Mercurial > repos > iuc > dexseq
changeset 4:7069d55968fb draft
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 |
files | dexseq.xml tool_dependencies.xml |
diffstat | 2 files changed, 29 insertions(+), 68 deletions(-) [+] |
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--- a/dexseq.xml Fri Sep 25 16:26:39 2015 -0400 +++ b/dexseq.xml Sun Sep 27 14:06:28 2015 -0400 @@ -13,9 +13,9 @@ source="both" level="fatal" description="Error in your input parameters: Make sure you only apply factors to selected samples." /> - <regex match="Error in" - source="both" - level="fatal" + <regex match="Error in" + source="both" + level="fatal" description="An undefined error occured, please check your intput carefully and contact your administrator." /> </stdio> <command> @@ -39,17 +39,18 @@ #end for -f '#echo json.dumps(temp_factor_names)#' -a $gtf + -c $fdr_cutoff + #if $report: -r ./html_out + && + mkdir $htmlreport.extra_files_path + && + cp ./html_out/testForDEU.html $htmlreport + && + cp -r ./html_out/* $htmlreport.extra_files_path #end if - -c $fdr_cutoff - && - mkdir $htmlreport.extra_files_path - && - cp ./html_out/testForDEU.html $htmlreport - && - cp -r ./html_out/* $htmlreport.extra_files_path - && + ]]> </command> <inputs> @@ -71,83 +72,43 @@ <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/> </repeat> </repeat> - <param name="report" type="boolean" truevalue="" falsevalue="" checked="true" + <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Visualise the analysis results?" - help="output an additional html file" /> - <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."/> + help="Output an additional HTML file." /> + <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"/> </inputs> <outputs> - <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/> + <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" /> <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}"> - <filter>report == True</filter> + <filter>report is True</filter> </data> </outputs> <tests> <test> <param name="gtf" value="dexseq.gtf" ftype="bed"/> <repeat name="rep_factorName"> - <param name="factorName" value="condition" ftype="bed"/> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="knockdown"/> - <param name="countsFile" ftype="tabular" value="treated1fb.txt"/> - </repeat> + <param name="factorName" value="condition"/> <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="knockdown"/> - <param name="countsFile" ftype="tabular" value="treated2fb.txt"/> - </repeat> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="knockdown"/> - <param name="countsFile" ftype="tabular" value="treated3fb.txt"/> + <param name="factorLevel" value="knockdown"/> + <param name="countsFile" value="treated1fb.txt,treated2fb.txt,treated3fb.txt"/> </repeat> <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="control"/> - <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/> - </repeat> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="control"/> - <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/> - </repeat> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="control"/> - <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/> - </repeat> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="control"/> - <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/> + <param name="factorLevel" value="control"/> + <param name="countsFile" value="untreated1fb.txt,untreated2fb.txt,untreated2fb.txt,untreated3fb.txt"/> </repeat> </repeat> <repeat name="rep_factorName"> - <param name="factorName" value="libtype" ftype="bed"/> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="singleend"/> - <param name="countsFile" ftype="tabular" value="treated1fb.txt"/> - </repeat> + <param name="factorName" value="libtype"/> <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="singleend"/> - <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/> - </repeat> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="singleend"/> - <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/> + <param name="factorLevel" value="singleend"/> + <param name="countsFile" ftype="tabular" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt"/> </repeat> <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="pairedend"/> - <param name="countsFile" ftype="tabular" value="treated2fb.txt"/> - </repeat> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="pairedend"/> - <param name="countsFile" ftype="tabular" value="treated3fb.txt"/> - </repeat> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="pairedend"/> - <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/> - </repeat> - <repeat name="rep_factorLevel"> - <param name="factorLevel" type="text" value="pairedend"/> - <param name="countsFile" ftype="tabular" value="untreated4fb.txt"/> + <param name="factorLevel" value="pairedend"/> + <param name="countsFile" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt"/> </repeat> </repeat> - <param name="report" type="boolean" value="False"/> + <param name="report" value="False"/> <param name="fdr_cutoff" value="0.05"/> <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> </test>
--- a/tool_dependencies.xml Fri Sep 25 16:26:39 2015 -0400 +++ b/tool_dependencies.xml Sun Sep 27 14:06:28 2015 -0400 @@ -7,6 +7,6 @@ <repository changeset_revision="025da27a2bb2" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="dexseq" version="1.14"> - <repository changeset_revision="cb7ad0ece9e8" name="package_dexseq_1_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d8a45cbc4208" name="package_dexseq_1_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>