[galaxy-commits] galaxy-dist commit 9638200fbfdc: Fixes for rgManQQ - manhattan and qqplot generator for

[commits-noreply at bitbucket.org]

# 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')