# HG changeset patch
# User fubar
# Date 1420697120 18000
# Node ID 445cb45d1bc09b93a2c065e9a10c04fea600d599
# Parent  12c26de8c872c3e7872b1689d7eccfeff1f6e609
Uploaded

diff -r 12c26de8c872 -r 445cb45d1bc0 rg_nri.xml
--- a/rg_nri.xml	Wed Jan 07 07:50:21 2015 -0500
+++ b/rg_nri.xml	Thu Jan 08 01:05:20 2015 -0500
@@ -48,8 +48,14 @@
   </outputs>
  <tests>
     <test>
+     <param name='title' value='nri_test1' />
      <param name='input1' value='nri_test1.xls' ftype='tabular' />
-     <param name='input2' value='nri_test2.xls' ftype='tabular' />
+     <param name='input2' value='nri_test1.xls' ftype='tabular' />
+     <param name='input1_id' value="1" />
+     <param name='input1_observed' value="2" />
+     <param name='input1_predicted' value="3" />
+     <param name='input2_observed' value="2" />
+     <param name='input2_predicted' value="4" />
      <output name='html_file' file='nri_test1_out.html'  compare='diff' lines_diff='10' />
      <output name='nri_file' file='nri_test1_out.xls' />
     </test>
diff -r 12c26de8c872 -r 445cb45d1bc0 test-data/genTest.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genTest.R	Thu Jan 08 01:05:20 2015 -0500
@@ -0,0 +1,10 @@
+ids=c(1:50)
+io1 = rep(c(0,0,0,0,1),10)
+ip2 = runif(50)+0.1
+ip2[which(ip2>1.0)] = 1.0
+ip1 = runif(50)+0.05
+ip1[which(ip1>1.0)] = 1.0
+df=data.frame(id=ids,input1_observed=io1,input1_predicted=ip1,input2_predicted=ip2)
+fout='test-data/nri_test1.xls'
+write.table(df,file=fout, quote=FALSE, sep="\t",row.names=F)
+# planemo test --job_output_files /home/rlazarus/tmp --test_output /home/rlazarus/tmp/startest/foo.html --update_test_data --galaxy_root /home/rlazarus/galaxy rg_nri.xml
diff -r 12c26de8c872 -r 445cb45d1bc0 test-data/nri_test1.xls
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nri_test1.xls	Thu Jan 08 01:05:20 2015 -0500
@@ -0,0 +1,51 @@
+id	input1_observed	input1_predicted	input2_predicted
+1	0	0.431491391919553	0.786344331596047
+2	0	0.235500678373501	0.37771512279287
+3	0	0.458084875205532	0.343597211781889
+4	0	0.400509147858247	0.50323077281937
+5	1	0.463376078708097	0.28904068809934
+6	0	0.638350193109363	0.745497886231169
+7	0	0.909975615050644	1
+8	0	0.0712537909392267	0.613464191928506
+9	0	0.475019342219457	0.757945845043287
+10	1	0.146289554610848	0.948540200153366
+11	0	0.947521302569658	0.452743433788419
+12	0	0.512624199455604	0.107415618747473
+13	0	0.260238706320524	0.165854234388098
+14	0	0.252348658815026	0.866530107706785
+15	1	0.552841167151928	0.781692814920098
+16	0	0.203356911847368	0.397802447108552
+17	0	0.138653858751059	0.966900746012107
+18	0	0.237485485337675	0.126699626818299
+19	0	0.317045996850356	0.646952681383118
+20	1	0.271802965737879	0.828731852956116
+21	0	0.522744563594461	0.421856845868751
+22	0	0.819749742234126	0.628745510149747
+23	0	0.27876661689952	0.826974717108533
+24	0	0.077877387823537	0.12339704008773
+25	1	0.911161796143279	1
+26	0	0.567042255960405	1
+27	0	0.223712538788095	0.738010874623433
+28	0	0.306199585506693	0.388159935269505
+29	0	0.305726604955271	0.618934138352051
+30	1	0.919456032756716	1
+31	0	0.493467168603092	0.470883537689224
+32	0	0.626042458415031	0.753118774993345
+33	0	0.739080456737429	0.812446624180302
+34	0	0.786149174161255	0.768807894224301
+35	1	0.65491428244859	0.855509085487574
+36	0	0.62289561489597	0.585996081028134
+37	0	0.297479379642755	0.357051227381453
+38	0	0.796507286094129	0.775113077275455
+39	0	0.581927774194628	0.569900369411334
+40	1	0.76229884494096	0.877794308261946
+41	0	0.845583727071062	0.804134764615446
+42	0	0.79128703516908	1
+43	0	0.0507813768461347	0.97111975508742
+44	0	0.49284805515781	0.101141295302659
+45	1	0.665627157501876	0.121852198988199
+46	0	0.059045681450516	0.996109608234838
+47	0	0.0814651515800506	0.852028644317761
+48	0	0.162336849560961	1
+49	0	0.577456943178549	0.343083152920008
+50	1	0.905623372131959	0.651731353392825
diff -r 12c26de8c872 -r 445cb45d1bc0 test-data/nri_test1_out.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nri_test1_out.html	Thu Jan 08 01:05:20 2015 -0500
@@ -0,0 +1,34 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 
+        <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 
+        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 
+        <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> 
+        <title></title> 
+        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
+        </head> 
+        <body> 
+        <div class="toolFormBody"> 
+        
+<div class="infomessage">Galaxy Tool "rg_NRI" run at 08/01/2015 16:12:57</div><br/>
+<div class="toolFormTitle">rg log output</div>
+
+<pre>
+
+Error in library("e1071") : there is no package called ‘e1071’
+
+Execution halted
+
+
+</pre>
+
+<div class="toolFormTitle">Other log output</div>
+/tmp/tmpq72Dni/job_working_directory/000/2/dataset_2_files/rg_NRI_runner.log is empty<br/>
+<div class="toolFormTitle">All output files available for downloading</div>
+
