
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
332 <conditional name="workMode">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
333 <param name="mode" type="select" label="Analysis Type"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
334 help="Classic Exact Tests are useful for simple comparisons across
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
335 two sampling groups. Generalised linear models allow for more
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
336 complex contrasts and gene level analysis to be made.">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
337 <option value="classic">Classic Exact Test</option>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
338 <option value="glm">Generalised Linear Model</option>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
339 </param>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
340
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
341 <when value="classic">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
342 <param name="pair1" type="text" label="Compare" size="40"/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
343 <param name="pair2" type="text" label="To" size="40"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
344 help="The analysis will subtract values of this group from those
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
345 in the group above to establish the difference."/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
346 </when>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
347
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
348 <when value="glm">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
349 <param name="contrast" type="text" size="60"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
350 label="Contrasts of interest"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
351 help="Specify equations defining contrasts to be made. Eg.
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
352 KD-Control will result in positive fold change if KD has
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
353 greater expression and negative if Control has greater
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
354 expression."/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
355
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
356 <conditional name="roast">
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
357 <param name="roastOption" type="select"
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
358 label="Perform Gene Level Analysis?"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
359 help="Analyse LogFC tendencies for target sequences belonging
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
360 to the same gene. NOTE: this is a slow procedure that
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
361 scales badly with the number of genes analysed.">
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
362 <option value="no">No</option>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
363 <option value="yes">Yes</option>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
364 </param>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
365
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
366 <when value="yes">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
367 <param name="hairpinReq" type="integer" value="2" min="2"
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
368 label="Minimum Targets Found"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
369 help="Only genes with at least this many target sequences
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
370 found will be analysed."/>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
371
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
372 <conditional name="select">
6
3d04308a99f9 - Added differentially expressed hairpin count output
shian_su <registertonysu@gmail.com>
parents: 2
diff changeset
373 <param name="selOption" type="select"
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
374 label="Gene Selection Method">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
375 <option value="rank">By p-value Rank</option>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
376 <option value="geneID">By Gene Identifier</option>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
377 </param>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
378 <when value="rank">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
379 <param name="selection" type="text" size="40" value="1:5"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
380 label="Ranks of Top Genes to Plot"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
381 help="Genes are ranked in ascending p-value for
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
382 differential representation, individual ranks can
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
383 be entered seperated by comma or a range seperated
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
384 by colon."/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
385 </when>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
386 <when value="geneID">
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
387 <param name="selection" type="text" size="80" value=""
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
388 label="Symbols of Genes to Plot"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
389 help="Select genes based on their identifier in the
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
390 'Gene' column of the sample information file.
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
391 Please ensure exact match with the values in input
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
392 file and separate selections with commas."/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
393 </when>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
394 </conditional>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
395
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
396
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
397 </when>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
398
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
399 <when value="no"/>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
400 </conditional>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
401 </when>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
402 </conditional>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
403
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
404 <param name="fdr" type="float" value="0.05" min="0" max="1"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
405 label="FDR Threshold"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
406 help="All observations below this threshold will be highlighted
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
407 in the smear plot."/>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
408
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
409 <param name="lfc" type="float" value="0" min="0"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
410 label="Absolute LogFC Threshold"
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
411 help="In additional to meeting the FDR requirement, the absolute
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
412 value of the log-fold-change of the observation must be above
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
413 this threshold to be highlighted."/>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
414
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
415 <param name="direction" type="select" label="Highlight Option"
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
416 help="Only hightlight positive or negative fold changes in smear plot?">
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
417 <option value="all">Default</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
418 <option value="up">Positive Only</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
419 <option value="down">Negative Only</option>
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
420 </param>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
421 </inputs>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
422
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
423 <outputs>
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
424 <data format="html" name="outFile" label="TagSeq Analysis"/>
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
425 </outputs>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
426 <help>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
427 .. class:: infomark
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
428
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
