[2] | 1 | #!/bin/sh |
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| 2 | # script to generate all functional test outputs for each rgenetics tool |
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| 3 | # could be run at installation to ensure all dependencies are in place? |
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| 4 | case $# in 0) echo "USAGE: ${0##*/} TooltoTest galaxyRoot outRoot"; exit 1;; |
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| 5 | [1-2]*) echo "Need ToolToTest and paths for galaxyRoot outRoot as parameters"; exit 2;; |
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| 6 | [5-10]*) echo "Too many arguments - ToolToTest and paths for galaxyRoot outRoot as parameters"; exit 2;; |
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| 7 | *) |
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| 8 | esac |
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| 9 | GALAXYROOT=$2 |
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| 10 | OUTROOT=$3 |
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| 11 | echo "using $GALAXYROOT" |
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| 12 | # change this as needed for your local install |
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| 13 | INPATH="${GALAXYROOT}/test-data" |
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| 14 | JARPATH="${GALAXYROOT}/tool-data/shared/jars" |
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| 15 | TOOLPATH="${GALAXYROOT}/tools/rgenetics" |
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| 16 | OROOT="${OUTROOT}/test-data/rgtestouts" |
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| 17 | NORMALOROOT="${OUTROOT}/test-data" |
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| 18 | case "$1" in |
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| 19 | 'rgManQQ') |
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| 20 | |
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| 21 | TOOL="rgManQQ" |
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| 22 | NPRE=${TOOL}test1 |
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| 23 | OUTPATH="$OROOT/$TOOL" |
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| 24 | rm -rf $OUTPATH/* |
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| 25 | CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0" |
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| 26 | # rgManQQ.py '$input_file' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' |
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| 27 | # '$pval_col' |
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| 28 | #python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1 |
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| 29 | #/opt/galaxy/test-data/rgtestouts/rgManQQ/rgManQQtest1.html /opt/galaxy/test-data/rgtestouts/rgManQQ 1 2 5,7 |
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| 30 | echo "Testing $TOOL using $CL" |
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| 31 | python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0 |
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| 32 | ;; |
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| 33 | |
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| 34 | 'rgfakePhe') |
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| 35 | TOOL="rgfakePhe" |
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| 36 | NPRE=${TOOL}test1 |
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| 37 | OUTPATH="$OROOT/$TOOL" |
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| 38 | rm -rf $OUTPATH/* |
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| 39 | PSSCRIPT="$OUTPATH/script_file" |
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| 40 | echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT |
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| 41 | echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT |
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| 42 | echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT |
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| 43 | echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT |
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| 44 | echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT |
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| 45 | echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT |
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| 46 | echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT |
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| 47 | echo "now doing $TOOL" |
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| 48 | python $TOOLPATH/$TOOL.py ${INPATH}/tinywga $NPRE $NPRE.pphe $OUTPATH $PSSCRIPT |
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| 49 | # <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name' |
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| 50 | # "$title1" '$ppheout' '$ppheout.files_path' '$script_file' |
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| 51 | # |
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| 52 | ;; |
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| 53 | 'rgQC') |
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| 54 | |
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| 55 | TOOL="rgQC" |
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| 56 | NPRE=${TOOL}test1 |
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| 57 | echo "now doing $TOOL" |
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| 58 | OUTPATH="$OROOT/$TOOL" |
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| 59 | rm -rf $OUTPATH/* |
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| 60 | CMD="python $TOOLPATH/$TOOL.py -i $INPATH/tinywga -o $NPRE -s ${OUTPATH}/${NPRE}.html -p $OUTPATH" |
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| 61 | echo "doing $CMD" |
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| 62 | $CMD |
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| 63 | # rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$out_prefix" |
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| 64 | # -s '$html_file' -p '$html_file.files_path' |
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| 65 | # |
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| 66 | ;; |
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| 67 | |
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| 68 | 'rgGRR') |
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| 69 | TOOL="rgGRR" |
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| 70 | NPRE=${TOOL}test1 |
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| 71 | echo "now doing $TOOL" |
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| 72 | OUTPATH="$OROOT/$TOOL" |
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| 73 | rm -rf $OUTPATH/* |
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| 74 | cmd="$TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6' 'true'" |
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| 75 | echo "Doing $cmd" |
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| 76 | python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6' |
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| 77 | # rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" |
