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comparison dexseq.xml @ 0:276833129f97 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
author iuc
date Thu, 24 Sep 2015 17:16:56 -0400
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-1:000000000000 0:276833129f97
1 <tool id="dexseq" name="DEXSeq" version="1.0">
2 <description>Determines differential exon usage from count tables</description>
3 <requirements>
4 <requirement type="package" version="3.2.0">R</requirement>
5 <requirement type="package" version="1.12.14">cairo</requirement>
6 <requirement type="package" version="4.0.3">tiff</requirement>
7 <requirement type="package" version="1.14.2">dexseq</requirement>
8 </requirements>
9 <code file="dexseq_helper.py" />
10 <command>
11 <![CDATA[
12 mkdir ./html_out &&
13 #import json
14 Rscript $__tool_directory__/dexseq.R
15 -o "$dexseq_out"
16 -p 6
17 #set $temp_factor_names = list()
18 #for $factor in $rep_factorName:
19 #set $temp_factor = list()
20 #for $level in $factor.rep_factorLevel:
21 #set $count_files = list()
22 #for $file in $level.countsFile:
23 $count_files.append(str($file))
24 #end for
25 $temp_factor.append( {str($level.factorLevel): $count_files} )
26 #end for
27 $temp_factor_names.append([str($factor.factorName), $temp_factor])
28 #end for
29 -f '#echo json.dumps(temp_factor_names)#'
30 -a $gtf
31 #if $report:
32 -r ./html_out
33 #end if
34 -c $fdr_cutoff
35 &&
36 mkdir $htmlreport.extra_files_path
37 &&
38 cp ./html_out/testForDEU.html $htmlreport
39 &&
40 cp -r ./html_out/* $htmlreport.extra_files_path
41 &&
42 ]]>
43 </command>
44 <stdio>
45 <regex match="Execution halted"
46 source="both"
47 level="fatal"
48 description="Execution halted." />
49 <regex match="Input-Error 01"
50 source="both"
51 level="fatal"
52 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
53 <regex match="Error in"
54 source="both"
55 level="fatal"
56 description="An undefined error occured, please check your intput carefully and contact your administrator." />
57 </stdio>
58 <inputs>
59 <param name="gtf" type="data" label="GTF file created from DEXSeq-Count tool"/>
60 <repeat name="rep_factorName" title="Factor" min="1">
61 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
62 help="Only letters, numbers and underscores will be retained in this field">
63 <sanitizer>
64 <valid initial="string.letters,string.digits"><add value="_" /></valid>
65 </sanitizer>
66 </param>
67 <repeat name="rep_factorLevel" title="Factor level" min="2" max="2" default="2">
68 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level"
69 help="Only letters, numbers and underscores will be retained in this field">
70 <sanitizer>
71 <valid initial="string.letters,string.digits"><add value="_" /></valid>
72 </sanitizer>
73 </param>
74 <param name="countsFile" type="data" multiple="true" label="Counts file"/>
75 </repeat>
76 </repeat>
77 <param name="report" type="boolean" truevalue="" falsevalue="" checked="true"
78 label="Visualise the analysis results?"
