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comparison dexseq.xml @ 4:251393b72616 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
author iuc
date Tue, 11 Dec 2018 00:19:18 -0500
parents 6e8b61c54ff3
children 278b189248cd
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3:f89c9b25feb4 4:251393b72616
1 <tool id="dexseq" name="DEXSeq" version="@VERSION@.0"> 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 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="1.20.0">r-getopt</requirement> 7 <requirement type="package" version="1.20.2">r-getopt</requirement>
8 <requirement type="package" version="0.2.15">r-rjson</requirement> 8 <requirement type="package" version="0.2.20">r-rjson</requirement>
9 </expand> 9 </expand>
10 <code file="dexseq_helper.py" /> 10 <code file="dexseq_helper.py" />
11 <stdio> 11 <stdio>
12 <regex match="Execution halted" 12 <regex match="Execution halted"
13 source="both" 13 source="both"
14 level="fatal" 14 level="fatal"
15 description="Execution halted." /> 15 description="Execution halted." />
16 <regex match="Input-Error 01" 16 <regex match="Input-Error 01"
17 source="both" 17 source="both"
18 level="fatal" 18 level="fatal"
19 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> 19 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
20 <regex match="Error in" 20 <regex match="Error in"
21 source="both" 21 source="both"
22 level="fatal" 22 level="fatal"
23 description="An undefined error occured, please check your input carefully and contact your administrator." /> 23 description="An undefined error occured, please check your input carefully and contact your administrator." />
24 <regex match="Error:" 24 <regex match="Error:"
25 source="both" 25 source="both"
26 level="fatal" 26 level="fatal"
27 description="Error in the R script." /> 27 description="Error in the R script." />
28 </stdio> 28 </stdio>
94 label="Visualise the analysis results?" 94 label="Visualise the analysis results?"
95 help="Output an additional HTML file." /> 95 help="Output an additional HTML file." />
96 <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"/> 96 <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 </inputs> 97 </inputs>
98 <outputs> 98 <outputs>
99 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" /> 99 <data name="dexseq_out" format="tabular" label="DEXSeq result file on ${on_string}" />
100 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}"> 100 <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}">
101 <filter>report is True</filter> 101 <filter>report is True</filter>
102 </data> 102 </data>
103 </outputs> 103 </outputs>
104 <tests> 104 <tests>
105 <!-- Ensure default output works--> 105 <!-- Ensure default output works-->
112 <param name="factorLevel2" value="control"/> 112 <param name="factorLevel2" value="control"/>
113 <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"/>
114 </repeat> 114 </repeat>
115 <param name="report" value="False"/> 115 <param name="report" value="False"/>
116 <param name="fdr_cutoff" value="1"/> 116 <param name="fdr_cutoff" value="1"/>
117 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> 117 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
118 </test> 118 </test>
119 <!-- Ensure report works--> 119 <!-- Ensure report works-->
120 <test expect_num_outputs="2"> 120 <test expect_num_outputs="2">
121 <param name="gtf" value="dexseq.gtf" ftype="gtf"/> 121 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
122 <repeat name="rep_factorName"> 122 <repeat name="rep_factorName">
126 <param name="factorLevel2" value="control"/> 126 <param name="factorLevel2" value="control"/>
127 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/> 127 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
128 </repeat> 128 </repeat>
129 <param name="report" value="True"/> 129 <param name="report" value="True"/>
130 <param name="fdr_cutoff" value="1"/> 130 <param name="fdr_cutoff" value="1"/>
131 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> 131 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
132 </test> 132 </test>
133 <!-- Ensure two factors works--> 133 <!-- Ensure two factors works-->
134 <test expect_num_outputs="1"> 134 <test expect_num_outputs="1">
135 <param name="gtf" value="dexseq.gtf" ftype="gtf"/> 135 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
136 <repeat name="rep_factorName"> 136 <repeat name="rep_factorName">
147 <param name="factorLevel2" value="pairedend"/> 147 <param name="factorLevel2" value="pairedend"/>
148 <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"/>
149 </repeat> 149 </repeat>
150 <param name="report" value="False"/> 150 <param name="report" value="False"/>
151 <param name="fdr_cutoff" value="0.05"/> 151 <param name="fdr_cutoff" value="0.05"/>
152 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular"/> 152 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/>
153 </test> 153 </test>
154 </tests> 154 </tests>
155 <help><![CDATA[ 155 <help><![CDATA[
156 .. class:: infomark 156 .. class:: infomark
157 157
161 161
162 162
163 **Inputs** 163 **Inputs**
164 164
165 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.
166 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 affect your experiment. The first factor you input is considered to be the primary
167 factor that affects gene expressions. You also input several secondary factors that might 167 factor that affects gene expressions. You can also input several secondary factors that might
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. 168 influence your experiment but the final output will be changes in genes due to primary factor in the presence of secondary factors. Each factor has two levels/states.
169 You need to select appropriate count table from your history for each factor level. 169 You need to select an appropriate count table from your history for each factor level.
170 170
171 The following table gives some examples of factors and their levels: 171 The following table gives some examples of factors and their levels:
172 172
173 ========= ============== =============== 173 ========= ============== ===============
174 Factor Factor level 1 Factor level 2 174 Factor Factor level 1 Factor level 2
182 SeqType SingleEnd PairedEnd 182 SeqType SingleEnd PairedEnd
183 --------- -------------- --------------- 183 --------- -------------- ---------------
184 Gender Female Male 184 Gender Female Male
185 ========= ============== =============== 185 ========= ============== ===============
186 186
187 *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. 187 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level 2. Here the order of factor levels is important. For example, for the factor 'condition' given in the 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.
188 188
189 **Output** 189 **Output**
190 190
191 DEXSeq_ generates a tabular file containing the different columns and an optional html report. 191 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
192 192