/tools/rgenetics/rgtest_one_tool.sh

https://bitbucket.org/cistrome/cistrome-harvard/ · Shell · 224 lines · 164 code · 17 blank · 43 comment · 2 complexity · b55f7e270dbd3a6cc42ca9952bb07e12 MD5 · raw file 

    

  1. #!/bin/sh
    2. 

  2. # script to generate all functional test outputs for each rgenetics tool
    3. 

  3. # could be run at installation to ensure all dependencies are in place?
    4. 

  4. case $# in 0) echo "USAGE: ${0##*/} TooltoTest galaxyRoot outRoot"; exit 1;;
    5. 

  5.            [1-2]*) echo "Need ToolToTest and paths for galaxyRoot outRoot as parameters"; exit 2;;
    6. 

  6.            [5-10]*) echo "Too many arguments - ToolToTest and paths for galaxyRoot outRoot as parameters"; exit 2;;
    7. 

  7.            *)
    8. 

  8. esac
    9. 

  9. GALAXYROOT=$2
    10. 

  10. OUTROOT=$3
    11. 

  11. echo "using $GALAXYROOT"
    12. 

  12. # change this as needed for your local install
    13. 

  13. INPATH="${GALAXYROOT}/test-data"
    14. 

  14. JARPATH="${GALAXYROOT}/tool-data/shared/jars"
    15. 

  15. TOOLPATH="${GALAXYROOT}/tools/rgenetics"
    16. 

  16. OROOT="${OUTROOT}/test-data/rgtestouts"
    17. 

  17. NORMALOROOT="${OUTROOT}/test-data"
    18. 

  18. case "$1" in
    19. 

  19. 'rgManQQ')
    20. 

  20. 

  21. TOOL="rgManQQ"
    22. 

  22. NPRE=${TOOL}test1
    23. 

  23. OUTPATH="$OROOT/$TOOL"
    24. 

  24. rm -rf $OUTPATH/*
    25. 

  25. CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0"
    26. 

  26. # rgManQQ.py '$input_file' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' 
    27. 

  27. # '$pval_col'
    28. 

  28. #python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1 
    29. 

  29. #/opt/galaxy/test-data/rgtestouts/rgManQQ/rgManQQtest1.html /opt/galaxy/test-data/rgtestouts/rgManQQ 1 2 5,7 
    30. 

  30. echo "Testing $TOOL using $CL"
    31. 

  31. python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0
    32. 

  32. ;;
    33. 

    34. 

  34. 'rgfakePhe')
    35. 

  35. TOOL="rgfakePhe"
    36. 

  36. NPRE=${TOOL}test1
    37. 

  37. OUTPATH="$OROOT/$TOOL"
    38. 

  38. rm -rf $OUTPATH/*
    39. 

  39. PSSCRIPT="$OUTPATH/script_file"
    40. 

  40. echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
    41. 

  41. echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
    42. 

  42. echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
    43. 

  43. echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
    44. 

  44. echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
    45. 

  45. echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
    46. 

  46. echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
    47. 

  47. echo "now doing $TOOL"
    48. 

  48. python $TOOLPATH/$TOOL.py ${INPATH}/tinywga $NPRE $NPRE.pphe $OUTPATH $PSSCRIPT
    49. 

  49. #   <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name'
    50. 

  50. #   "$title1" '$ppheout' '$ppheout.files_path' '$script_file'
    51. 

  51. #
    52. 

  52. ;;
    53. 

  53. 'rgQC')
    54. 

    55. 

  55. TOOL="rgQC"
    56. 

  56. NPRE=${TOOL}test1
    57. 

  57. echo "now doing $TOOL"
    58. 

  58. OUTPATH="$OROOT/$TOOL"
    59. 

  59. rm -rf $OUTPATH/*
    60. 

  60. CMD="python $TOOLPATH/$TOOL.py -i $INPATH/tinywga -o $NPRE -s ${OUTPATH}/${NPRE}.html -p $OUTPATH"
    61. 

  61. echo "doing $CMD"
    62. 

  62. $CMD
    63. 

  63. # rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$out_prefix" 
    64. 

  64. # -s '$html_file' -p '$html_file.files_path' 
    65. 

  65. #
    66. 

  66. ;;
    67. 

    68. 

  68. 'rgGRR')
    69. 

  69. TOOL="rgGRR"
    70. 

  70. NPRE=${TOOL}test1
    71. 

  71. echo "now doing $TOOL"
    72. 

  72. OUTPATH="$OROOT/$TOOL"
    73. 

  73. rm -rf $OUTPATH/*
    74. 

  74. cmd="$TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6' 'true'"
    75. 

