Mercurial > repos > fubar > rglasso_1_9_8
changeset 13:445cb45d1bc0 draft
Uploaded
| author | fubar |
|---|---|
| date | Thu, 08 Jan 2015 01:05:20 -0500 |
| parents | 12c26de8c872 |
| children | a061150f1d94 |
| files | rg_nri.xml test-data/genTest.R test-data/nri_test1.xls test-data/nri_test1_out.html test-data/nri_test1_out.xls tool_dependencies.xml |
| diffstat | 5 files changed, 141 insertions(+), 15 deletions(-) [+] |
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--- 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>
--- /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
--- /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
--- /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> +
--- 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> + 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