--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/rgtest.sh	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,201 @@
+#!/bin/sh
+# script to generate all functional test outputs for each rgenetics tool
+# could be run at installation to ensure all dependencies are in place?
+if test $# -lt 2
+then
+   echo "We need to agree on 2 parameters - GalaxyRoot and OutRoot - use paths to galaxy and galaxy to re-create all test outputs"
+   echo "or more prudently, galaxy and /tmp/foo for checking without updating all your test-data"
+   echo "Exiting with no changes"
+   exit 1
+fi
+if [ $1 ]
+then
+  GALAXYROOT=$1
+else
+  GALAXYROOT=`pwd`
+fi
+if [ $2 ]
+then
+  OUTROOT=$2
+else
+  OUTROOT=`pwd`
+  OUTROOT="$OUTROOT/test-data"
+fi
+echo "using $GALAXYROOT as galaxyroot and $OUTROOT as outroot"
+# change this as needed for your local install
+INPATH="${GALAXYROOT}/test-data"
+JARPATH="${GALAXYROOT}/tool-data/shared/jars"
+TOOLPATH="${GALAXYROOT}/tools/rgenetics"
+OROOT="${OUTROOT}/test-data/rgtestouts"
+NORMALOROOT="${OUTROOT}/test-data"
+mkdir -p $OROOT
+rm -rf $OROOT/*
+# needed for testing - but tool versions should be bumped if this is rerun?
+TOOL="rgManQQ"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0"
+# rgManQQ.py '$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 $OUTPATH 1 2 7 0
+TOOL="rgfakePhe"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+PSSCRIPT="$OUTPATH/script_file"
+echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
+echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
+echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
+echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
+echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
+echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
+echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py ${INPATH}/tinywga $NPRE $NPRE.pphe $OUTPATH $PSSCRIPT
+#   <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name'
+#   "$title1" '$ppheout' '$ppheout.files_path' '$script_file'
+#
+#
+TOOL="rgQC"
+NPRE=${TOOL}test1
+echo "now doing $TOOL"
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga" -o $NPRE -s ${OUTPATH}/${NPRE}.html -p $OUTPATH
+# rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$out_prefix" 
+# -s '$html_file' -p '$html_file.files_path' 
+#
+TOOL="rgGRR"
+NPRE=${TOOL}test1
+echo "now doing $TOOL"
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+CMD="python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" 100 6 true" 
+echo "doing $CMD"
+$CMD
+# rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name"
+#'$out_file1' '$out_file1.files_path' "$title"  '$n' '$Z' '$force'
+#
+TOOL="rgLDIndep"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+python $TOOLPATH/$TOOL.py "$INPATH" "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 10000 5000 0.1 
+#rgLDIndep.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
+# '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1'
+#'$out_file1.files_path'  '$window' '$step' '$r2' 
+TOOL="rgPedSub"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+PSSCRIPT="$OUTPATH/pedsub.script"
+echo "title~~~~$NPRE" > $PSSCRIPT
+echo "output1~~~~${OUTPATH}/${NPRE}.lped" >> $PSSCRIPT
+echo "outformat~~~~lped" >> $PSSCRIPT
+echo "basename~~~~tinywga" >> $PSSCRIPT
+echo "inped~~~~$INPATH/tinywga" >> $PSSCRIPT
+echo "outdir~~~~$OUTPATH" >> $PSSCRIPT
+echo "region~~~~" >> $PSSCRIPT
+echo "relfilter~~~~all" >> $PSSCRIPT
+echo "rslist~~~~rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" >> $PSSCRIPT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py $PSSCRIPT
+rm -rf $PSSCRIPT
+#
+TOOL="rgfakePhe"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+PSSCRIPT="$OUTPATH/script_file"
+echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
+echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
+echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
+echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
+echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
+echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
+echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py $PSSCRIPT
+#
+echo "Now doing rgclean"
+TOOL="rgClean"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+python $TOOLPATH/$TOOL.py $INPATH "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 0 0 0 0
+# rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
+#        '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path'
+#        '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' '$relfilter' '$afffilter' '$sexfilter' '$fixaff'
+#
+echo "Now doing rgEigPCA"
+TOOL="rgEigPCA"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "$NPRE" ${OUTPATH}/${NPRE}.html $OUTPATH 4 2 2 2 $OUTPATH/rgEigPCAtest1.txt
+#    rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1"
+#    "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca" 
+#
+TOOL="rgfakePed"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py --title "$NPRE" -o $OUTPATH/${NPRE}.lped -p $OUTPATH -c "20" -n "40" -s "10" -w "0" -v "0" -l "pbed" -d "T" -m "0" -M "0"
+#rgfakePed.py --title '$title1' 
+#  -o '$out_file1' -p '$out_file1.extra_files_path' -c '$ncases' -n '$ntotal'
+#  -s '$nsnp'  -w '$lowmaf' -v '$missingValue' -l '$outFormat'
+#  -d '$mafdist' -m '$missingRate' -M '$mendelRate'
+#
+TOOL="rgHaploView"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py ""  "rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" \
+"$NPRE" $OUTPATH/${NPRE}.html  "$INPATH" "tinywga" 0.0 200000 "RSQ" "lo" "2048" "$OUTPATH" "noinfo" "0.8" "YRI" $JARPATH/haploview.jar
+#  rgHaploView.py "$ucsc_region" "$rslist" "$title" "$output1"  
+#  "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name"
+#  "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$output1.files_path" 
+#  "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/rg/bin/haploview.jar
+# note these statistical tools do NOT generate composite outputs
+TOOL="rgGLM"
+NPRE=${TOOL}test1
+OUTPATH=$NORMALOROOT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py "$INPATH/tinywga" $INPATH/tinywga "$NPRE" "c1" "" $OUTPATH/${NPRE}_GLM.xls \
+$OUTPATH/${NPRE}_GLM_log.txt "tinywga" "" "" "" 1 1 0 0 $OUTPATH/${NPRE}_GLM_topTable.gff 
+##        rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name'
+##        "$title1" '$predvar' '$covar' '$out_file1' '$logf' '$dbkey' '$i.metadata.base_name'
+##        '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$gffout'
+#
+TOOL="rgTDT"
+NPRE=${TOOL}test1
+OUTPATH=$NORMALOROOT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga"  -o "$NPRE" -r $OUTPATH/${NPRE}_TDT.xls \
+-l $OUTPATH/${NPRE}_TDT_log.txt -g $OUTPATH/${NPRE}_TDT_topTable.gff
+##        rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title'
+##        -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
+##        -g '$gffout'
+#
+TOOL="rgCaCo"
+NPRE=${TOOL}test1
+OUTPATH=$NORMALOROOT
+echo "now doing $TOOL"
+python $TOOLPATH/rgCaCo.py $INPATH/tinywga "$NPRE" $OUTPATH/${NPRE}_CaCo.xls $OUTPATH/${NPRE}_CaCo_log.txt $OUTPATH $OUTPATH/${NPRE}_CaCo_topTable.gff
+# rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name"  '$out_file1' '$logf' '$logf.files_path' '$gffout'
+#
+TOOL="rgQQ"
+echo "now doing $TOOL"
+NPRE=${TOOL}test1
+OUTPATH=$NORMALOROOT
+CL="python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH"
+echo "running $TOOL using $CL"
+python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH
+# rgQQ.py "$input1" "$name" $sample "$cols" $allqq $height $width $log $allqq.id $__new_file_path__ 
+#