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comparison tools/rgenetics/rgtest.sh @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/bin/sh
2 # script to generate all functional test outputs for each rgenetics tool
3 # could be run at installation to ensure all dependencies are in place?
4 if test $# -lt 2
5 then
6 echo "We need to agree on 2 parameters - GalaxyRoot and OutRoot - use paths to galaxy and galaxy to re-create all test outputs"
7 echo "or more prudently, galaxy and /tmp/foo for checking without updating all your test-data"
8 echo "Exiting with no changes"
9 exit 1
10 fi
11 if [ $1 ]
12 then
13 GALAXYROOT=$1
14 else
15 GALAXYROOT=`pwd`
16 fi
17 if [ $2 ]
18 then
19 OUTROOT=$2
20 else
21 OUTROOT=`pwd`
22 OUTROOT="$OUTROOT/test-data"
23 fi
24 echo "using $GALAXYROOT as galaxyroot and $OUTROOT as outroot"
25 # change this as needed for your local install
26 INPATH="${GALAXYROOT}/test-data"
27 JARPATH="${GALAXYROOT}/tool-data/shared/jars"
28 TOOLPATH="${GALAXYROOT}/tools/rgenetics"
29 OROOT="${OUTROOT}/test-data/rgtestouts"
30 NORMALOROOT="${OUTROOT}/test-data"
31 mkdir -p $OROOT
32 rm -rf $OROOT/*
33 # needed for testing - but tool versions should be bumped if this is rerun?
34 TOOL="rgManQQ"
35 NPRE=${TOOL}test1
36 OUTPATH="$OROOT/$TOOL"
37 mkdir $OUTPATH
38 CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0"
39 # rgManQQ.py '$input_file' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col'
40 # '$pval_col'
41 #python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1
42 #/opt/galaxy/test-data/rgtestouts/rgManQQ/rgManQQtest1.html /opt/galaxy/test-data/rgtestouts/rgManQQ 1 2 5,7
43 echo "Testing $TOOL using $CL"
44 python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0
45 TOOL="rgfakePhe"
46 NPRE=${TOOL}test1
47 OUTPATH="$OROOT/$TOOL"
48 mkdir $OUTPATH
49 PSSCRIPT="$OUTPATH/script_file"
50 echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
51 echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
52 echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
53 echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
54 echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
55 echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
56 echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
57 echo "now doing $TOOL"
58 python $TOOLPATH/$TOOL.py ${INPATH}/tinywga $NPRE $NPRE.pphe $OUTPATH $PSSCRIPT
59 # <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name'
60 # "$title1" '$ppheout' '$ppheout.files_path' '$script_file'
61 #
62 #
63 TOOL="rgQC"
64 NPRE=${TOOL}test1
65 echo "now doing $TOOL"
66 OUTPATH="$OROOT/$TOOL"
67 mkdir $OUTPATH
68 python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga" -o $NPRE -s ${OUTPATH}/${NPRE}.html -p $OUTPATH
69 # rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$out_prefix"
70 # -s '$html_file' -p '$html_file.files_path'
71 #
72 TOOL="rgGRR"
73 NPRE=${TOOL}test1
74 echo "now doing $TOOL"
75 OUTPATH="$OROOT/$TOOL"
76 mkdir $OUTPATH
77 CMD="python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" 100 6 true"
78 echo "doing $CMD"
79 $CMD
80 # rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name"
81 #'$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' '$force'
82 #
83 TOOL="rgLDIndep"
84 NPRE=${TOOL}test1
85 OUTPATH="$OROOT/$TOOL"
86 mkdir $OUTPATH
87 python $TOOLPATH/$TOOL.py "$INPATH" "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 10000 5000 0.1
88 #rgLDIndep.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
89 # '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1'
90 #'$out_file1.files_path' '$window' '$step' '$r2'
91 TOOL="rgPedSub"
92 NPRE=${TOOL}test1
93 OUTPATH="$OROOT/$TOOL"
94 mkdir $OUTPATH
95 PSSCRIPT="$OUTPATH/pedsub.script"
96 echo "title~~~~$NPRE" > $PSSCRIPT
97 echo "output1~~~~${OUTPATH}/${NPRE}.lped" >> $PSSCRIPT
98 echo "outformat~~~~lped" >> $PSSCRIPT
99 echo "basename~~~~tinywga" >> $PSSCRIPT
100 echo "inped~~~~$INPATH/tinywga" >> $PSSCRIPT
101 echo "outdir~~~~$OUTPATH" >> $PSSCRIPT
102 echo "region~~~~" >> $PSSCRIPT
103 echo "relfilter~~~~all" >> $PSSCRIPT
104 echo "rslist~~~~rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" >> $PSSCRIPT
105 echo "now doing $TOOL"
106 python $TOOLPATH/$TOOL.py $PSSCRIPT
107 rm -rf $PSSCRIPT
108 #
109 TOOL="rgfakePhe"
110 NPRE=${TOOL}test1
111 OUTPATH="$OROOT/$TOOL"
