# HG changeset patch
# User sanbi-uwc
# Date 1485175607 18000
# Node ID 642a39a927c9721669d401b874e4331216cadb1c
# Parent f6cb99d6afd363fe6860a3772dc04d5797c97137
planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
diff -r f6cb99d6afd3 -r 642a39a927c9 README.rst
--- a/README.rst Mon Jan 23 06:31:29 2017 -0500
+++ b/README.rst Mon Jan 23 07:46:47 2017 -0500
@@ -58,6 +58,8 @@
========== ======================================================================
Version Changes
---------- ----------------------------------------------------------------------
+0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version
+ is still supported for now).
0.36.0 - Update to Trimmomatic 0.36.
0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input
diff -r f6cb99d6afd3 -r 642a39a927c9 package_trimmomatic.sh
--- a/package_trimmomatic.sh Mon Jan 23 06:31:29 2017 -0500
+++ b/package_trimmomatic.sh Mon Jan 23 07:46:47 2017 -0500
@@ -11,7 +11,7 @@
tar cvzf $TGZ \
README.rst \
trimmomatic.xml \
- trimmomatic.sh \
+ trimmomatic_macros.xml \
tool_dependencies.xml \
test-data
if [ -f $TGZ ] ; then
diff -r f6cb99d6afd3 -r 642a39a927c9 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Jan 23 06:31:29 2017 -0500
+++ b/tool_dependencies.xml Mon Jan 23 07:46:47 2017 -0500
@@ -4,7 +4,7 @@
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
-
+
trimmomatic-0.36.jar
$INSTALL_DIR
@@ -13,10 +13,10 @@
$INSTALL_DIR/adapters
- $INSTALL_DIR
+ $INSTALL_DIR
- $INSTALL_DIR/adapters
+ $INSTALL_DIR/adapters
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic.sh
--- a/trimmomatic.sh Mon Jan 23 06:31:29 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-#!/bin/sh
-#
-# Shell wrapper to run Trimmomatic jar file as a Galaxy tool
-echo Arguments:
-for i in $@ ; do
- echo "*" $i
-done
-
-if [ -n "$CONDA_PREFIX" ] ; then
- # bioconda installs trimmomatic in a share directory
- # with a jarfile called trimmomatic.jar
- TRIMMOMATIC_DIR="$CONDA_PREFIX/share/trimmomatic"
- JARFILE="trimmomatic.jar"
-else
- JARFILE="trimmomatic-0.36.jar"
-fi
-
-if [ -z "$TRIMMOMATIC_DIR" ] ; then
- echo "TRIMMOMATIC_DIR variable not set, can't find jar file"
- exit 1
-fi
-
-java -mx16G -jar $TRIMMOMATIC_DIR/$JARFILE $@ 2>&1 | tee trimmomatic.log
-status=$?
-echo "Exit status: $status"
-# Check for successful completion
-if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
- echo "Trimmomatic did not finish successfully" >&2
- exit 1
-fi
-exit $status
-##
-#
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic.xml
--- a/trimmomatic.xml Mon Jan 23 06:31:29 2017 -0500
+++ b/trimmomatic.xml Mon Jan 23 07:46:47 2017 -0500
@@ -1,5 +1,8 @@
flexible read trimming tool for Illumina NGS data
+
+ trimmomatic_macros.xml
+
trimmomatic
@@ -17,7 +20,9 @@
#else
ln -s '$fastq_in' fastq_in.'$fastq_in.extension' &&
#end if
- bash '${__tool_directory__}/trimmomatic.sh'
+ @CONDA_TRIMMOMATIC_JAR_PATH@ &&
+ @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&
+ java -mx16G -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
#if $readtype.single_or_paired in ["pair_of_files","collection"]
PE -threads \${GALAXY_SLOTS:-6} -phred33
fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
@@ -28,7 +33,7 @@
#end if
## ILLUMINACLIP option
#if $illuminaclip.do_illuminaclip
- ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
+ ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
#end if
## Other operations
#for $op in $operations
@@ -81,19 +86,19 @@
-
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diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic.xml.orig Mon Jan 23 07:46:47 2017 -0500
@@ -0,0 +1,426 @@
+<<<<<<< HEAD
+
+=======
+
+>>>>>>> upstream/master
