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comparison hairpinTool.xml @ 6:3d04308a99f9

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- Added differentially expressed hairpin count output - Added running time output - Added counts table output
author shian_su <registertonysu@gmail.com>
date Fri, 11 Apr 2014 17:17:15 +1000
parents 076ca575208f
children 91e411fcdecc
comparison
equal deleted inserted replaced
5:17befe9f8b03 6:3d04308a99f9
1 <tool id="shRNAseq" name="shRNAseq Tool" version="1.0.5"> 1 <tool id="shRNAseq" name="shRNAseq Tool" version="1.0.7">
2 <description> 2 <description>
3 Analyse hairpin differential representation using edgeR 3 Analyse hairpin differential representation using edgeR
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
7 <requirement type="R-module">edgeR</requirement> 7 <requirement type="R-module" version="3.5.27">edgeR</requirement>
8 <requirement type="R-module">limma</requirement> 8 <requirement type="R-module" version="3.18.13">limma</requirement>
9 </requirements> 9 </requirements>
10 10
11 <stdio> 11 <stdio>
12 <exit_code range="1:" level="fatal" description="Tool exception" /> 12 <exit_code range="1:" level="fatal" description="Tool exception" />
13 </stdio> 13 </stdio>
14 14
15 <command interpreter="Rscript"> 15 <command interpreter="Rscript">
16 hairpinTool.R $inputOpt.type 16 hairpinTool.R $inputOpt.inputType
17 #if $inputOpt.type=="fastq": 17 #if $inputOpt.inputType=="fastq":
18 #for $i, $fas in enumerate($inputOpt.fastq): 18 #for $i, $fas in enumerate($inputOpt.fastq):
19 fastq::$fas.file 19 fastq::$fas.file
20 #end for 20 #end for
21 21
22 $inputOpt.hairpin 22 $inputOpt.hairpin
23 $inputOpt.samples 23 $inputOpt.samples
24 24
25 #if $inputOpt.positions.option=="yes": 25 #if $inputOpt.positions.posOption=="yes":
26 $inputOpt.positions.barstart 26 $inputOpt.positions.barstart
27 $inputOpt.positions.barend 27 $inputOpt.positions.barend
28 $inputOpt.positions.hpstart 28 $inputOpt.positions.hpstart
29 $inputOpt.positions.hpend 29 $inputOpt.positions.hpend
30 #else: 30 #else:
33 37 33 37
34 57 34 57
35 #end if 35 #end if
36 #else: 36 #else:
37 $inputOpt.counts 37 $inputOpt.counts
38 $inputOpt.anno 38 $inputOpt.hairpin
39 "$inputOpt.factors" 39 $inputOpt.samples
40 0 0 0 40 0 0 0
41 #end if 41 #end if
42 42
43 #if $filterCPM.option=="yes": 43 #if $filterCPM.filtOption=="yes":
44 $filterCPM.cpmReq 44 $filterCPM.cpmReq
45 $filterCPM.sampleReq 45 $filterCPM.sampleReq
46 #else: 46 #else:
47 -Inf 47 -Inf
48 -Inf 48 -Inf
55 $outFile.files_path 55 $outFile.files_path
56 56
57 #if $workMode.mode=="classic": 57 #if $workMode.mode=="classic":
58 "$workMode.pair1" 58 "$workMode.pair1"
59 "$workMode.pair2" 59 "$workMode.pair2"
60 #else: 60 #elif $workMode.mode=="glm":
61 "$workMode.contrast" 61 "$workMode.contrast"
62 $workMode.roast.option 62 $workMode.roast.roastOption
63 #if $workMode.roast.option=="yes": 63 #if $workMode.roast.roastOption=="yes":
64 $workMode.roast.hairpinReq 64 $workMode.roast.hairpinReq
65 $workMode.roast.select.option 65 $workMode.roast.select.selOption
66 "$workMode.roast.select.selection" 66 "$workMode.roast.select.selection"
67 #else: 67 #else:
68 0 68 0
69 0 69 0
70 0 70 0
72 #end if 72 #end if
73 </command> 73 </command>
74 74
75 <inputs> 75 <inputs>
76 <conditional name="inputOpt"> 76 <conditional name="inputOpt">
77 <param name="type" type="select" label="Input File Type"> 77 <param name="inputType" type="select" label="Input File Type">
78 <option value="fastq">FastQ File</option> 78 <option value="fastq">FastQ File</option>
79 <option value="counts">Table of Counts</option> 79 <option value="counts">Table of Counts</option>
80 </param> 80 </param>
81 81
82 <when value="fastq"> 82 <when value="fastq">
90 <repeat name="fastq" title="FastQ Files"> 90 <repeat name="fastq" title="FastQ Files">
91 <param name="file" type="data" format="fastq"/> 91 <param name="file" type="data" format="fastq"/>
92 </repeat> 92 </repeat>
93 93
94 <conditional name="positions"> 94 <conditional name="positions">
95 <param name="option" type="select" 95 <param name="posOption" type="select"
96 label="Specify Barcode and Hairpin Locations?" 96 label="Specify Barcode and Hairpin Locations?"
