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comparison dexseq.xml @ 4:7069d55968fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
author iuc
date Sun, 27 Sep 2015 14:06:28 -0400
parents a26a82bed63f
children 28a2181df3b9
comparison
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3:a26a82bed63f 4:7069d55968fb
11 description="Execution halted." /> 11 description="Execution halted." />
12 <regex match="Input-Error 01" 12 <regex match="Input-Error 01"
13 source="both" 13 source="both"
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 intput carefully and contact your administrator." />
20 </stdio> 20 </stdio>
21 <command> 21 <command>
22 <![CDATA[ 22 <![CDATA[
23 mkdir ./html_out && 23 mkdir ./html_out &&
37 #end for 37 #end for
38 $temp_factor_names.append([str($factor.factorName), $temp_factor]) 38 $temp_factor_names.append([str($factor.factorName), $temp_factor])
39 #end for 39 #end for
40 -f '#echo json.dumps(temp_factor_names)#' 40 -f '#echo json.dumps(temp_factor_names)#'
41 -a $gtf 41 -a $gtf
42 -c $fdr_cutoff
43
42 #if $report: 44 #if $report:
43 -r ./html_out 45 -r ./html_out
46 &&
47 mkdir $htmlreport.extra_files_path
48 &&
49 cp ./html_out/testForDEU.html $htmlreport
50 &&
51 cp -r ./html_out/* $htmlreport.extra_files_path
44 #end if 52 #end if
45 -c $fdr_cutoff 53
46 &&
47 mkdir $htmlreport.extra_files_path
48 &&
49 cp ./html_out/testForDEU.html $htmlreport
50 &&
51 cp -r ./html_out/* $htmlreport.extra_files_path
52 &&
53 ]]> 54 ]]>
54 </command> 55 </command>
55 <inputs> 56 <inputs>
56 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/> 57 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
57 <repeat name="rep_factorName" title="Factor" min="1"> 58 <repeat name="rep_factorName" title="Factor" min="1">
69 </sanitizer> 70 </sanitizer>
70 </param> 71 </param>
71 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/> 72 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/>
72 </repeat> 73 </repeat>
73 </repeat> 74 </repeat>
74 <param name="report" type="boolean" truevalue="" falsevalue="" checked="true" 75 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
75 label="Visualise the analysis results?" 76 label="Visualise the analysis results?"
76 help="output an additional html file" /> 77 help="Output an additional HTML file." />
77 <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."/> 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"/>
78 </inputs> 79 </inputs>
79 <outputs> 80 <outputs>
80 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/> 81 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" />
81 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}"> 82 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
82 <filter>report == True</filter> 83 <filter>report is True</filter>
83 </data> 84 </data>
84 </outputs> 85 </outputs>
85 <tests> 86 <tests>
86 <test> 87 <test>
87 <param name="gtf" value="dexseq.gtf" ftype="bed"/> 88 <param name="gtf" value="dexseq.gtf" ftype="bed"/>
88 <repeat name="rep_factorName"> 89 <repeat name="rep_factorName">
89 <param name="factorName" value="condition" ftype="bed"/> 90 <param name="factorName" value="condition"/>
90 <repeat name="rep_factorLevel"> 91 <repeat name="rep_factorLevel">
91 <param name="factorLevel" type="text" value="knockdown"/> 92 <param name="factorLevel" value="knockdown"/>
92 <param name="countsFile" ftype="tabular" value="treated1fb.txt"/> 93 <param name="countsFile" value="treated1fb.txt,treated2fb.txt,treated3fb.txt"/>
93 </repeat> 94 </repeat>
94 <repeat name="rep_factorLevel"> 95 <repeat name="rep_factorLevel">
95 <param name="factorLevel" type="text" value="knockdown"/> 96 <param name="factorLevel" value="control"/>
96 <param name="countsFile" ftype="tabular" value="treated2fb.txt"/> 97 <param name="countsFile" value="untreated1fb.txt,untreated2fb.txt,untreated2fb.txt,untreated3fb.txt"/>
97 </repeat>
98 <repeat name="rep_factorLevel">
99 <param name="factorLevel" type="text" value="knockdown"/>
100 <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
101 </repeat>
102 <repeat name="rep_factorLevel">
103 <param name="factorLevel" type="text" value="control"/>
104 <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
105 </repeat>
106 <repeat name="rep_factorLevel">
107 <param name="factorLevel" type="text" value="control"/>
108 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
109 </repeat>
110 <repeat name="rep_factorLevel">
111 <param name="factorLevel" type="text" value="control"/>
112 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
113 </repeat>
114 <repeat name="rep_factorLevel">
115 <param name="factorLevel" type="text" value="control"/>
116 <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
117 </repeat> 98 </repeat>
118 </repeat> 99 </repeat>
119 <repeat name="rep_factorName"> 100 <repeat name="rep_factorName">
120 <param name="factorName" value="libtype" ftype="bed"/> 101 <param name="factorName" value="libtype"/>
121 <repeat name="rep_factorLevel"> 102 <repeat name="rep_factorLevel">
122 <param name="factorLevel" type="text" value="singleend"/> 103 <param name="factorLevel" value="singleend"/>
123 <param name="countsFile" ftype="tabular" value="treated1fb.txt"/> 104 <param name="countsFile" ftype="tabular" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt"/>
124 </repeat> 105 </repeat>
125 <repeat name="rep_factorLevel"> 106 <repeat name="rep_factorLevel">
126 <param name="factorLevel" type="text" value="singleend"/> 107 <param name="factorLevel" value="pairedend"/>
127 <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/> 108 <param name="countsFile" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt"/>
128 </repeat>
129 <repeat name="rep_factorLevel">
130 <param name="factorLevel" type="text" value="singleend"/>
131 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
132 </repeat>
133 <repeat name="rep_factorLevel">
134 <param name="factorLevel" type="text" value="pairedend"/>
135 <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
136 </repeat>
137 <repeat name="rep_factorLevel">
138 <param name="factorLevel" type="text" value="pairedend"/>
139 <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
140 </repeat>
141 <repeat name="rep_factorLevel">
142 <param name="factorLevel" type="text" value="pairedend"/>
143 <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
144 </repeat>
145 <repeat name="rep_factorLevel">
146 <param name="factorLevel" type="text" value="pairedend"/>
147 <param name="countsFile" ftype="tabular" value="untreated4fb.txt"/>
148 </repeat> 109 </repeat>
149 </repeat> 110 </repeat>
150 <param name="report" type="boolean" value="False"/> 111 <param name="report" value="False"/>
151 <param name="fdr_cutoff" value="0.05"/> 112 <param name="fdr_cutoff" value="0.05"/>
152 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> 113 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
153 </test> 114 </test>
154 </tests> 115 </tests>
155 <help> 116 <help>