Mercurial > repos > fubar > rglasso_1_9_8

changeset 15:1948c6a82a9b draft

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Uploaded
author iuc
date Wed, 18 Feb 2015 11:37:11 -0500
parents a061150f1d94
children fa6d1e1a84c9
files rg_nri.xml rglasso_cox.xml test-data/coxlassotest.html tool_dependencies.xml
diffstat 4 files changed, 19 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/rg_nri.xml	Tue Jan 27 06:16:16 2015 -0500
+++ b/rg_nri.xml	Wed Feb 18 11:37:11 2015 -0500
@@ -1,7 +1,7 @@
-<tool id="rg_nri" name="NRI" version="0.04">
+<tool id="rg_nri" name="NRI" version="0.03">
   <description>and other model improvement measures</description>
   <requirements>
-      <requirement type="package" version="3.1.2">R</requirement>
+      <requirement type="package" version="3.1.1">R_3_1_1</requirement>
       <requirement type="package" version="1.3.18">graphicsmagick</requirement>
       <requirement type="package" version="9.10">ghostscript</requirement>
       <requirement type="package" version="2.14">glmnet_lars_2_14</requirement>
--- a/rglasso_cox.xml	Tue Jan 27 06:16:16 2015 -0500
+++ b/rglasso_cox.xml	Wed Feb 18 11:37:11 2015 -0500
@@ -1,7 +1,7 @@
-<tool id="rglasso_cox" name="Lasso" version="0.04">
+<tool id="rglasso_cox" name="Lasso" version="0.03">
   <description>and cox regression using elastic net</description>
   <requirements>
-      <requirement type="package" version="3.1.2">R</requirement>
+      <requirement type="package" version="3.1.1">R_3_1_1</requirement>
       <requirement type="package" version="1.3.18">graphicsmagick</requirement>
       <requirement type="package" version="9.10">ghostscript</requirement>
       <requirement type="package" version="2.14">glmnet_lars_2_14</requirement>
@@ -132,7 +132,7 @@
      <param name='do_standard' value="True" />
      <param name='cox_time' value='1' />
      <param name='cox_status' value='2' />
-     <param name='cox_id' value='2' />
+     <param name='cox_id' value='1' />
      <param name='predict_at' value='' />
      <param name='fam' value='cox' />
      <param name='yvar_cols' value='' />
@@ -150,7 +150,7 @@
                 <has_n_columns n="7" />
            </assert_contents>
      </output>
-     <output name='html_file' file='coxlassotest.html'  compare='diff' lines_diff='10' />
+     <output name='html_file' file='coxlassotest.html'  compare='diff' lines_diff='16' />
     </test>
 </tests>
 <help>
--- a/test-data/coxlassotest.html	Tue Jan 27 06:16:16 2015 -0500
+++ b/test-data/coxlassotest.html	Wed Feb 18 11:37:11 2015 -0500
@@ -8,7 +8,7 @@
         <body> 
         <div class="toolFormBody"> 
         
-<div class="infomessage">Galaxy Tool "rglasso" run at 28/12/2014 13:07:57</div><br/>
+<div class="infomessage">Galaxy Tool "rglasso" run at 18/02/2015 22:06:08</div><br/>
 <div class="toolFormTitle">cox images and outputs</div>
 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
 <div><table class="simple" cellpadding="2" cellspacing="2">
@@ -34,9 +34,7 @@
 
 rhubarb               10              10
 
-vegemite               3              10
-
-apple                  0               1
+vegemite               6               6
 
 [1] @@@ Results preview:
 
@@ -104,9 +102,9 @@
 
 [1] @@@ SessionInfo for this R session:
 
-R version 3.0.2 (2013-09-25)
+R version 3.1.0 (2014-04-10)
 
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-unknown-linux-gnu (64-bit)
 
 locale:
 
@@ -118,11 +116,11 @@
 
 other attached packages:
 
-[1] pec_2.4.4       survival_2.37-7 lars_1.2        glmnet_1.9-8    Matrix_1.1-4   
+[1] pec_2.4.4       survival_2.37-7 lars_1.2        glmnet_1.9-8    Matrix_1.1-5   
 
 loaded via a namespace (and not attached):
 
-[1] codetools_0.2-9 foreach_1.4.2   grid_3.0.2      iterators_1.0.7 lattice_0.20-29 lava_1.3        prodlim_1.5.1  
+[1] codetools_0.2-10 foreach_1.4.2    grid_3.1.0       iterators_1.0.7  lattice_0.20-29  lava_1.3         prodlim_1.5.1   
 
 Warning messages:
 
@@ -157,10 +155,10 @@
 
 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
 
-<tr><td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf">cox_Coxglmnettest_glmnet_cvdeviance.pdf</a></td><td>6.3 KB</td></tr>
+<tr><td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf">cox_Coxglmnettest_glmnet_cvdeviance.pdf</a></td><td>6.4 KB</td></tr>
 <tr class="odd_row"><td><a href="cox_Coxglmnettest_glmnetdev.pdf">cox_Coxglmnettest_glmnetdev.pdf</a></td><td>5.3 KB</td></tr>
-<tr><td><a href="cox_cross_validation_model_counts.xls">cox_cross_validation_model_counts.xls</a></td><td>47 B</td></tr>
-<tr class="odd_row"><td><a href="cox_rglasso.log">cox_rglasso.log</a></td><td>563 B</td></tr>
+<tr><td><a href="cox_cross_validation_model_counts.xls">cox_cross_validation_model_counts.xls</a></td><td>42 B</td></tr>
+<tr class="odd_row"><td><a href="cox_rglasso.log">cox_rglasso.log</a></td><td>522 B</td></tr>
 <tr><td><a href="rglasso.Rscript">rglasso.Rscript</a></td><td>21.5 KB</td></tr>
 <tr class="odd_row"><td><a href="rglasso_error.log">rglasso_error.log</a></td><td>803 B</td></tr>
 <tr><td><a href="rglasso_runner.log">rglasso_runner.log</a></td><td>1.7 KB</td></tr>
--- a/tool_dependencies.xml	Tue Jan 27 06:16:16 2015 -0500
+++ b/tool_dependencies.xml	Wed Feb 18 11:37:11 2015 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R" version="3.1.2">
-        <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="R_3_1_1" version="3.1.1">
+        <repository changeset_revision="63cdb9b2234c" name="package_r_3_1_1" owner="fubar" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="graphicsmagick" version="1.3.18">
         <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -13,8 +13,8 @@
         <install version="1.0">
             <actions>
                 <action type="setup_r_environment">
-                    <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="R" version="3.1.2" />
+                    <repository changeset_revision="63cdb9b2234c" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="R_3_1_1" version="3.1.1" />
                     </repository>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/RColorBrewer_1.1-2.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/MASS_7.3-35.tar.gz?raw=true</package>
@@ -79,8 +79,6 @@
         </install>
         <readme>
         Yee-Haw! Lasso for Galaxy!
-        Uses glmnet from the R CRAN.
-        See http://web.stanford.edu/~hastie/glmnet/glmnet_alpha.html
         </readme>
     </package>
 </tool_dependency>