112 mkdir $OUTPATH
113 PSSCRIPT="$OUTPATH/script_file"
114 echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
115 echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
116 echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
117 echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
118 echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
119 echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
120 echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
121 echo "now doing $TOOL"
122 python $TOOLPATH/$TOOL.py $PSSCRIPT
123 #
124 echo "Now doing rgclean"
125 TOOL="rgClean"
126 NPRE=${TOOL}test1
127 OUTPATH="$OROOT/$TOOL"
128 mkdir $OUTPATH
129 python $TOOLPATH/$TOOL.py $INPATH "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 0 0 0 0
130 # rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
131 # '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path'
132 # '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' '$relfilter' '$afffilter' '$sexfilter' '$fixaff'
133 #
134 echo "Now doing rgEigPCA"
135 TOOL="rgEigPCA"
136 NPRE=${TOOL}test1
137 OUTPATH="$OROOT/$TOOL"
138 mkdir $OUTPATH
139 python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "$NPRE" ${OUTPATH}/${NPRE}.html $OUTPATH 4 2 2 2 $OUTPATH/rgEigPCAtest1.txt
140 # rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1"
141 # "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca"
142 #
143 TOOL="rgfakePed"
144 NPRE=${TOOL}test1
145 OUTPATH="$OROOT/$TOOL"
146 mkdir $OUTPATH
147 echo "now doing $TOOL"
148 python $TOOLPATH/$TOOL.py --title "$NPRE" -o $OUTPATH/${NPRE}.lped -p $OUTPATH -c "20" -n "40" -s "10" -w "0" -v "0" -l "pbed" -d "T" -m "0" -M "0"
149 #rgfakePed.py --title '$title1'
150 # -o '$out_file1' -p '$out_file1.extra_files_path' -c '$ncases' -n '$ntotal'
151 # -s '$nsnp' -w '$lowmaf' -v '$missingValue' -l '$outFormat'
152 # -d '$mafdist' -m '$missingRate' -M '$mendelRate'
153 #
154 TOOL="rgHaploView"
155 NPRE=${TOOL}test1
156 OUTPATH="$OROOT/$TOOL"
157 mkdir $OUTPATH
158 echo "now doing $TOOL"
159 python $TOOLPATH/$TOOL.py "" "rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" \
160 "$NPRE" $OUTPATH/${NPRE}.html "$INPATH" "tinywga" 0.0 200000 "RSQ" "lo" "2048" "$OUTPATH" "noinfo" "0.8" "YRI" $JARPATH/haploview.jar
161 # rgHaploView.py "$ucsc_region" "$rslist" "$title" "$output1"
162 # "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name"
163 # "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$output1.files_path"
164 # "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/rg/bin/haploview.jar
165 # note these statistical tools do NOT generate composite outputs
166 TOOL="rgGLM"
167 NPRE=${TOOL}test1
168 OUTPATH=$NORMALOROOT
169 echo "now doing $TOOL"
170 python $TOOLPATH/$TOOL.py "$INPATH/tinywga" $INPATH/tinywga "$NPRE" "c1" "" $OUTPATH/${NPRE}_GLM.xls \
171 $OUTPATH/${NPRE}_GLM_log.txt "tinywga" "" "" "" 1 1 0 0 $OUTPATH/${NPRE}_GLM_topTable.gff
172 ## rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name'
173 ## "$title1" '$predvar' '$covar' '$out_file1' '$logf' '$dbkey' '$i.metadata.base_name'
174 ## '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$gffout'
175 #
176 TOOL="rgTDT"
177 NPRE=${TOOL}test1
178 OUTPATH=$NORMALOROOT
179 echo "now doing $TOOL"
180 python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga" -o "$NPRE" -r $OUTPATH/${NPRE}_TDT.xls \
181 -l $OUTPATH/${NPRE}_TDT_log.txt -g $OUTPATH/${NPRE}_TDT_topTable.gff
182 ## rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title'
183 ## -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
184 ## -g '$gffout'
185 #
186 TOOL="rgCaCo"
187 NPRE=${TOOL}test1
188 OUTPATH=$NORMALOROOT
189 echo "now doing $TOOL"
190 python $TOOLPATH/rgCaCo.py $INPATH/tinywga "$NPRE" $OUTPATH/${NPRE}_CaCo.xls $OUTPATH/${NPRE}_CaCo_log.txt $OUTPATH $OUTPATH/${NPRE}_CaCo_topTable.gff
191 # rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name" '$out_file1' '$logf' '$logf.files_path' '$gffout'
192 #
193 TOOL="rgQQ"
194 echo "now doing $TOOL"
195 NPRE=${TOOL}test1
196 OUTPATH=$NORMALOROOT
197 CL="python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH"
198 echo "running $TOOL using $CL"
199 python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH
200 # rgQQ.py "$input1" "$name" $sample "$cols" $allqq $height $width $log $allqq.id $__new_file_path__
201 #