Mercurial > repos > iuc > deseq2
changeset 15:d856341e03c8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit dd85747b08272b72c7161de9b18d19598bb49de1
author | iuc |
---|---|
date | Tue, 31 May 2016 06:24:39 -0400 |
parents | 0fb62f07f8b7 |
children | a7bf54ecfa9d |
files | deseq2.xml tool_dependencies.xml |
diffstat | 2 files changed, 8 insertions(+), 5 deletions(-) [+] |
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--- a/deseq2.xml Wed Dec 02 17:41:10 2015 -0500 +++ b/deseq2.xml Tue May 31 06:24:39 2016 -0400 @@ -52,6 +52,9 @@ #if $outlier_filter_off: -b #end if + #if $auto_mean_filter_off: + -c + #end if #if $many_contrasts: -m #end if @@ -59,7 +62,7 @@ </command> <inputs> <repeat name="rep_factorName" title="Factor" min="1"> - <param name="factorName" type="text" value="FactorName" label="Specify a factor name" + <param name="factorName" type="text" value="FactorName" label="Specify a factor name" help="Only letters, numbers and underscores will be retained in this field"> <sanitizer> <valid initial="string.letters,string.digits"><add value="_" /></valid> @@ -105,7 +108,7 @@ </data> <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> <filter>many_contrasts is True</filter> - <discover_datasets pattern="vs" visible="true"/> + <discover_datasets pattern="None.(?P<designation>.+_vs_.+)" format="tabular" directory="." visible="false"/> </collection> <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> <filter>pdf == True</filter> @@ -133,7 +136,7 @@ <![CDATA[ .. class:: infomark -**What it does** +**What it does** Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution @@ -145,7 +148,7 @@ The following table gives some examples of factors and their levels: ========= ============== =============== -Factor Factor level 1 Factor level 2 +Factor Factor level 1 Factor level 2 --------- -------------- --------------- Treatment Treated Untreated --------- -------------- ---------------
--- a/tool_dependencies.xml Wed Dec 02 17:41:10 2015 -0500 +++ b/tool_dependencies.xml Tue May 31 06:24:39 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="deseq2" version="1.8.2"> - <repository changeset_revision="acbeda52bf87" name="package_deseq2_1_8_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="81a3e281bf21" name="package_deseq2_1_8_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>