diff shell-script-template.sh @ 7:3f92c10de274 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shell-script-template.sh	Mon Apr 30 10:15:54 2018 -0400
@@ -0,0 +1,36 @@
+# SHELL_SCRIPT file name
+SHELL_SCRIPT='fastqc.sh'
+
+# run SHELL_SCRIPT within tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+# build job-script.sh
+cat >temp.sh <<EOF
+
+cp ${X_r} read_1.fq
+cp ${X_R} read_2.fq
+
+fastqc \\
+  -q \\
+  -c ${X_c} \\
+  -l ${X_l} \\
+  ${X_d}/read_1.fq > /dev/null 2>&1
+  
+fastqc \\
+  -q \\
+  -c ${X_c} \\
+  -l ${X_l} \\
+  ${X_d}/read_2.fq > /dev/null 2>&1
+
+EOF
+
+grep -v None temp.sh > ${SHELL_SCRIPT}
+rm temp.sh
+
+# run SHELL_SCRIPT
+sh ${SHELL_SCRIPT}
+
+
+# unzip outputs
+unzip -q read_1_fastqc.zip
+unzip -q read_2_fastqc.zip
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