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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
author iuc
date Sun, 28 Jan 2018 04:04:39 -0500
parents f1c406f9554c
children 251393b72616
comparison
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1:f1c406f9554c 2:6e8b61c54ff3
1 <tool id="dexseq" name="DEXSeq" version="1.20.1"> 1 <tool id="dexseq" name="DEXSeq" version="@VERSION@.0">
2 <description>Determines differential exon usage from count tables</description> 2 <description>Determines differential exon usage from count tables</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
5 <requirement type="package" version="1.20.0">r-getopt</requirement> 7 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <requirement type="package" version="0.2.15">r-rjson</requirement> 8 <requirement type="package" version="0.2.15">r-rjson</requirement>
7 </requirements> 9 </expand>
8 <code file="dexseq_helper.py" /> 10 <code file="dexseq_helper.py" />
9 <stdio> 11 <stdio>
10 <regex match="Execution halted" 12 <regex match="Execution halted"
11 source="both" 13 source="both"
12 level="fatal" 14 level="fatal"
22 <regex match="Error:" 24 <regex match="Error:"
23 source="both" 25 source="both"
24 level="fatal" 26 level="fatal"
25 description="Error in the R script." /> 27 description="Error in the R script." />
26 </stdio> 28 </stdio>
27 <version_command> 29 <version_command><![CDATA[
28 <![CDATA[ 30 echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
29 echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")" 31 ]]></version_command>
30 ]]> 32 <command><![CDATA[
31 </version_command> 33 mkdir ./html_out &&
32 <command> 34 #import json
33 <![CDATA[ 35 Rscript '$__tool_directory__/dexseq.R'
34 mkdir ./html_out && 36 -o '$dexseq_out'
35 #import json 37 -p \${GALAXY_SLOTS:-4}
36 Rscript '$__tool_directory__/dexseq.R' 38 #set $temp_factor_names = list()
37 -o '$dexseq_out' 39 #for $factor in $rep_factorName:
38 -p \${GALAXY_SLOTS:-4} 40 #set $temp_factor = list()
39 #set $temp_factor_names = list() 41 #set $count_files1 = list()
40 #for $factor in $rep_factorName: 42 #for $file in $factor.countFiles1:
41 #set $temp_factor = list() 43 $count_files1.append(str($file))
42 #set $count_files1 = list() 44 #end for
43 #for $file in $factor.countFiles1: 45 $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
44 $count_files1.append(str($file)) 46
45 #end for 47 #set $count_files2 = list()
46 $temp_factor.append( {str($factor.factorLevel1): $count_files1} ) 48 #for $file in $factor.countFiles2:
47 49 $count_files2.append(str($file))
48 #set $count_files2 = list() 50 #end for
49 #for $file in $factor.countFiles2: 51 $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
50 $count_files2.append(str($file)) 52 $temp_factor_names.append([str($factor.factorName), $temp_factor])
51 #end for 53 #end for
52 $temp_factor.append( {str($factor.factorLevel2): $count_files2} ) 54 -f '#echo json.dumps(temp_factor_names)#'
53 $temp_factor_names.append([str($factor.factorName), $temp_factor]) 55 -a $gtf
54 #end for 56 -c $fdr_cutoff
55 -f '#echo json.dumps(temp_factor_names)#' 57
56 -a $gtf 58 #if $report:
57 -c $fdr_cutoff 59 -r ./html_out
58 60 &&
59 #if $report: 61 mkdir '$htmlreport.extra_files_path'
60 -r ./html_out 62 &&
61 && 63 cp ./html_out/testForDEU.html $htmlreport
62 mkdir '$htmlreport.extra_files_path' 64 &&
63 && 65 cp -r ./html_out/* '$htmlreport.extra_files_path'
64 cp ./html_out/testForDEU.html $htmlreport 66 #end if
65 && 67 ]]></command>
66 cp -r ./html_out/* '$htmlreport.extra_files_path'
67 #end if
68
69 ]]>
70 </command>
71 <inputs> 68 <inputs>
72 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/> 69 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
73 <repeat name="rep_factorName" title="Factor" min="1"> 70 <repeat name="rep_factorName" title="Factor" min="1">
74 <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 71 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
75 help="Only letters, numbers and underscores will be retained in this field"> 72 help="Only letters, numbers and underscores will be retained in this field">
103 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}"> 100 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
104 <filter>report is True</filter> 101 <filter>report is True</filter>
105 </data> 102 </data>
106 </outputs> 103 </outputs>
107 <tests> 104 <tests>
108 <test> 105 <!-- Ensure default output works-->
106 <test expect_num_outputs="1">
109 <param name="gtf" value="dexseq.gtf" ftype="gtf"/> 107 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
110 <repeat name="rep_factorName"> 108 <repeat name="rep_factorName">
