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comparison dexseq.xml @ 5:28a2181df3b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
author iuc
date Thu, 08 Oct 2015 16:49:40 -0400
parents 7069d55968fb
children 469c0d7489bd
comparison
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4:7069d55968fb 5:28a2181df3b9
14 level="fatal" 14 level="fatal"
15 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> 15 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
16 <regex match="Error in" 16 <regex match="Error in"
17 source="both" 17 source="both"
18 level="fatal" 18 level="fatal"
19 description="An undefined error occured, please check your intput carefully and contact your administrator." /> 19 description="An undefined error occured, please check your input carefully and contact your administrator." />
20 <regex match="Error:"
21 source="both"
22 level="fatal"
23 description="Error in the R script." />
20 </stdio> 24 </stdio>
25 <version_command>
26 <![CDATA[
27 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: ")")"
28 ]]>
29 </version_command>
21 <command> 30 <command>
22 <![CDATA[ 31 <![CDATA[
23 mkdir ./html_out && 32 mkdir ./html_out &&
24 #import json 33 #import json
25 Rscript $__tool_directory__/dexseq.R 34 Rscript $__tool_directory__/dexseq.R
26 -o "$dexseq_out" 35 -o "$dexseq_out"
27 -p 6 36 -p \${GALAXY_SLOTS:-4}
28 #set $temp_factor_names = list() 37 #set $temp_factor_names = list()
29 #for $factor in $rep_factorName: 38 #for $factor in $rep_factorName:
30 #set $temp_factor = list() 39 #set $temp_factor = list()
31 #for $level in $factor.rep_factorLevel: 40 #set $count_files1 = list()
32 #set $count_files = list() 41 #for $file in $factor.countFiles1:
33 #for $file in $level.countsFile: 42 $count_files1.append(str($file))
34 $count_files.append(str($file))
35 #end for
36 $temp_factor.append( {str($level.factorLevel): $count_files} )
37 #end for 43 #end for
44 $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
45
46 #set $count_files2 = list()
47 #for $file in $factor.countFiles2:
48 $count_files2.append(str($file))
49 #end for
50 $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
38 $temp_factor_names.append([str($factor.factorName), $temp_factor]) 51 $temp_factor_names.append([str($factor.factorName), $temp_factor])
39 #end for 52 #end for
40 -f '#echo json.dumps(temp_factor_names)#' 53 -f '#echo json.dumps(temp_factor_names)#'
41 -a $gtf 54 -a $gtf
42 -c $fdr_cutoff 55 -c $fdr_cutoff
60 help="Only letters, numbers and underscores will be retained in this field"> 73 help="Only letters, numbers and underscores will be retained in this field">
61 <sanitizer> 74 <sanitizer>
62 <valid initial="string.letters,string.digits"><add value="_" /></valid> 75 <valid initial="string.letters,string.digits"><add value="_" /></valid>
63 </sanitizer> 76 </sanitizer>
64 </param> 77 </param>
65 <repeat name="rep_factorLevel" title="Factor level" min="2" max="2" default="2"> 78 <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"
66 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level" 79 help="Only letters, numbers and underscores will be retained in this field">
67 help="Only letters, numbers and underscores will be retained in this field"> 80 <sanitizer>
68 <sanitizer> 81 <valid initial="string.letters,string.digits"><add value="_" /></valid>
69 <valid initial="string.letters,string.digits"><add value="_" /></valid> 82 </sanitizer>
70 </sanitizer> 83 </param>
71 </param> 84 <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>
72 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/> 85
73 </repeat> 86 <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify a factor level"
87 help="Only letters, numbers and underscores will be retained in this field">
88 <sanitizer>
89 <valid initial="string.letters,string.digits"><add value="_" /></valid>
90 </sanitizer>
91 </param>
92 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
74 </repeat> 93 </repeat>
75 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true" 94 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
76 label="Visualise the analysis results?" 95 label="Visualise the analysis results?"
77 help="Output an additional HTML file." /> 96 help="Output an additional HTML file." />
78 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/> 97 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
83 <filter>report is True</filter> 102 <filter>report is True</filter>
84 </data> 103 </data>
85 </outputs> 104 </outputs>
86 <tests> 105 <tests>
87 <test> 106 <test>
88 <param name="gtf" value="dexseq.gtf" ftype="bed"/> 107 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
89 <repeat name="rep_factorName"> 108 <repeat name="rep_factorName">
90 <param name="factorName" value="condition"/> 109 <param name="factorName" value="condition"/>
91 <repeat name="rep_factorLevel"> 110 <param name="factorLevel1" value="knockdown"/>
92 <param name="factorLevel" value="knockdown"/> 111 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
93 <param name="countsFile" value="treated1fb.txt,treated2fb.txt,treated3fb.txt"/> 112 <param name="factorLevel2" value="control"/>
94 </repeat> 113 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
95 <repeat name="rep_factorLevel">
96 <param name="factorLevel" value="control"/>
97 <param name="countsFile" value="untreated1fb.txt,untreated2fb.txt,untreated2fb.txt,untreated3fb.txt"/>
98 </repeat>
99 </repeat> 114 </repeat>
100 <repeat name="rep_factorName"> 115 <repeat name="rep_factorName">
101 <param name="factorName" value="libtype"/> 116 <param name="factorName" value="libtype"/>
102 <repeat name="rep_factorLevel"> 117 <param name="factorLevel1" value="singleend"/>
103 <param name="factorLevel" value="singleend"/> 118 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
104 <param name="countsFile" ftype="tabular" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt"/> 119 <param name="factorLevel2" value="pairedend"/>
105 </repeat> 120 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
106 <repeat name="rep_factorLevel">
107 <param name="factorLevel" value="pairedend"/>
108 <param name="countsFile" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt"/>
109 </repeat>
110 </repeat> 121 </repeat>
111 <param name="report" value="False"/> 122 <param name="report" value="False"/>
112 <param name="fdr_cutoff" value="0.05"/> 123 <param name="fdr_cutoff" value="0.05"/>
113 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> 124 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
114 </test> 125 </test>
122 Inference of differential exon usage in RNA-Seq. 133 Inference of differential exon usage in RNA-Seq.
123 134
124 135
125 **Inputs** 136 **Inputs**
126 137
127 DEXSeq_ takes count tables that generated from the dexseq_count as input. Count tables must be generated for each sample individually. 138 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
128 DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary 139 DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary
129 factor that affects gene expressions. Primary factor should always be named as 'condition'. You also input several secondary factors that might 140 factor that affects gene expressions. Primary factor should always be named as 'condition'. You also input several secondary factors that might
130 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. 141 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.
131 You need to select appropriate count table from your history for each factor level. 142 You need to select appropriate count table from your history for each factor level.
132 143