+ flexible read trimming tool for Illumina NGS data
+
+ trimmomatic_macros.xml
+
+
+ trimmomatic
+
+<<<<<<< HEAD
+
+
+
+ >>>>>> upstream/master
+ PE -threads \${GALAXY_SLOTS:-6} -phred33
+ fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
+ fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
+ fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
+ #else
+ SE -threads \${GALAXY_SLOTS:-6} -phred33 fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
+ #end if
+ ## ILLUMINACLIP option
+ #if $illuminaclip.do_illuminaclip
+ ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
+ #end if
+ ## Other operations
+ #for $op in $operations
+ ## SLIDINGWINDOW
+ #if str( $op.operation.name ) == "SLIDINGWINDOW"
+ SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality
+ #end if
+ ## MINLEN:36
+ #if str( $op.operation.name ) == "MINLEN"
+ MINLEN:$op.operation.minlen
+ #end if
+ #if str( $op.operation.name ) == "LEADING"
+ LEADING:$op.operation.leading
+ #end if
+ #if str( $op.operation.name ) == "TRAILING"
+ TRAILING:$op.operation.trailing
+ #end if
+ #if str( $op.operation.name ) == "CROP"
+ CROP:$op.operation.crop
+ #end if
+ #if str( $op.operation.name ) == "HEADCROP"
+ HEADCROP:$op.operation.headcrop
+ #end if
+ #if str( $op.operation.name ) == "AVGQUAL"
+ AVGQUAL:$op.operation.avgqual
+ #end if
+ #if str( $op.operation.name ) == "MAXINFO"
+ MAXINFO:$op.operation.target_length:$op.operation.strictness
+ #end if
+ #end for
+<<<<<<< HEAD
+ &&
+ #if $readtype.single_or_paired == "pair_of_files"
+ mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
+ mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
+ mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
+ mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
+ #elif $readtype.single_or_paired == "collection"
+ mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
+ mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
+ mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
+ mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
+ #else
+ mv fastq_out.'$fastq_in.extension' '${fastq_out}'
+ #end if
+=======
+ 2>&1 | tee trimmomatic.log &&
+ if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
+>>>>>>> upstream/master
+ ]]>
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+ readtype['single_or_paired'] == "pair_of_files"
+
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+ readtype['single_or_paired'] == "pair_of_files"
+
+
+ readtype['single_or_paired'] == "pair_of_files"
+
+
+ readtype['single_or_paired'] == "pair_of_files"
+
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+ readtype['single_or_paired'] == 'se'
+
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+ readtype['single_or_paired'] == "collection"
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+ readtype['single_or_paired'] == "collection"
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+ 10.1093/bioinformatics/btu170
+
+
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic_BACKUP_16831.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_BACKUP_16831.sh Mon Jan 23 07:46:47 2017 -0500
@@ -0,0 +1,33 @@
+#!/bin/sh
+#
+# Shell wrapper to run Trimmomatic jar file as a Galaxy tool
+echo Arguments:
+for i in $@ ; do
+ echo "*" $i
+done
+
+if [ -n "$CONDA_PREFIX" ] ; then
+ # bioconda installs trimmomatic in a share directory
+ # with a jarfile called trimmomatic.jar
+ TRIMMOMATIC_DIR="$CONDA_PREFIX/share/trimmomatic"
+ JARFILE="trimmomatic.jar"
+else
+ JARFILE="trimmomatic-0.36.jar"
+fi
+
+if [ -z "$TRIMMOMATIC_DIR" ] ; then
+ echo "TRIMMOMATIC_DIR variable not set, can't find jar file"
+ exit 1
+fi
+
+java -mx16G -jar $TRIMMOMATIC_DIR/$JARFILE $@ 2>&1 | tee trimmomatic.log
+status=$?