429 **What it does**
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
430
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
431 Given tables containing information about the hairpins/sgRNA and their
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
432 associated sample indices, information about the samples and fastq file
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
433 containing the sequencing reads. This tool will generate plots and tables for
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
434 the analysis of differential representation.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
435
7
91e411fcdecc Version 1.0.8
shian_su <registertonysu@gmail.com>
parents: 6
diff changeset
436 .. class:: infomark
91e411fcdecc Version 1.0.8
shian_su <registertonysu@gmail.com>
parents: 6
diff changeset
437
91e411fcdecc Version 1.0.8
shian_su <registertonysu@gmail.com>
parents: 6
diff changeset
438 A tutorial of how to use this tool is available at:
91e411fcdecc Version 1.0.8
shian_su <registertonysu@gmail.com>
parents: 6
diff changeset
439 http://bioinf.wehi.edu.au/shRNAseq/galaxy.html
91e411fcdecc Version 1.0.8
shian_su <registertonysu@gmail.com>
parents: 6
diff changeset
440
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
441 -----
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
442
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
443 .. class:: infomark
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
444
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
445 **INPUTS**
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
446
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
447 **Input File Type:**
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
448
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
449 This tool is able to either generate counts from a raw FastQ file given the
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
450 information regarding the samples and hairpins/sgRNA. Alternatively if a table
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
451 of counts has already been generated it can also be used.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
452
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
453 **Counts Table (Counts Input):**
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
454
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
455 A tab delimited text table of information regarding the counts of
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
456 hairpins/sgRNA. Should have a column 'ID' to denote the hairpins/sgRNA that
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
457 counts correspond to. Each additional column should have titles corresponding to
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
458 the label for the sample.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
459
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
460 Example::
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
461
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
462 ID Sample1 Sample2 Sample3
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
463 Control1 49802 48014 40148
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
464 Control2 12441 16352 14232
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
465 Control3 9842 9148 9111
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
466 Hairpin1 3300 3418 2914
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
467 Hairpin2 91418 95812 93174
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
468 Hairpin3 32985 31975 35104
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
469 Hairpin4 12082 14081 14981
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
470 Hairpin5 2491 2769 2691
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
471 Hairpin6 1294 1486 1642
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
472 Hairpin7 49501 49076 47611
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
473 ...
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
474
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
475 **Target Sequence Annotation:**
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
476
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
477 A tab delimited text table of information regarding the targetted
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
478 hairpins/sgRNA sequence. Should have columns 'ID', 'Sequences' and 'Gene' to
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
479 uniquely identify the target, align it with the reads to produce counts and
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
480 identify which gene the target acts on.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
481
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
482 NOTE: the column names are case sensitive and should be input exactly as they
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
483 are shown here.
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
484
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
485 Example::
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
486
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
487 ID Sequences Gene
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
488 Control1 TCTCGCTTGGGCGAGAGTAAG 2
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
489 Control2 CCGCCTGAAGTCTCTGATTAA 2
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
490 Control3 AGGAATTATAATGCTTATCTA 2
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
491 Hairpin1 AAGGCAGAGACTGACCACCTA 4
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
492 Hairpin2 GAGCGACCTGGTGTTACTCTA 4
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
493 Hairpin3 ATGGTGTAAATAGAGCTGTTA 4
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
494 Hairpin4 CAGCTCATCTTCTGTGAAGAA 4
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
495 Hairpin5 CAGCTCTGTGGGTCAGAAGAA 4
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
496 Hairpin6 CCAGGCACAGATCTCAAGATA 4
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
497 Hairpin7 ATGACAAGAAAGACATCTCAA 7
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
498 ...
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
499
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
500 **Sample Annotation (FastQ Input):**
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
501
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
502 A tab delimited text table of information regarding the samples. Should have
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
503 columns 'ID', 'Sequences' and 'group' to uniquely identify each sample, identify
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
504 the sample in the reads by its sample index sequence and correctly group
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
505 replicates for analysis. Additional columns may inserted for annotation purposes
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
506 and will not interfere with analysis as long as the necessary columns are
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
507 present.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
508
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
509 NOTE: With the exception of other_group, column names are case sensitive and
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
510 should be input exactly as they are shown here. The other_group column can be
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
511 named by the user and specified in the "Include Secondary Factor" option of the
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
512 tool.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
513
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
514 Example::
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
515
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
516 ID Sequences group other_group Replicate
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
517 3 GAAAG Day 2 male 1
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
518 6 GAACC Day 10 female 1
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
519 9 GAAGA Day 5 GFP neg male 1
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
520 16 GAATT Day 5 GFP pos male 1
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
521 18 GACAC Day 2 female 2
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
522 21 GACCA Day 10 male 2
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
523 28 GACGT Day 5 GFP neg male 2
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
524 31 GACTG Day 5 GFP pos female 2
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
525 33 GAGAA Day 2 male 3
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
526 40 GAGCT Day 10 female 3
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
527 ...
