# HG changeset patch
# User fubar
# Date 1374893258 14400
# Node ID c4f8c9a00c0eec130e858d35f12f9761d780f6f6
# Parent  91e77df18a7fb3af6c0597885f43c87a09c9c5c0
Uploaded

diff -r 91e77df18a7f -r c4f8c9a00c0e rgedgeR/rgedgeRpaired.xml
--- a/rgedgeR/rgedgeRpaired.xml	Fri Jul 26 22:04:58 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Fri Jul 26 22:47:38 2013 -0400
@@ -2,7 +2,7 @@
   <description>models using BioConductor packages</description>
   <requirements>
       <requirement type="package" version="2.12">biocbasics</requirement>
-      <requirement type="package" version="3.0.1">package_r3</requirement>
+      <requirement type="package" version="3.0.1">r3</requirement>
   </requirements>
   
   <command interpreter="python">
@@ -76,45 +76,6 @@
       <option value="F" selected="true">Do not run VOOM</option>
       <option value="T">Run VOOM</option>
      </param>
-    <conditional name="camera">
-    <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets" 
-        help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history">
-    <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option>
-    <option value="T">Run GSEA tests with the Camera algorithm</option>
-    </param>
-     <when value="T">
-     <conditional name="gmtSource">
-      <param name="refgmtSource" type="select" 
-         label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set">
-        <option value="indexed" selected="true">Use a built-in gene set</option>
-        <option value="history">Use a gene set from my history</option>
-        <option value="both">Add a gene set from my history to a built in gene set</option>
-      </param>
-      <when value="indexed">
-        <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
-          <options from_data_table="gseaGMT_3.1">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
-      </when>
-      <when value="both">
-        <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" />
-        <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
-          <options from_data_table="gseaGMT_4">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No GMT v4 files are available - please fix tool_data_table and loc files"/>
-          </options>
-        </param>
-       </when>
-     </conditional>
-     </when>
-     <when value="F"> 
-     </when>
-    </conditional>
     <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
      help="Conventional default value of 0.05 recommended"/>
     <param name="fdrtype" type="select" label="FDR (Type II error) control method" 
@@ -145,7 +106,6 @@
  <param name='doedgeR' value='T' />
  <param name='doVoom' value='T' />
  <param name='doDESeq2' value='T' />
- <param name='doCamera' value='T' />
  <param name='fdrtype' value='fdr' />
  <param name='edgeR_priordf' value="8" />
  <param name='fdrthresh' value="0.05" />
@@ -691,7 +651,7 @@
 history_gmt=""
 doDESeq2 = $DESeq2.doDESeq2 # make these T or F
 doVoom = $doVoom
-doCamera = $camera.doCamera
+doCamera = F 
 doedgeR = $edgeR.doedgeR
 edgeR_priordf = 0
 
@@ -702,17 +662,6 @@
 edgeR_priordf = $edgeR.edgeR_priordf
 #end if
 
-#if $camera.doCamera == 'T'
-#if $camera.gmtSource.refgmtSource == "indexed" or $camera.gmtSource.refgmtSource == "both":
-  builtin_gmt = "${camera.gmtSource.builtinGMT.fields.path}"
-#end if
-#if $camera.gmtSource.refgmtSource == "history" or $camera.gmtSource.refgmtSource == "both":
-    history_gmt = "${camera.gmtSource.ownGMT}"
-    history_gmt_name = "${camera.gmtSource.ownGMT.name}"
-  #end if
-#end if
-
-
 
 Out_Dir = "$html_file.files_path"
 Input =  "$input1"
diff -r 91e77df18a7f -r c4f8c9a00c0e rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Fri Jul 26 22:04:58 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Fri Jul 26 22:47:38 2013 -0400
@@ -1,21 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="package_r3" version="3.0.1">
-        <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    <package name="r3" version="3.0.1">
+        <repository changeset_revision="1ffaf8412079" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="biocbasics" version="2.12">
         <install version="1.0"> 
             <actions>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="1ffaf8412079" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="r3" version="3.0.1" />
                     </repository>
                 </action>
                 <action type="make_directory">$INSTALL_DIR</action>
                 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2','gplots')" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T)" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>                
                 <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R  </action>
             </actions>