Mercurial > repos > iuc > deseq2
changeset 2:9c706d3721ab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 521ea70d49fee701db4d832823644c8c3050f8f2-dirty
| author | iuc |
|---|---|
| date | Fri, 04 Sep 2015 07:11:53 -0400 |
| parents | 522aa36eb845 |
| children | 1ae1da9a5e66 |
| files | deseq2.xml tool_dependencies.xml |
| diffstat | 2 files changed, 12 insertions(+), 4 deletions(-) [+] |
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--- a/deseq2.xml Sun Jul 26 14:33:36 2015 -0400 +++ b/deseq2.xml Fri Sep 04 07:11:53 2015 -0400 @@ -5,7 +5,14 @@ <requirement type="package" version="3.1.0">R</requirement> <requirement type="package" version="1.8.1">deseq2</requirement> </requirements> + <version_command> + <![CDATA[ + echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2) && + cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]> + </version_command> <command interpreter="Rscript"> + <![CDATA[ #import json deseq2.R -o "$deseq_out" @@ -35,6 +42,7 @@ #if $many_contrasts: -m #end if + ]]> </command> <stdio> <regex match="Execution halted" @@ -119,7 +127,7 @@ </test> </tests> <help> - +<![CDATA[ .. class:: infomark **What it does** @@ -167,7 +175,7 @@ .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html - +]]> </help> <citations> <citation type="doi">10.1186/s13059-014-0550-8</citation>
--- a/tool_dependencies.xml Sun Jul 26 14:33:36 2015 -0400 +++ b/tool_dependencies.xml Fri Sep 04 07:11:53 2015 -0400 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="R" version="3.2.0"> - <repository changeset_revision="b689e15fa6fe" name="package_r_3_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d973c8e9b29e" name="package_r_3_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="deseq2" version="1.8.1"> - <repository changeset_revision="747cc19f6fd9" name="package_deseq2_1_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="388cc9221c2c" name="package_deseq2_1_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>