97 help="Default Positions: Barcode: 1 to 5, Hairpin: 37 to 57."> 97 help="Default Positions: Barcode: 1 to 5, Hairpin: 37 to 57.">
98 <option value="no" selected="True">No</option> 98 <option value="no" selected="True">No</option>
99 <option value="yes">Yes</option> 99 <option value="yes">Yes</option>
100 </param> 100 </param>
116 </conditional> 116 </conditional>
117 </when> 117 </when>
118 118
119 <when value="counts"> 119 <when value="counts">
120 <param name="counts" type="data" format="tabular" label="Counts Table"/> 120 <param name="counts" type="data" format="tabular" label="Counts Table"/>
121 <param name="anno" type="data" format="tabular" 121 <param name="hairpin" type="data" format="tabular"
122 label="Hairpin Annotation"/> 122 label="Hairpin Annotation"/>
123 <param name="factors" type="data" format="tabular" 123 <param name="samples" type="data" format="tabular"
124 label="Sample Annotation"/> 124 label="Sample Annotation"/>
125 </when> 125 </when>
126 </conditional> 126 </conditional>
127 127
128 <conditional name="filterCPM"> 128 <conditional name="filterCPM">
129 <param name="option" type="select" label="Filter Low CPM?" 129 <param name="filtOption" type="select" label="Filter Low CPM?"
130 help="Ignore hairpins with very low representation when performing 130 help="Ignore hairpins with very low representation when performing
131 analysis."> 131 analysis.">
132 <option value="yes">Yes</option> 132 <option value="yes">Yes</option>
133 <option value="no">No</option> 133 <option value="no">No</option>
134 </param> 134 </param>
170 KD-Control will result in positive fold change if KD has 170 KD-Control will result in positive fold change if KD has
171 greater expression and negative if Control has greater 171 greater expression and negative if Control has greater
172 expression."/> 172 expression."/>
173 173
174 <conditional name="roast"> 174 <conditional name="roast">
175 <param name="option" type="select" 175 <param name="roastOption" type="select"
176 label="Perform Gene Level Analysis?" 176 label="Perform Gene Level Analysis?"
177 help="Analyse LogFC tendencies for hairpins belonging 177 help="Analyse LogFC tendencies for hairpins belonging
178 to the same gene."> 178 to the same gene.">
179 <option value="no">No</option> 179 <option value="no">No</option>
180 <option value="yes">Yes</option> 180 <option value="yes">Yes</option>
185 label="Minimum Hairpins" 185 label="Minimum Hairpins"
186 help="Only genes with at least this many hairpins will 186 help="Only genes with at least this many hairpins will
187 be analysed."/> 187 be analysed."/>
188 188
189 <conditional name="select"> 189 <conditional name="select">
190 <param name="option" type="select" 190 <param name="selOption" type="select"
191 label="Gene Selection Method"> 191 label="Gene Selection Method">
192 <option value="rank">By p-value Rank</option> 192 <option value="rank">By p-value Rank</option>
193 <option value="geneID">By Gene Identifier</option> 193 <option value="geneID">By Gene Identifier</option>
194 </param> 194 </param>
195 <when value="rank"> 195 <when value="rank">
230 </inputs> 230 </inputs>
231 231
232 <outputs> 232 <outputs>
233 <data format="html" name="outFile" label="shRNAseq Analysis"/> 233 <data format="html" name="outFile" label="shRNAseq Analysis"/>
234 </outputs> 234 </outputs>
235
236 <help> 235 <help>
237 .. class:: infomark 236 .. class:: infomark
238 237
239 **What it does** 238 **What it does**
240 239