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| 78 | #'$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' |
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| 79 | ;; |
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| 80 | 'rgLDIndep') |
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| 81 | TOOL="rgLDIndep" |
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| 82 | NPRE=${TOOL}test1 |
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| 83 | OUTPATH="$OROOT/$TOOL" |
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| 84 | rm -rf $OUTPATH/* |
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| 85 | python $TOOLPATH/$TOOL.py "$INPATH" "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 10000 5000 0.1 |
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| 86 | #rgLDIndep.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind' |
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| 87 | # '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' |
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| 88 | #'$out_file1.files_path' '$window' '$step' '$r2' |
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| 89 | ;; |
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| 90 | |
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| 91 | 'rgPedSub') |
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| 92 | TOOL="rgPedSub" |
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| 93 | NPRE=${TOOL}test1 |
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| 94 | OUTPATH="$OROOT/$TOOL" |
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| 95 | rm -rf $OUTPATH/* |
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| 96 | PSSCRIPT="$OUTPATH/pedsub.script" |
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| 97 | echo "title~~~~$NPRE" > $PSSCRIPT |
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| 98 | echo "output1~~~~${OUTPATH}/${NPRE}.lped" >> $PSSCRIPT |
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| 99 | echo "outformat~~~~lped" >> $PSSCRIPT |
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| 100 | echo "basename~~~~tinywga" >> $PSSCRIPT |
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| 101 | echo "inped~~~~$INPATH/tinywga" >> $PSSCRIPT |
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| 102 | echo "outdir~~~~$OUTPATH" >> $PSSCRIPT |
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| 103 | echo "region~~~~" >> $PSSCRIPT |
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| 104 | echo "relfilter~~~~all" >> $PSSCRIPT |
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| 105 | echo "rslist~~~~rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" >> $PSSCRIPT |
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| 106 | echo "now doing $TOOL" |
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| 107 | python $TOOLPATH/$TOOL.py $PSSCRIPT |
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| 108 | rm -rf $PSSCRIPT |
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| 109 | ;; |
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| 110 | |
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| 111 | 'rgfakePhe') |
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| 112 | |
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| 113 | TOOL="rgfakePhe" |
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| 114 | NPRE=${TOOL}test1 |
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| 115 | OUTPATH="$OROOT/$TOOL" |
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| 116 | rm -rf $OUTPATH/* |
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| 117 | PSSCRIPT="$OUTPATH/script_file" |
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| 118 | echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT |
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| 119 | echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT |
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| 120 | echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT |
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| 121 | echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT |
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| 122 | echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT |
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| 123 | echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT |
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| 124 | echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT |
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| 125 | echo "now doing $TOOL" |
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| 126 | python $TOOLPATH/$TOOL.py $PSSCRIPT |
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| 127 | ;; |
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| 128 | |
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| 129 | 'rgClean') |
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| 130 | TOOL="rgClean" |
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| 131 | NPRE=${TOOL}test1 |
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| 132 | OUTPATH="$OROOT/$TOOL" |
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| 133 | rm -rf $OUTPATH/* |
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| 134 | python $TOOLPATH/$TOOL.py $INPATH "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 0 0 0 0 |
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| 135 | # rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind' |
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| 136 | # '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path' |
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| 137 | # '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' '$relfilter' '$afffilter' '$sexfilter' '$fixaff' |
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| 138 | # |
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| 139 | ;; |
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| 140 | |
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| 141 | 'rgEigPCA') |
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| 142 | |
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| 143 | TOOL="rgEigPCA" |
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| 144 | NPRE=${TOOL}test1 |
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| 145 | OUTPATH="$OROOT/$TOOL" |
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| 146 | rm -rf $OUTPATH/* |
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| 147 | python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "$NPRE" ${OUTPATH}/${NPRE}.html $OUTPATH 4 2 2 2 $OUTPATH/rgEigPCAtest1.txt |
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| 148 | # rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1" |
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| 149 | # "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca" |
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| 150 | # |
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| 151 | ;; |
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| 152 | |
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| 153 | 'rgfakePed') |
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| 154 | TOOL="rgfakePed" |
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| 155 | NPRE=${TOOL}test1 |
