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40
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1 #echo "1: " $1" 2: " $2" 3: " $3" 4: "$4" 5: "$5 " 6: "$6 "7: "$7" 8: "$8 " 9: "$9" 10: "${10}" 11: "${11} "12: "${12}
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2 #echo " 13: "${13}" 14: "${14}" 15: "${15}" 16: "${16} "17: "${17}" 18: "${18}" 19: "${19}" 20: "${20}" 21: "${21} " 22: "${22}" 23:" ${23}
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3
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4 #Count total number of parameters and classification parameters
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5 parmSize=0
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6 classSize=0
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7 matrixSize=0
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8 for i in "$@"; do
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9 currParm=$(cut -d'|' -f1 <<< $i)
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10 parmSize=$((parmSize+1))
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11 if [ $currParm = "classification" ]
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12 then
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13 classSize=$((classSize+1))
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14 fi
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15 done
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16
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17 #Get tool data and tool install directories
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18 tooldir=$1
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19 tooldata=$2
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20 #create temp directory for row and col order and dendro files.
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21 tdir=$tooldata/$(date +%y%m%d%M%S)
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22 mkdir $tdir
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23 #echo "tdir: "$tdir
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24
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25 #Extract parameters for row and column order and dendro files
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26 rowOrderFile=$tdir/ROfile.txt
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27 rowDendroFile=$tdir/RDfile.txt
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28 colOrderFile=$tdir/COfile.txt
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29 colDendroFile=$tdir/CDfile.txt
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30 rowOrderJson='"order_file": "'$rowOrderFile'",'
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31 rowDendroJson='"dendro_file": "'$rowDendroFile'",'
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32 colOrderJson='"order_file": "'$colOrderFile'",'
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33 colDendroJson='"dendro_file": "'$colDendroFile'",'
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34
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35 #BEGIN: Construct JSON for all non-repeating parameters
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36 parmJson='{'
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37 rowConfigJson='"row_configuration": {'
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38 colConfigJson='"col_configuration": {'
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39
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40 ctr=0
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41 for i in "$@"; do
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42 if [ $ctr -gt 1 ]
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43 then
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44 currParm=$(cut -d'|' -f1 <<< $i)
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41
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45 if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "chm_name" ]
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40
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46 then
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47 #Parse pipe-delimited parameter parameter
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48 parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",'
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49 fi
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41
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50 if [ $currParm = "chm_name" ]
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51 then
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52 currVal=$(cut -d'|' -f2 <<< $i)
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53 currEdit=$(echo "$currVal" | sed 's/\//_/g')
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54 parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$currEdit'",'
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55 fi
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40
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56 if [ $currParm = "row_configuration" ]
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57 then
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58 rowOrder=$(cut -d'|' -f3 <<< $i)
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59 rowDistance=$(cut -d'|' -f5 <<< $i)
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60 rowAgglomeration=$(cut -d'|' -f7 <<< $i)
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61 rowCuts=$(cut -d'|' -f9 <<< $i)
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62 rowLabels=$(cut -d'|' -f11 <<< $i)
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63 dataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$rowLabels'"]'
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64 if [ $rowOrder = 'Hierarchical' ]
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65 then
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66 rowConfigJson=$rowConfigJson$rowOrderJson$rowDendroJson
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67 fi
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68 rowConfigJson=$rowConfigJson'"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'",'$dataTypeJson'},'
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69 fi
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70 if [ $currParm = "col_configuration" ]
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71 then
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72 colOrder=$(cut -d'|' -f3 <<< $i)