  75. echo "Doing $cmd"
    76. 

  76. python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6' 
    77. 

  77. # rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name"
    78. 

  78. #'$out_file1' '$out_file1.files_path' "$title"  '$n' '$Z' 
    79. 

  79. ;;
    80. 

  80. 'rgLDIndep')
    81. 

  81. TOOL="rgLDIndep"
    82. 

  82. NPRE=${TOOL}test1
    83. 

  83. OUTPATH="$OROOT/$TOOL"
    84. 

  84. rm -rf $OUTPATH/*
    85. 

  85. python $TOOLPATH/$TOOL.py "$INPATH" "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 10000 5000 0.1 
    86. 

  86. #rgLDIndep.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
    87. 

  87. # '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1'
    88. 

  88. #'$out_file1.files_path'  '$window' '$step' '$r2' 
    89. 

  89. ;;
    90. 

    91. 

  91. 'rgPedSub')
    92. 

  92. TOOL="rgPedSub"
    93. 

  93. NPRE=${TOOL}test1
    94. 

  94. OUTPATH="$OROOT/$TOOL"
    95. 

  95. rm -rf $OUTPATH/*
    96. 

  96. PSSCRIPT="$OUTPATH/pedsub.script"
    97. 

  97. echo "title~~~~$NPRE" > $PSSCRIPT
    98. 

  98. echo "output1~~~~${OUTPATH}/${NPRE}.lped" >> $PSSCRIPT
    99. 

  99. echo "outformat~~~~lped" >> $PSSCRIPT
    100. 

  100. echo "basename~~~~tinywga" >> $PSSCRIPT
    101. 

  101. echo "inped~~~~$INPATH/tinywga" >> $PSSCRIPT
    102. 

  102. echo "outdir~~~~$OUTPATH" >> $PSSCRIPT
    103. 

  103. echo "region~~~~" >> $PSSCRIPT
    104. 

  104. echo "relfilter~~~~all" >> $PSSCRIPT
    105. 

  105. echo "rslist~~~~rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" >> $PSSCRIPT
    106. 

  106. echo "now doing $TOOL"
    107. 

  107. python $TOOLPATH/$TOOL.py $PSSCRIPT
    108. 

  108. rm -rf $PSSCRIPT
    109. 

  109. ;;
    110. 

    111. 

  111. 'rgfakePhe')
    112. 

    113. 

  113. TOOL="rgfakePhe"
    114. 

  114. NPRE=${TOOL}test1
    115. 

  115. OUTPATH="$OROOT/$TOOL"
    116. 

  116. rm -rf $OUTPATH/*
    117. 

  117. PSSCRIPT="$OUTPATH/script_file"
    118. 

  118. echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
    119. 

  119. echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
    120. 

  120. echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
    121. 

  121. echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
    122. 

  122. echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
    123. 

  123. echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
    124. 

  124. echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
    125. 

  125. echo "now doing $TOOL"
    126. 

  126. python $TOOLPATH/$TOOL.py $PSSCRIPT
    127. 

  127. ;;
    128. 

    129. 

  129. 'rgClean')
    130. 

  130. TOOL="rgClean"
    131. 

  131. NPRE=${TOOL}test1
    132. 

  132. OUTPATH="$OROOT/$TOOL"
    133. 

  133. rm -rf $OUTPATH/*
    134. 

  134. python $TOOLPATH/$TOOL.py $INPATH "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 0 0 0 0
    135. 

  135. # rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
    136. 

  136. #        '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path'
    137. 

  137. #        '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' '$relfilter' '$afffilter' '$sexfilter' '$fixaff'
    138. 

  138. #
    139. 

  139. ;;
    140. 

    141. 

  141. 'rgEigPCA')
    142. 

    143. 

  143. TOOL="rgEigPCA"
    144. 

  144. NPRE=${TOOL}test1
    145. 

  145. OUTPATH="$OROOT/$TOOL"
    146. 

  146. rm -rf $OUTPATH/*
    147. 

  147. python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "$NPRE" ${OUTPATH}/${NPRE}.html $OUTPATH 4 2 2 2 $OUTPATH/rgEigPCAtest1.txt
    148. 

  148. #    rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1"
    149. 

  149. #    "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca" 
    150. 

  150. #
    151. 

  151. ;;
    152. 

    153. 

  153. 'rgfakePed')
    154. 

  154. TOOL="rgfakePed"
    155. 

  155. NPRE=${TOOL}test1
    156. 

  156. OUTPATH="$OROOT/$TOOL"
    157. 

  157. rm -rf $OUTPATH/*
    158. 

  158. echo "now doing $TOOL"
    159. 