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| 156 | OUTPATH="$OROOT/$TOOL" |
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| 157 | rm -rf $OUTPATH/* |
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| 158 | echo "now doing $TOOL" |
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| 159 | python $TOOLPATH/$TOOL.py --title "$NPRE" -o $OUTPATH/${NPRE}.lped -p $OUTPATH -c "20" -n "40" -s "10" -w "0" -v "0" -l "pbed" -d "T" -m "0" -M "0" |
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| 160 | #rgfakePed.py --title '$title1' |
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| 161 | # -o '$out_file1' -p '$out_file1.extra_files_path' -c '$ncases' -n '$ntotal' |
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| 162 | # -s '$nsnp' -w '$lowmaf' -v '$missingValue' -l '$outFormat' |
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| 163 | # -d '$mafdist' -m '$missingRate' -M '$mendelRate' |
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| 164 | ;; |
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| 165 | |
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| 166 | 'rgHaploView') |
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| 167 | |
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| 168 | TOOL="rgHaploView" |
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| 169 | NPRE=${TOOL}test1 |
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| 170 | OUTPATH="$OROOT/$TOOL" |
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| 171 | rm -rf $OUTPATH/* |
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| 172 | CL="python $TOOLPATH/$TOOL.py '' 'rs2283802 rs2267000 rs16997606 rs4820537 rs3788347 rs756632 rs4820539 rs2283804 rs2267006 rs4822363' '$NPRE' $OUTPATH/${NPRE}.html '$INPATH' 'tinywga' 0.0 200000 'RSQ' 'lo' '2048' '$OUTPATH' 'noinfo' '0.8' 'YRI' $JARPATH/haploview.jar" |
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| 173 | echo "Testing $TOOL using $CL" |
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| 174 | python $TOOLPATH/$TOOL.py "" "rs2283802 rs2267000 rs16997606 rs4820537 rs3788347 rs756632 rs4820539 rs2283804 rs2267006 rs4822363" \ |
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| 175 | "$NPRE" $OUTPATH/${NPRE}.html "$INPATH" "tinywga" 0.0 200000 "RSQ" "lo" "2048" "$OUTPATH" "noinfo" "0.8" "YRI" $JARPATH/haploview.jar |
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| 176 | # rgHaploView.py "$ucsc_region" "$rslist" "$title" "$output1" |
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| 177 | # "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name" |
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| 178 | # "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$output1.files_path" |
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| 179 | # "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/rg/bin/haploview.jar |
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| 180 | # note these statistical tools do NOT generate composite outputs |
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| 181 | ;; |
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| 182 | |
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| 183 | 'rgGLM') |
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| 184 | TOOL="rgGLM" |
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| 185 | NPRE=${TOOL}test1 |
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| 186 | OUTPATH=$NORMALOROOT |
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| 187 | python $TOOLPATH/$TOOL.py "$INPATH/tinywga" $INPATH/tinywga "$NPRE" "c1" "" $OUTPATH/${NPRE}_GLM.xls \ |
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| 188 | $OUTPATH/${NPRE}_GLM_log.txt "tinywga" "" "" "" 1 1 0 0 $OUTPATH/${NPRE}_GLM_topTable.gff |
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| 189 | ## rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name' |
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| 190 | ## "$title1" '$predvar' '$covar' '$out_file1' '$logf' '$dbkey' '$i.metadata.base_name' |
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| 191 | ## '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$gffout' |
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| 192 | ;; |
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| 193 | |
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| 194 | 'rgTDT') |
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| 195 | TOOL="rgTDT" |
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| 196 | NPRE=${TOOL}test1 |
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| 197 | OUTPATH=$NORMALOROOT |
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| 198 | python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga" -o "$NPRE" -r $OUTPATH/${NPRE}_TDT.xls \ |
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| 199 | -l $OUTPATH/${NPRE}_TDT_log.txt -g $OUTPATH/${NPRE}_TDT_topTable.gff |
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| 200 | ## rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title' |
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| 201 | ## -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' |
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| 202 | ## -g '$gffout' |
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| 203 | ;; |
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| 204 | |
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| 205 | 'rgCaCo') |
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| 206 | TOOL="rgCaCo" |
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| 207 | NPRE=${TOOL}test1 |
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| 208 | OUTPATH=$NORMALOROOT |
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| 209 | echo "now doing $TOOL" |
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| 210 | python $TOOLPATH/rgCaCo.py $INPATH/tinywga "$NPRE" $OUTPATH/${NPRE}_CaCo.xls $OUTPATH/${NPRE}_CaCo_log.txt $OUTPATH $OUTPATH/${NPRE}_CaCo_topTable.gff |
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| 211 | # rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name" '$out_file1' '$logf' '$logf.files_path' '$gffout' |
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| 212 | ;; |
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| 213 | |
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| 214 | 'rgQQ') |
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| 215 | TOOL="rgQQ" |
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| 216 | echo "now doing $TOOL" |
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| 217 | NPRE=${TOOL}test1 |
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| 218 | OUTPATH=$NORMALOROOT |
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| 219 | CL="python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH" |
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| 220 | echo "running $TOOL using $CL" |
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| 221 | python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH |
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| 222 | # rgQQ.py "$input1" "$name" $sample "$cols" $allqq $height $width $log $allqq.id $__new_file_path__ |
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| 223 | ;; |
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| 224 | esac |
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