Mercurial > repos > dereeper > blup_calculator
comparison blupcal.sh @ 0:45d215f2be74 draft
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author | dereeper |
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date | Sat, 29 Dec 2018 18:44:05 -0500 |
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-1:000000000000 | 0:45d215f2be74 |
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1 #!/bin/bash | |
2 tool_directory=$1 | |
3 galaxy_tabular_file=$2 | |
4 galaxy_replication_vector_column_index=$3 | |
5 galaxy_genotype_vector_column_index=$4 | |
6 galaxy_first_y_vector_column_index=$5 | |
7 galaxy_last_y_vector_column_index=$6 | |
8 galaxy_design=$7 | |
9 galaxy_summarize_by=$8 | |
10 galaxy_summarize_by_vector_column_index=$9 | |
11 galaxy_group_variable_1=${10} | |
12 galaxy_group_variable_1_vector_column_index=${11} | |
13 galaxy_group_variable_2=${12} | |
14 galaxy_group_variable_2_vector_column_index=${13} | |
15 galaxy_output_file_path=${14} | |
16 block_vector_column_index=${15} | |
17 | |
18 directory=`dirname $0` | |
19 mkdir tmpdir$$ | |
20 | |
21 | |
22 counter=$galaxy_first_y_vector_column_index | |
23 | |
24 previous="tmpdir$$/output" | |
25 echo '' >$previous | |
26 while [ $counter -le $galaxy_last_y_vector_column_index ] | |
27 do | |
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$$/output.$counter --block_vector_column_index $block_vector_column_index | |
29 #cat tmpdir$$/output.$counter >>$galaxy_output_file_path | |
30 if [ "$counter" -gt "$galaxy_first_y_vector_column_index" ];then | |
31 if [[ "$galaxy_summarize_by" == "true" ]];then | |
32 cut -f 3-7 tmpdir$$/output.$counter >>tmpdir$$/output.$counter.cut | |
33 fi | |
34 if [[ "$galaxy_summarize_by" == "false" ]];then | |
35 cut -f 2-6 tmpdir$$/output.$counter >>tmpdir$$/output.$counter.cut | |
36 fi | |
37 mv tmpdir$$/output.$counter.cut tmpdir$$/output.$counter | |
38 fi | |
39 if [ "$counter" -gt "$galaxy_first_y_vector_column_index" ];then | |
40 paste $previous tmpdir$$/output.$counter >>tmpdir$$/output.$counter.$counter | |
41 fi | |
42 if [ "$counter" -eq "$galaxy_first_y_vector_column_index" ];then | |
43 cp tmpdir$$/output.$counter tmpdir$$/output.$counter.$counter | |
44 fi | |
45 previous="tmpdir$$/output.$counter.$counter" | |
46 cp -rf tmpdir$$/output.$counter.$counter $galaxy_output_file_path | |
47 #paste $galaxy_output_file_path tmpdir$$/output.$counter >>$galaxy_output_file_path | |
48 #cut -f 3-7 tmpdir$$/output.$counter >tmpdir$$/output.$counter.cut | |
49 ((counter++)) | |
50 done | |
51 | |
52 | |
53 echo $galaxy_summarize_by | |
54 | |
55 | |
56 |