111 <param name="factorName" value="condition"/> 109 <param name="factorName" value="condition"/>
112 <param name="factorLevel1" value="knockdown"/> 110 <param name="factorLevel1" value="knockdown"/>
113 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/> 111 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
114 <param name="factorLevel2" value="control"/> 112 <param name="factorLevel2" value="control"/>
115 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/> 113 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
116 </repeat> 114 </repeat>
115 <param name="report" value="False"/>
116 <param name="fdr_cutoff" value="1"/>
117 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
118 </test>
119 <!-- Ensure report works-->
120 <test expect_num_outputs="2">
121 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
122 <repeat name="rep_factorName">
123 <param name="factorName" value="Treatment"/>
124 <param name="factorLevel1" value="knockdown"/>
125 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
126 <param name="factorLevel2" value="control"/>
127 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
128 </repeat>
129 <param name="report" value="True"/>
130 <param name="fdr_cutoff" value="1"/>
131 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
132 </test>
133 <!-- Ensure two factors works-->
134 <test expect_num_outputs="1">
135 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
136 <repeat name="rep_factorName">
137 <param name="factorName" value="condition"/>
138 <param name="factorLevel1" value="knockdown"/>
139 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
140 <param name="factorLevel2" value="control"/>
141 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
142 </repeat>
117 <repeat name="rep_factorName"> 143 <repeat name="rep_factorName">
118 <param name="factorName" value="libtype"/> 144 <param name="factorName" value="libtype"/>
119 <param name="factorLevel1" value="singleend"/> 145 <param name="factorLevel1" value="singleend"/>
120 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/> 146 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
121 <param name="factorLevel2" value="pairedend"/> 147 <param name="factorLevel2" value="pairedend"/>
122 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/> 148 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
123 </repeat> 149 </repeat>
124 <param name="report" value="False"/> 150 <param name="report" value="False"/>
125 <param name="fdr_cutoff" value="0.05"/> 151 <param name="fdr_cutoff" value="0.05"/>
126 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> 152 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular"/>
127 </test> 153 </test>
128 </tests> 154 </tests>
129 <help> 155 <help><![CDATA[
130 <![CDATA[
131 .. class:: infomark 156 .. class:: infomark
132 157
133 **What it does** 158 **What it does**
134 159
135 Inference of differential exon usage in RNA-Seq. 160 Inference of differential exon usage in RNA-Seq.
137 162
138 **Inputs** 163 **Inputs**
139 164
140 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually. 165 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
141 DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary 166 DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary
142 factor that affects gene expressions. Primary factor should always be named as 'condition'. You also input several secondary factors that might 167 factor that affects gene expressions. You also input several secondary factors that might
143 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. 168 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.
144 You need to select appropriate count table from your history for each factor level. 169 You need to select appropriate count table from your history for each factor level.
145 170
146 The following table gives some examples of factors and their levels: 171 The following table gives some examples of factors and their levels:
147 172
184 14 list of transcripts overlapping with the exon 209 14 list of transcripts overlapping with the exon
185 ====== ========================================================== 210 ====== ==========================================================
186 211
187 212
188 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html 213 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
189 ]]> 214 ]]></help>
190 </help>
191 <citations> 215 <citations>
192 <citation type="doi">10.1101/gr.133744.111</citation> 216 <citation type="doi">10.1101/gr.133744.111</citation>
193 </citations> 217 </citations>
194 </tool> 218 </tool>