# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User fubar: ross Lazarus at gmail period com # Date 1279184288 14400 # Node ID 9638200fbfdcc470675ca6b65f0220f28ed1809c # Parent c0eb25264f919b2e7cac25b65483aa1ce4c6f54d Fixes for rgManQQ - manhattan and qqplot generator for interval pvalues New qqplot image Fixes to fix test output generators to only provide one set of pval columns --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -38,13 +38,13 @@ <param name='i' value='smallwgaP.xls' ftype='tabular' ></param><param name='name' value='rgManQQtest1' /> - <param name='pval_col' value='5,7' /> + <param name='pval_col' value='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" /> + delta = "4000" /><extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" delta = "4000" /><extra_files type="file" name='Armitagep_manhattan.png' value='rgtestouts/rgManQQ/Armitagep_manhattan.png' compare="sim_size" --- a/tools/rgenetics/rgtest.sh +++ b/tools/rgenetics/rgtest.sh @@ -35,7 +35,7 @@ TOOL="rgManQQ" NPRE=${TOOL}test1 OUTPATH="$OROOT/$TOOL" mkdir $OUTPATH -CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0" +CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0" # rgManQQ.py '$input_file' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' # '$pval_col' #python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1 Binary file test-data/rgtestouts/rgManQQ/Allelep_qqplot.png has changed --- a/tools/rgenetics/rgtest_one_tool.sh +++ b/tools/rgenetics/rgtest_one_tool.sh @@ -2,7 +2,7 @@ # script to generate all functional test outputs for each rgenetics tool # could be run at installation to ensure all dependencies are in place? case $# in 0) echo "USAGE: ${0##*/} TooltoTest galaxyRoot outRoot"; exit 1;; - [1-3]*) echo "Need ToolToTest and paths for galaxyRoot outRoot as parameters"; exit 2;; + [1-2]*) echo "Need ToolToTest and paths for galaxyRoot outRoot as parameters"; exit 2;; [5-10]*) echo "Too many arguments - ToolToTest and paths for galaxyRoot outRoot as parameters"; exit 2;; *) esac @@ -22,13 +22,13 @@ TOOL="rgManQQ" NPRE=${TOOL}test1 OUTPATH="$OROOT/$TOOL" rm -rf $OUTPATH/* -CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0" +CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0" # rgManQQ.py '$input_file' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' # '$pval_col' #python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1 #/opt/galaxy/test-data/rgtestouts/rgManQQ/rgManQQtest1.html /opt/galaxy/test-data/rgtestouts/rgManQQ 1 2 5,7 echo "Testing $TOOL using $CL" -python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0 +python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0 ;; 'rgfakePhe')