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1 #!/bin/bash
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2 tool_directory=$1
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3 galaxy_tabular_file=$2
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4 galaxy_replication_vector_column_index=$3
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5 galaxy_genotype_vector_column_index=$4
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6 galaxy_first_y_vector_column_index=$5
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7 galaxy_last_y_vector_column_index=$6
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8 galaxy_design=$7
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9 galaxy_summarize_by=$8
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10 galaxy_summarize_by_vector_column_index=$9
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11 galaxy_group_variable_1=${10}
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12 galaxy_group_variable_1_vector_column_index=${11}
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13 galaxy_group_variable_2=${12}
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14 galaxy_group_variable_2_vector_column_index=${13}
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15 galaxy_output_file_path=${14}
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16 block_vector_column_index=${15}
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17
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18 directory=`dirname $0`
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19 mkdir tmpdir$$
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20
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21
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22 counter=$galaxy_first_y_vector_column_index
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23
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24 previous="tmpdir$$/output"
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25 echo '' >$previous
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26 while [ $counter -le $galaxy_last_y_vector_column_index ]
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27 do
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28 Rscript --vanilla $directory/blupcal_wrapper.R --tool_directory $tool_directory --tabular_file $galaxy_tabular_file --replication_vector_column_index $galaxy_replication_vector_column_index --genotype_vector_column_index $galaxy_genotype_vector_column_index --y_vector_column_index $counter --design $galaxy_design --summarize_by $galaxy_summarize_by --summarize_by_vector_column_index $galaxy_summarize_by_vector_column_index --group_variable_1 $galaxy_group_variable_1 --group_variable_1_vector_column_index $galaxy_group_variable_1_vector_column_index --group_variable_2 $galaxy_group_variable_2 --group_variable_2_vector_column_index $galaxy_group_variable_2_vector_column_index --output_file_path tmpdir$$/output.$counter --block_vector_column_index $block_vector_column_index
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29 #cat tmpdir$$/output.$counter >>$galaxy_output_file_path
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30 if [ "$counter" -gt "$galaxy_first_y_vector_column_index" ];then
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31 if [[ "$galaxy_summarize_by" == "true" ]];then
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32 cut -f 3-7 tmpdir$$/output.$counter >>tmpdir$$/output.$counter.cut
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33 fi
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34 if [[ "$galaxy_summarize_by" == "false" ]];then
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35 cut -f 2-6 tmpdir$$/output.$counter >>tmpdir$$/output.$counter.cut
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36 fi
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37 mv tmpdir$$/output.$counter.cut tmpdir$$/output.$counter
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38 fi
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39 if [ "$counter" -gt "$galaxy_first_y_vector_column_index" ];then
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40 paste $previous tmpdir$$/output.$counter >>tmpdir$$/output.$counter.$counter
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41 fi
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42 if [ "$counter" -eq "$galaxy_first_y_vector_column_index" ];then
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43 cp tmpdir$$/output.$counter tmpdir$$/output.$counter.$counter
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44 fi
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45 previous="tmpdir$$/output.$counter.$counter"
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46 cp -rf tmpdir$$/output.$counter.$counter $galaxy_output_file_path
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47 #paste $galaxy_output_file_path tmpdir$$/output.$counter >>$galaxy_output_file_path
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48 #cut -f 3-7 tmpdir$$/output.$counter >tmpdir$$/output.$counter.cut
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49 ((counter++))
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50 done
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51
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52
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53 echo $galaxy_summarize_by
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54
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55
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56
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