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