diff shell-script-template.sh @ 7:c5c297020c36 draft

planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311

--- a/shell-script-template.sh	Wed Apr 25 17:20:11 2018 -0400
+++ b/shell-script-template.sh	Thu Apr 26 12:49:35 2018 -0400
@@ -1,47 +1,48 @@
+# SHELL_SCRIPT file name
+SHELL_SCRIPT='skewer.sh'
+
 # run SHELL_SCRIPT within tool outputs directory
 cd ${REPORT_FILES_PATH}
 
-#--------- index genome --------
-# create genome directory for genome indexes
-mkdir -p ${X_d}/genomeDir
-
+# build job-script.sh
 cat >temp.sh <<EOF
-STAR \\
-  --runMode genomeGenerate \\
-  --genomeDir ${X_d}/genomeDir \\
-  --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\
-  --sjdbGTFfile ${X_B} \\
-  --sjdbOverhang ${X_C} \\
-  > /dev/null 2>&1
+skewer \\
+	${X_A} \\
+	${X_B} \\
+	-x ${X_x} \\ 
+	-y ${X_y} \\
+	-m ${X_m} \\
+	-r ${X_r} \\
+	-d ${X_D} \\
+	-q ${X_q} \\
+	-Q ${X_Q} \\
+	-l ${X_l} \\
+	-j ${X_j} \\
+	-M ${X_M} \\
+	-b ${X_b} \\
+	-c ${X_b} \\
+	-n ${X_n} \\
+	-u ${X_u} \\
+	-f ${X_f} \\
+	-z ${X_z} \\
+	-qiime ${X_E} \\
+	-quiet ${X_F} \\
+	-i ${X_i} \\
+	-o trim > /dev/null 2>&1 
 EOF
 
-grep -v None temp.sh > index-genome.sh
-
-# run star
-sh index-genome.sh
+# remove empty input lines
+grep -v '\-M  \\' temp.sh |\
+  grep -v 'None' |\
+  grep -v 'NO_ARGUMENT_NO' |\
+  sed 's/NO_ARGUMENT_YES//g' > ${SHELL_SCRIPT}
 
-#---- mapping ---------
-cat >temp.sh <<EOF
-STAR \\
-  --genomeDir ${X_d}/genomeDir \\
-  --readFilesIn \\
-  ${X_F} \\
-  ${X_R} \\
-  > /dev/null 2>&1
-EOF
-
-grep -v None temp.sh > mapping.sh
-
-# run mapping
-sh mapping.sh
-
-# remove temp.sh
 rm temp.sh
 
-#----- SAM to sorted BAM ------
-echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
-sh sam2bam.sh
+# run SHELL_SCRIPT
+sh ${SHELL_SCRIPT}
 
-#----- evaluate mapping -------
-echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh
-sh flagstat.sh
+# rename log file
+if [ -e trim-trimmed.log ]; then
+  cp trim-trimmed.log trim-trimmed.txt
+fi
\ No newline at end of file