diff blupcal.sh @ 0:45d215f2be74 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blupcal.sh	Sat Dec 29 18:44:05 2018 -0500
@@ -0,0 +1,56 @@
+#!/bin/bash
+tool_directory=$1
+galaxy_tabular_file=$2
+galaxy_replication_vector_column_index=$3
+galaxy_genotype_vector_column_index=$4
+galaxy_first_y_vector_column_index=$5
+galaxy_last_y_vector_column_index=$6
+galaxy_design=$7
+galaxy_summarize_by=$8
+galaxy_summarize_by_vector_column_index=$9
+galaxy_group_variable_1=${10}
+galaxy_group_variable_1_vector_column_index=${11}
+galaxy_group_variable_2=${12}
+galaxy_group_variable_2_vector_column_index=${13}
+galaxy_output_file_path=${14}
+block_vector_column_index=${15}
+
+directory=`dirname $0`
+mkdir tmpdir$$
+
+
+counter=$galaxy_first_y_vector_column_index
+
+previous="tmpdir$$/output"
+echo '' >$previous
+while [ $counter -le $galaxy_last_y_vector_column_index ]
+do
+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$$/output.$counter --block_vector_column_index $block_vector_column_index
+#cat tmpdir$$/output.$counter >>$galaxy_output_file_path
+if [ "$counter" -gt "$galaxy_first_y_vector_column_index" ];then
+if [[ "$galaxy_summarize_by" == "true" ]];then 
+cut -f 3-7 tmpdir$$/output.$counter >>tmpdir$$/output.$counter.cut
+fi
+if [[ "$galaxy_summarize_by" == "false" ]];then
+cut -f 2-6 tmpdir$$/output.$counter >>tmpdir$$/output.$counter.cut
+fi
+mv tmpdir$$/output.$counter.cut tmpdir$$/output.$counter
+fi
+if [ "$counter" -gt "$galaxy_first_y_vector_column_index" ];then
+paste $previous tmpdir$$/output.$counter >>tmpdir$$/output.$counter.$counter
+fi
+if [ "$counter" -eq "$galaxy_first_y_vector_column_index" ];then
+cp tmpdir$$/output.$counter tmpdir$$/output.$counter.$counter
+fi
+previous="tmpdir$$/output.$counter.$counter"
+cp -rf tmpdir$$/output.$counter.$counter $galaxy_output_file_path
+#paste $galaxy_output_file_path tmpdir$$/output.$counter >>$galaxy_output_file_path
+#cut -f 3-7 tmpdir$$/output.$counter >tmpdir$$/output.$counter.cut
+((counter++))
+done
+
+
+echo $galaxy_summarize_by
+
+
+