  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"
    160. 

  160. #rgfakePed.py --title '$title1' 
    161. 

  161. #  -o '$out_file1' -p '$out_file1.extra_files_path' -c '$ncases' -n '$ntotal'
    162. 

  162. #  -s '$nsnp'  -w '$lowmaf' -v '$missingValue' -l '$outFormat'
    163. 

  163. #  -d '$mafdist' -m '$missingRate' -M '$mendelRate'
    164. 

  164. ;;
    165. 

    166. 

  166. 'rgHaploView')
    167. 

    168. 

  168. TOOL="rgHaploView"
    169. 

  169. NPRE=${TOOL}test1
    170. 

  170. OUTPATH="$OROOT/$TOOL"
    171. 

  171. rm -rf $OUTPATH/*
    172. 

  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"
    173. 

  173. echo "Testing $TOOL using $CL"
    174. 

  174. python $TOOLPATH/$TOOL.py ""  "rs2283802 rs2267000 rs16997606 rs4820537 rs3788347 rs756632 rs4820539 rs2283804 rs2267006 rs4822363" \
    175. 

  175. "$NPRE" $OUTPATH/${NPRE}.html  "$INPATH" "tinywga" 0.0 200000 "RSQ" "lo" "2048" "$OUTPATH" "noinfo" "0.8" "YRI" $JARPATH/haploview.jar
    176. 

  176. #  rgHaploView.py "$ucsc_region" "$rslist" "$title" "$output1"  
    177. 

  177. #  "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name"
    178. 

  178. #  "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$output1.files_path" 
    179. 

  179. #  "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/rg/bin/haploview.jar
    180. 

  180. # note these statistical tools do NOT generate composite outputs
    181. 

  181. ;;
    182. 

    183. 

  183. 'rgGLM')
    184. 

  184. TOOL="rgGLM"
    185. 

  185. NPRE=${TOOL}test1
    186. 

  186. OUTPATH=$NORMALOROOT
    187. 

  187. python $TOOLPATH/$TOOL.py "$INPATH/tinywga" $INPATH/tinywga "$NPRE" "c1" "" $OUTPATH/${NPRE}_GLM.xls \
    188. 

  188. $OUTPATH/${NPRE}_GLM_log.txt "tinywga" "" "" "" 1 1 0 0 $OUTPATH/${NPRE}_GLM_topTable.gff 
    189. 

  189. ##        rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name'
    190. 

  190. ##        "$title1" '$predvar' '$covar' '$out_file1' '$logf' '$dbkey' '$i.metadata.base_name'
    191. 

  191. ##        '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$gffout'
    192. 

  192. ;;
    193. 

    194. 

  194. 'rgTDT')
    195. 

  195. TOOL="rgTDT"
    196. 

  196. NPRE=${TOOL}test1
    197. 

  197. OUTPATH=$NORMALOROOT
    198. 

  198. python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga"  -o "$NPRE" -r $OUTPATH/${NPRE}_TDT.xls \
    199. 

  199. -l $OUTPATH/${NPRE}_TDT_log.txt -g $OUTPATH/${NPRE}_TDT_topTable.gff
    200. 

  200. ##        rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title'
    201. 

  201. ##        -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
    202. 

  202. ##        -g '$gffout'
    203. 

  203. ;;
    204. 

    205. 

  205. 'rgCaCo')
    206. 

  206. TOOL="rgCaCo"
    207. 

  207. NPRE=${TOOL}test1
    208. 

  208. OUTPATH=$NORMALOROOT
    209. 

  209. echo "now doing $TOOL"
    210. 

  210. python $TOOLPATH/rgCaCo.py $INPATH/tinywga "$NPRE" $OUTPATH/${NPRE}_CaCo.xls $OUTPATH/${NPRE}_CaCo_log.txt $OUTPATH $OUTPATH/${NPRE}_CaCo_topTable.gff
    211. 

  211. # rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name"  '$out_file1' '$logf' '$logf.files_path' '$gffout'
    212. 

  212. ;;
    213. 

    214. 

  214. 'rgQQ')
    215. 

  215. TOOL="rgQQ"
    216. 

  216. echo "now doing $TOOL"
    217. 

  217. NPRE=${TOOL}test1
    218. 

  218. OUTPATH=$NORMALOROOT
    219. 

  219. CL="python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH"
    220. 

  220. echo "running $TOOL using $CL"
    221. 

  221. python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH
    222. 

  222. # rgQQ.py "$input1" "$name" $sample "$cols" $allqq $height $width $log $allqq.id $__new_file_path__ 
    223. 

  223. ;;
    224. 

  224. esac
    225.