79 help="output an additional html file" />
80 <param name="fdr_cutoff" type="float" min="0" max="1" value="0.05" label="All the genes under this FDR threshold will be shown in the html report."/>
81 </inputs>
82
83 <outputs>
84 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/>
85 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
86 <filter>report == True</filter>
87 </data>
88 </outputs>
89
90 <code file="dexseq_helper.py" />
91 <tests>
92 <test>
93 <param name="gtf" value="dexseq.gtf" ftype="bed"/>
94 <repeat name="rep_factorName">
95 <param name="factorName" value="condition" ftype="bed"/>
96 <repeat name="rep_factorLevel">
97 <param name="factorLevel" type="text" value="knockdown"/>
98 <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
99 </repeat>
100 <repeat name="rep_factorLevel">
101 <param name="factorLevel" type="text" value="knockdown"/>
102 <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
103 </repeat>
104 <repeat name="rep_factorLevel">
105 <param name="factorLevel" type="text" value="knockdown"/>
106 <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
107 </repeat>
108 <repeat name="rep_factorLevel">
109 <param name="factorLevel" type="text" value="control"/>
110 <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
111 </repeat>
112 <repeat name="rep_factorLevel">
113 <param name="factorLevel" type="text" value="control"/>
114 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
115 </repeat>
116 <repeat name="rep_factorLevel">
117 <param name="factorLevel" type="text" value="control"/>
118 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
119 </repeat>
120 <repeat name="rep_factorLevel">
121 <param name="factorLevel" type="text" value="control"/>
122 <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
123 </repeat>
124 </repeat>
125 <repeat name="rep_factorName">
126 <param name="factorName" value="libtype" ftype="bed"/>
127 <repeat name="rep_factorLevel">
128 <param name="factorLevel" type="text" value="singleend"/>
129 <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
130 </repeat>
131 <repeat name="rep_factorLevel">
132 <param name="factorLevel" type="text" value="singleend"/>
133 <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
134 </repeat>
135 <repeat name="rep_factorLevel">
136 <param name="factorLevel" type="text" value="singleend"/>
137 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
138 </repeat>
139 <repeat name="rep_factorLevel">
140 <param name="factorLevel" type="text" value="pairedend"/>
141 <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
142 </repeat>
143 <repeat name="rep_factorLevel">
144 <param name="factorLevel" type="text" value="pairedend"/>
145 <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
146 </repeat>
147 <repeat name="rep_factorLevel">
148 <param name="factorLevel" type="text" value="pairedend"/>
149 <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
150 </repeat>
151 <repeat name="rep_factorLevel">
152 <param name="factorLevel" type="text" value="pairedend"/>
153 <param name="countsFile" ftype="tabular" value="untreated4fb.txt"/>
154 </repeat>
155 </repeat>
156 <param name="report" type="boolean" value="False"/>
157 <param name="fdr_cutoff" value="0.05"/>
158 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
159 </test>
160 </tests>
161 <help>
162 <![CDATA[
163 .. class:: infomark
164
165 **What it does**
166
167 Inference of differential exon usage in RNA-Seq.
168
169
170 **Inputs**
171
172 DEXSeq_ takes count tables that generated from the dexseq_count as input. Count tables must be generated for each sample individually.
173 DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary
174 factor that affects gene expressions. Primary factor should always be named as 'condition'. You also input several secondary factors that might
175 influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states.
176 You need to select appropriate count table from your history for each factor level.
177
178 The following table gives some examples of factors and their levels:
179
180 ========= ============== ===============
181 Factor Factor level 1 Factor level 2
182 --------- -------------- ---------------
183 condition Knockdown Wildtype
184 --------- -------------- ---------------
185 treatment Treated Untreated
186 --------- -------------- ---------------
187 timePoint Day4 Day1
188 --------- -------------- ---------------
189 SeqType SingleEnd PairedEnd
190 --------- -------------- ---------------
191 Gender Female Male
192 ========= ============== ===============
193
194 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'condition' given in above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples.
195
196 **Output**
197
198 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
199
200 ====== ==========================================================
201 Column Description
202 ------ ----------------------------------------------------------
203 1 Gene and exon Identifiers
204 2 group/gene identifier
205 3 feature/exon identifier
206 4 mean of the counts across samples in each feature/exon
207 5 exon dispersion estimate
208 6 LRT statistic
209 7 LRT p-value
210 8 BH adjusted p-values
211 9 exon usage coefficient factorLevel 2
212 10 exon usage coefficient factorLevel 1
213 11 relative exon usage fold changes
214 12 GRanges object of the coordinates of the exon/feature
215 13 matrix of integer counts, of each column containing a sample
216 14 list of transcripts overlapping with the exon
217 ====== ==========================================================
218
219
220 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
221 ]]>
222 </help>
223 <citations>
224 <citation type="doi">10.1101/gr.133744.111</citation>
225 </citations>
226 </tool>