Mercurial > repos > mingchen0919 > aurora_deseq2

changeset 4:f4b8887aac56 draft

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add deseq2 package
author mingchen0919
date Thu, 08 Mar 2018 21:04:53 -0500
parents caae0a188548
children f4b64fff0dd0
files deseq2.xml
diffstat 1 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/deseq2.xml	Thu Mar 08 21:03:01 2018 -0500
+++ b/deseq2.xml	Thu Mar 08 21:04:53 2018 -0500
@@ -4,6 +4,7 @@
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
         <requirement type="package" version="1.6">r-rmarkdown</requirement>
+        <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
         <requirement type="package" version="4.5.6">r-plotly</requirement>
         <requirement type="package" version="2.2.1">r-ggplot2</requirement>
     </requirements>
@@ -27,7 +28,8 @@
   -F '$untreated'
   -G '$test_type'
   -H '$fit_type'
-  -I '$alpha']]></command>
+  -I '$alpha'
+  -J '$significant_genes']]></command>
     <inputs>
         <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
                label="Display analysis code in report?"/>
@@ -73,6 +75,7 @@
     <outputs>
         <data format="html" name="report" label="tool report"/>
         <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
+        <data name="significant_genes" format="csv" label="signficant genes from ${on_string} " hidden="false"/>
     </outputs>
     <citations>
         <citation type="bibtex"><![CDATA[