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73 colDistance=$(cut -d'|' -f5 <<< $i)
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74 colAgglomeration=$(cut -d'|' -f7 <<< $i)
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75 colCuts=$(cut -d'|' -f9 <<< $i)
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76 colLabels=$(cut -d'|' -f11 <<< $i)
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77 dataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$colLabels'"]'
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78 if [ $colOrder = 'Hierarchical' ]
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79 then
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80 colConfigJson=$colConfigJson$colOrderJson$colDendroJson
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81 fi
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82 colConfigJson=$colConfigJson'"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'",'$dataTypeJson'},'
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83 fi
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84 fi
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85 ctr=$((ctr+1))
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86 done
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87 #END: Construct JSON for all non-repeating parameters
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88 #echo "rowCuts: "$rowCuts
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89 #echo "colCuts: "$colCuts
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90 #echo "ROW CONFIG JSON: "$rowConfigJson
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91 #echo "COL CONFIG JSON: "$colConfigJson
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92
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93 #BEGIN: Construct JSON for data layers
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94 matrixJson='"matrix_files": [ '
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95 inputMatrix=''
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96 for i in "$@"; do
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97 currParm=$(cut -d'|' -f1 <<< $i)
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98 if [ $currParm = "matrix_files" ]
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99 then
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100 #Parse pipe-delimited parameter parameter
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101 matrixJson=$matrixJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'"}'
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102 inputMatrix=$(cut -d'|' -f3 <<< $i)
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103 fi
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104 done
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105 matrixJson=$matrixJson"],"
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106 #END: Construct JSON for data layers
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107
|
|
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108 #BEGIN: Construct JSON for classification files
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|
|
109 classJson='"classification_files": [ '
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110 classIter=0
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111 for i in "$@"; do
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112 currParm=$(cut -d'|' -f1 <<< $i)
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113 if [ $currParm = "classification" ]
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114 then
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115 classIter=$((classIter+1))
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|
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116 #Parse pipe-delimited 3-part classification bar parameter
|
|
41
|
117 className=$(cut -d'|' -f3 <<< $i)
|
|
|
118 if [[ -z "$className" ]]; then
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|
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119 className="covar"$classIter
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|
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120 fi
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121 classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$className'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'"'
|
|
40
|
122 classCat=$(cut -d'|' -f7 <<< $i)
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|
|
123 classColorType=$(cut -d'_' -f2 <<< $classCat)
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|
|
124 classJson=$classJson','
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|
|
125 classJson=$classJson' "position":"'$(cut -d'_' -f1 <<< $classCat)'","color_map": {"type":"'$classColorType'"}}'
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|
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126 if [ $classIter -lt $classSize ]
|
|
|
127 then
|
|
|
128 classJson=$classJson','
|
|
|
129 fi
|
|
|
130 fi
|
|
|
131 done
|
|
|
132 classJson=$classJson']'
|
|
|
133 #END: Construct JSON for classification files
|
|
|
134
|
|
42
|
135 #Add build platform JSON for distinction between GenePattern and Galaxy Builders
|
|
|
136 platformJson='"build_platform": "Galaxy",'
|
|
|
137
|
|
|
138 parmJson=$parmJson$matrixJson$rowConfigJson$colConfigJson$platformJson$classJson
|
|
40
|
139 parmJson=$parmJson'}'
|
|
|
140 #echo "HEATMAP PARAMETERS JSON: "$parmJson
|
|
|
141
|
|
|
142 #run R to cluster matrix
|
|
|
143 output="$(R --slave --vanilla --file=$tooldir/CHM.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)"
|
|
|
144 rc=$?;
|
|
|
145 if [ $rc != 0 ]
|
|
|
146 then
|
|
|
147 echo $output;
|
|
|
148 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
|
|
|
149 then
|
|
|
150 echo "";
|
|
41
|
151 echo "R CLUSTERING: Error in clustering the matrix provided (View Details - stdout). "
|
|
|
152 echo "Note: This error can occur when:"
|
|
|
153 echo " 1. There is invalid numeric data in the matrix provided. Try using Matrix Manipulation tools to fix invalid data.";
|
|
|
154 echo " 2. There is no variation in a row or column in the matrix. Try a different distance measure or remove rows/columns without variation using Matrix Manipulation tools.";
|
|
|
155 echo " 3. A covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry.";
|
|
40
|
156 fi
|
|
|
157 exit $rc;
|
|
|
158 fi
|
|
|
159
|
|
|
160 #call java program to generate NGCHM viewer files.
|
|
|
161 java -jar $tooldir/GalaxyMapGen.jar "$parmJson"
|
|
|
162 #clean up tempdir
|
|
|
163 rm -rf $tdir
|
