details: http://www.bx.psu.edu/hg/galaxy/rev/b95a24c9187e changeset: 3602:b95a24c9187e user: fubar: ross Lazarus at gmail period com date: Fri Apr 02 14:23:55 2010 -0400 description: Two small fixes for WGA/SNP tools needed so they work on test. Remove bogus extra_ from file_path for output files - works on rgenetics.org but breaks on test - fixed Need to create output extra_files_path in rgGRR.py diffstat: tools/rgenetics/rgGRR.py | 4 ++++ tools/rgenetics/rgGRR.xml | 2 +- tools/rgenetics/rgfakePed.xml | 2 +- 3 files changed, 6 insertions(+), 2 deletions(-) diffs (38 lines): diff -r 6bbe3704b015 -r b95a24c9187e tools/rgenetics/rgGRR.py --- a/tools/rgenetics/rgGRR.py Fri Apr 02 12:24:39 2010 -0400 +++ b/tools/rgenetics/rgGRR.py Fri Apr 02 14:23:55 2010 -0400 @@ -1037,6 +1037,10 @@ basename = sys.argv[2] outhtml = sys.argv[3] newfilepath = sys.argv[4] + try: + os.makedirs(newfilepath) + except: + pass title = sys.argv[5].translate(ptran) logfname = 'Log_%s.txt' % title logpath = os.path.join(newfilepath,logfname) # log was a child - make part of html extra_files_path zoo diff -r 6bbe3704b015 -r b95a24c9187e tools/rgenetics/rgGRR.xml --- a/tools/rgenetics/rgGRR.xml Fri Apr 02 12:24:39 2010 -0400 +++ b/tools/rgenetics/rgGRR.xml Fri Apr 02 14:23:55 2010 -0400 @@ -3,7 +3,7 @@ <description>Pairwise Allele Sharing</description> <command interpreter="python"> rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" - '$out_file1' '$out_file1.extra_files_path' "$title1" '$n' '$Z' + '$out_file1' '$out_file1.files_path' "$title1" '$n' '$Z' </command> <inputs> <param name="i" type="data" label="Genotype data file from your current history" diff -r 6bbe3704b015 -r b95a24c9187e tools/rgenetics/rgfakePed.xml --- a/tools/rgenetics/rgfakePed.xml Fri Apr 02 12:24:39 2010 -0400 +++ b/tools/rgenetics/rgfakePed.xml Fri Apr 02 14:23:55 2010 -0400 @@ -2,7 +2,7 @@ <description>for testing</description> <code file="rgfakePed_code.py"/> <command interpreter="python">rgfakePed.py --title '$title1' - -o '$out_file1' -p '$out_file1.extra_files_path' -c '$ncases' -n '$ntotal' + -o '$out_file1' -p '$out_file1.files_path' -c '$ncases' -n '$ntotal' -s '$nsnp' -w '$lowmaf' -v '$missingValue' -l '$outFormat' -d '$mafdist' -m '$missingRate' -M '$mendelRate' </command> <inputs>