details: http://www.bx.psu.edu/hg/galaxy/rev/bda77e05c7c0 changeset: 3574:bda77e05c7c0 user: fubar: ross Lazarus at gmail period com date: Sat Mar 27 11:42:45 2010 -0400 description: Two small tweaks to WGA/SNP tests - for rgQC and for rgManQQ diffstat: tools/rgenetics/rgManQQ.py | 5 ++--- tools/rgenetics/rgManQQ.xml | 1 + tools/rgenetics/rgQC.xml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diffs (39 lines): diff -r b5757fb7ab13 -r bda77e05c7c0 tools/rgenetics/rgManQQ.py --- a/tools/rgenetics/rgManQQ.py Fri Mar 26 22:40:46 2010 -0400 +++ b/tools/rgenetics/rgManQQ.py Sat Mar 27 11:42:45 2010 -0400 @@ -189,10 +189,9 @@ if chrom_col == 1 or offset_col == 1: # was passed as zero - do not do manhattan plots chrom_col = 0 offset_col = 0 - if sys.argv[8].lower() in ['1','true']: + grey = 0 + if (sys.argv[8].lower() in ['1','true']): grey = 1 - else: - grey = 0 rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey)) rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir) flist.sort() diff -r b5757fb7ab13 -r bda77e05c7c0 tools/rgenetics/rgManQQ.xml --- a/tools/rgenetics/rgManQQ.xml Fri Mar 26 22:40:46 2010 -0400 +++ b/tools/rgenetics/rgManQQ.xml Sat Mar 27 11:42:45 2010 -0400 @@ -41,6 +41,7 @@ <param name='pval_col' value='5,7' /> <param name='chrom_col' value='1' /> <param name='offset_col' value='2' /> + <param name='grey' value='0' /> <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='17'> <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" delta = "100" /> diff -r b5757fb7ab13 -r bda77e05c7c0 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml Fri Mar 26 22:40:46 2010 -0400 +++ b/tools/rgenetics/rgQC.xml Sat Mar 27 11:42:45 2010 -0400 @@ -37,7 +37,7 @@ <extra_files type="file" name='tinywga.imiss' value="rgtestouts/rgQC/tinywga.imiss" compare="diff" /> <extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" /> <extra_files type="file" name='tinywga.lmiss' value="rgtestouts/rgQC/tinywga.lmiss" compare="diff" /> - <extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="diff" lines_diff="1112"/> + <extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="diff" lines_diff="2660"/> <extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" /> <extra_files type="file" name='ldp_tinywga.bim' value="rgtestouts/rgQC/ldp_tinywga.bim" compare="diff" /> <extra_files type="file" name='ldp_tinywga.fam' value="rgtestouts/rgQC/ldp_tinywga.fam" compare="diff" />