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
528
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
529 **Include Secondary Factor**
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
530 If there are two factors involved in the experiment (i.e. Age and Gender) then
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
531 then secondary factor should be included to improve the statistical analysis.
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
532 The secondary factor should be specified as a column in the sample annotation
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
533 file and the corresponding column name should be input exactly as it is into
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
534 the provided field in the tool.
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
535
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
536 NOTE: Currently the secondary factor is used only to improve statistical
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
537 analysis, comparisons can only be made in the primary factor specified as
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
538 "group" in the sample annotation.
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
539
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
540 **Specify Sample Index and Target Sequence Locations (FastQ Input):**
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
541
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
542 It is assumed that in the sequencing reads that the first 5 bases are the
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
543 sample index sequence and that bases 37-57 are the hairpins/sgRNA. If this is
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
544 not the case then the values of the positions can be changed, however it still
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
545 requires the sample indices and hairpins/sgRNA to be in a consistent location an
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
546 in a continuous sequence.
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
547
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
548 NOTE: position values start at 1 for the first base.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
549
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
550 **Filter Low CPM?:**
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
551
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
552 Often in a large screen there may members with very low counts which are of no
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
553 interest in the experiment, these may be filtered out to speed up computations.
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
554 Filtering will be based on counts per million in a required number of samples.
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
555
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
556 **Analysis Type:**
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
557
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
558 * **Classic Exact Test:** This allows two experimental groups to be compared
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
559 and p-values for differential representation derivec for each target
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
560 sequence. Simple and fast for straightforward comparisons. In this option you
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
561 will have the option of "*Compare* x *To* y" which implicitly subtracts the
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
562 data from y from that of x to produce the comparison.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
563
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
564 * **Generalised Linear Model:** This allow for complex contrasts to be specified
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
565 and also gene level analysis to be performed. If this option is chosen then
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
566 contrasts must be explicitly stated in equations and multiple contrasts can
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
567 be made. In addition there will be the option to analyse hairpins/sgRNA on a
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
568 per-gene basis to see if hairpins/sgRNA belonging to a particular gene have
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
569 any overall tendencies for the direction of their log-fold-change.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
570
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
571 **FDR Threshold:**
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
572 The smear plot in the output will have hairpins/sgRNA highlighted to signify
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
573 significant differential representation. The significance is determined by
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
574 contorlling the false discovery rate, only those with a FDR lower than the
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
575 threshold will be highlighted in the plot.
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
576
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
577 -----
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
578
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
579 **Citations:**
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
580
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
581 .. class:: infomark
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
582
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
583 limma
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
584
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
585 Please cite the paper below for the limma software itself. Please also try
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
586 to cite the appropriate methodology articles that describe the statistical
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
587 methods implemented in limma, depending on which limma functions you are
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
588 using. The methodology articles are listed in Section 2.1 of the limma
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
589 User's Guide.
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
590
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
591 * Smyth, GK (2005). Limma: linear models for microarray data. In:
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
592 'Bioinformatics and Computational Biology Solutions using R and
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
593 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
594 W. Huber (eds), Springer, New York, pages 397-420.
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
595
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
596 .. class:: infomark
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
597
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
598 edgeR
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
599
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
600 Please cite the first paper for the software itself and the other papers for
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
601 the various original statistical methods implemented in edgeR. See
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
602 Section 1.2 in the User's Guide for more detail.
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
603
13
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
604 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
605 package for differential expression analysis of digital gene expression
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
606 data. Bioinformatics 26, 139-140
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
607
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
608 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
609 differences in tag abundance. Bioinformatics 23, 2881-2887
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
610
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
611 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
612 binomial dispersion, with applications to SAGE data.
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
613 Biostatistics, 9, 321-332
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
614
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
615 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
616 of multifactor RNA-Seq experiments with respect to biological variation.
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
617 Nucleic Acids Research 40, 4288-4297
7aaa9bc23e3c Added support for paired end reads
shian_su <registertonysu@gmail.com>
parents: 11
diff changeset
618
8
548802b3492f Version 1.0.9
shian_su <registertonysu@gmail.com>
parents: 7
diff changeset
619 Report problems to: su.s@wehi.edu.au
2
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
620
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
621 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
622 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
623 </help>
076ca575208f First commit
shian_su <registertonysu@gmail.com>
parents:
diff changeset
624 </tool>