+<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="rg_NRI.Rscript">rg_NRI.Rscript</a></td><td>18.1 KB</td></tr>
+<tr class="odd_row"><td><a href="rg_NRI_error.log">rg_NRI_error.log</a></td><td>84 B</td></tr>
+<tr><td><a href="rg_NRI_runner.log">rg_NRI_runner.log</a></td><td>48 B</td></tr>
+</table></div><br/>
+</div></body></html>
+
diff -r 12c26de8c872 -r 445cb45d1bc0 test-data/nri_test1_out.xls
diff -r 12c26de8c872 -r 445cb45d1bc0 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jan 07 07:50:21 2015 -0500
+++ b/tool_dependencies.xml	Thu Jan 08 01:05:20 2015 -0500
@@ -17,29 +17,54 @@
                         <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>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/class_7.3-11.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/e1071_1.6-4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/latticeExtra_0.6-26.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/Rcpp_0.11.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/plyr_1.8.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/digest_0.6.8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/gtable_0.1.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/stringr_0.6.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/reshape2_1.4.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/dichromat_2.0-0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/colorspace_1.2-4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/munsell_0.4.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/labeling_0.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/scales_0.2.4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/proto_0.3-10.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/ggplot2_1.0.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/nnet_7.3-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/caret_6.0-41.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/codetools_0.2-9.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/iterators_1.0.7.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/foreach_1.4.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/nlme_3.1-118.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/Matrix_1.1-4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/minqa_1.2.4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/nloptr_1.0.4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/lme4_1.1-7.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/profileModel_0.5-9.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/brglm_0.5-9.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/gtools_3.4.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/BradleyTerry2_1.0-5.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/pROC_1.7.3.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/survival_2.37-7.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/Formula_1.1-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/cluster_1.15.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/rpart_4.1-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/acepack_1.3-3.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/foreign_0.8-62.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/Hmisc_3.14-6.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/pracma_1.7.9.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/lars_1.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/lattice_0.20-29.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/latticeExtra_0.6-26.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/Matrix_1.1-4.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/glmnet_1.9-8.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/KernSmooth_2.23-13.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/numDeriv_2012.9-1.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/lava_1.3.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/prodlim_1.5.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/codetools_0.2-9.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/iterators_1.0.7.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/foreach_1.4.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/Formula_1.1-2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/cluster_1.15.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/rpart_4.1-8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/nnet_7.3-8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/acepack_1.3-3.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/foreign_0.8-61.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/Hmisc_3.14-6.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/SparseM_1.6.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/quantreg_5.05.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/nlme_3.1-118.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/polspline_1.1.9.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/mvtnorm_1.0-2.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/TH.data_1.0-6.tar.gz?raw=true</package>