Mercurial > repos > iuc > dexseq

comparison dexseq.xml @ 11:577d1c8baab4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
author iuc
date Mon, 14 Jan 2019 05:01:42 -0500
parents 6f684b3b0a6d
children e5fe98b50c21
comparison
equal deleted inserted replaced
10:6f684b3b0a6d 11:577d1c8baab4
1 <tool id="dexseq" name="DEXSeq" version="@VERSION@.0"> 1 <tool id="dexseq" name="DEXSeq" version="@VERSION@+galaxy1">
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">
52 $temp_factor_names.append([str($factor.factorName), $temp_factor]) 52 $temp_factor_names.append([str($factor.factorName), $temp_factor])
53 #end for 53 #end for
54 -f '#echo json.dumps(temp_factor_names)#' 54 -f '#echo json.dumps(temp_factor_names)#'
55 -a $gtf 55 -a $gtf
56 -c $fdr_cutoff 56 -c $fdr_cutoff
57 -d $rds
57 58
58 #if $report: 59 #if $report:
59 -r ./html_out 60 -r ./html_out
60 && 61 &&
61 mkdir '$htmlreport.extra_files_path' 62 mkdir '$htmlreport.extra_files_path'
91 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/> 92 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
92 </repeat> 93 </repeat>
93 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true" 94 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
94 label="Visualise the analysis results?" 95 label="Visualise the analysis results?"
95 help="Output an additional HTML file." /> 96 help="Output an additional HTML file." />
97 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false"
98 label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" />
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"/> 99 <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> 100 </inputs>
98 <outputs> 101 <outputs>
99 <data name="dexseq_out" format="tabular" label="DEXSeq result file on ${on_string}" /> 102 <data name="dexseq_out" format="tabular" label="DEXSeq result file on ${on_string}" />
100 <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}"> 103 <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}">
101 <filter>report is True</filter> 104 <filter>report is True</filter>
102 </data> 105 </data>
106 <data name="rds_out" format="rdata" from_work_dir="DEXSeqResults.rds" label="DEXSeq rds file on ${on_string}">
107 <filter>rds is True</filter>
108 </data>
103 </outputs> 109 </outputs>
104 <tests> 110 <tests>
105 <!-- Ensure default output works--> 111 <!-- Ensure default output works-->
106 <test expect_num_outputs="1"> 112 <test expect_num_outputs="1">
107 <param name="gtf" value="dexseq.gtf" ftype="gtf"/> 113 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
149 </repeat> 155 </repeat>
150 <param name="report" value="False"/> 156 <param name="report" value="False"/>
151 <param name="fdr_cutoff" value="0.05"/> 157 <param name="fdr_cutoff" value="0.05"/>
152 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/> 158 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/>
153 </test> 159 </test>
160 <!-- Ensure rds output works-->
161 <test expect_num_outputs="2">
162 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
163 <repeat name="rep_factorName">
164 <param name="factorName" value="condition"/>
165 <param name="factorLevel1" value="knockdown"/>
166 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
167 <param name="factorLevel2" value="control"/>
168 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
169 </repeat>
170 <param name="report" value="False"/>
171 <param name="rds" value="True"/>
172 <param name="fdr_cutoff" value="0.05"/>
173 <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/>
174 <output name="rds_out" ftype="rdata" file="dexseq.rds" compare="sim_size"/>
175 </test>
154 </tests> 176 </tests>
155 <help><![CDATA[ 177 <help><![CDATA[
156 .. class:: infomark 178 .. class:: infomark
157 179
158 **What it does** 180 **What it does**
186 208
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. 209 *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.
188 210
189 **Output** 211 **Output**
190 212
191 DEXSeq_ generates a tabular file containing the different columns and an optional html report. 213 DEXSeq_ generates a tabular file containing the different columns and an optional html report. It can also ouput the DEXSeqResults R object that can be used with the plotDEXSeq tool to visualise individual genes.
192 214
193 ====== ========================================================== 215 ====== ==========================================================
194 Column Description 216 Column Description
195 ------ ---------------------------------------------------------- 217 ------ ----------------------------------------------------------
196 1 Gene and exon Identifiers 218 1 Gene and exon Identifiers