+echo "Exit status: $status"
+# Check for successful completion
+if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
+ echo "Trimmomatic did not finish successfully" >&2
+ exit 1
+fi
+exit $status
+##
+#
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic_BACKUP_16925.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_BACKUP_16925.sh Mon Jan 23 07:46:47 2017 -0500
@@ -0,0 +1,33 @@
+#!/bin/sh
+#
+# Shell wrapper to run Trimmomatic jar file as a Galaxy tool
+echo Arguments:
+for i in $@ ; do
+ echo "*" $i
+done
+
+if [ -n "$CONDA_PREFIX" ] ; then
+ # bioconda installs trimmomatic in a share directory
+ # with a jarfile called trimmomatic.jar
+ TRIMMOMATIC_DIR="$CONDA_PREFIX/share/trimmomatic"
+ JARFILE="trimmomatic.jar"
+else
+ JARFILE="trimmomatic-0.36.jar"
+fi
+
+if [ -z "$TRIMMOMATIC_DIR" ] ; then
+ echo "TRIMMOMATIC_DIR variable not set, can't find jar file"
+ exit 1
+fi
+
+java -mx16G -jar $TRIMMOMATIC_DIR/$JARFILE $@ 2>&1 | tee trimmomatic.log
+status=$?
+echo "Exit status: $status"
+# Check for successful completion
+if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
+ echo "Trimmomatic did not finish successfully" >&2
+ exit 1
+fi
+exit $status
+##
+#
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic_BASE_16831.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_BASE_16831.sh Mon Jan 23 07:46:47 2017 -0500
@@ -0,0 +1,18 @@
+#!/bin/sh
+#
+# Shell wrapper to run Trimmomatic jar file as a Galaxy tool
+echo Arguments:
+for i in $@ ; do
+ echo "*" $i
+done
+java $@ 2>&1 | tee trimmomatic.log
+status=$?
+echo "Exit status: $status"
+# Check for successful completion
+if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
+ echo "Trimmomatic did not finish successfully" >&2
+ exit 1
+fi
+exit $status
+##
+#
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic_BASE_16925.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_BASE_16925.sh Mon Jan 23 07:46:47 2017 -0500
@@ -0,0 +1,18 @@
+#!/bin/sh
+#
+# Shell wrapper to run Trimmomatic jar file as a Galaxy tool
+echo Arguments:
+for i in $@ ; do
+ echo "*" $i
+done
+java $@ 2>&1 | tee trimmomatic.log
+status=$?
+echo "Exit status: $status"
+# Check for successful completion
+if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
+ echo "Trimmomatic did not finish successfully" >&2
+ exit 1
+fi
+exit $status
+##
+#
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic_LOCAL_16831.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_LOCAL_16831.sh Mon Jan 23 07:46:47 2017 -0500
@@ -0,0 +1,33 @@
+#!/bin/sh
+#
+# Shell wrapper to run Trimmomatic jar file as a Galaxy tool
+echo Arguments:
+for i in $@ ; do
+ echo "*" $i
+done
+
+if [ -n "$CONDA_PREFIX" ] ; then
+ # bioconda installs trimmomatic in a share directory
+ # with a jarfile called trimmomatic.jar
+ TRIMMOMATIC_DIR="$CONDA_PREFIX/share/trimmomatic"
+ JARFILE="trimmomatic.jar"
+else
+ JARFILE="trimmomatic-0.36.jar"
+fi
+
+if [ -z "$TRIMMOMATIC_DIR" ] ; then
+ echo "TRIMMOMATIC_DIR variable not set, can't find jar file"
+ exit 1
+fi
+
+java -mx16G -jar $TRIMMOMATIC_DIR/$JARFILE $@ 2>&1 | tee trimmomatic.log
+status=$?
+echo "Exit status: $status"
+# Check for successful completion
+if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
+ echo "Trimmomatic did not finish successfully" >&2
+ exit 1
+fi
+exit $status
+##
+#
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic_LOCAL_16925.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_LOCAL_16925.sh Mon Jan 23 07:46:47 2017 -0500
@@ -0,0 +1,33 @@
+#!/bin/sh
+#
+# Shell wrapper to run Trimmomatic jar file as a Galaxy tool
+echo Arguments:
+for i in $@ ; do
+ echo "*" $i
+done
+
+if [ -n "$CONDA_PREFIX" ] ; then
+ # bioconda installs trimmomatic in a share directory
+ # with a jarfile called trimmomatic.jar
+ TRIMMOMATIC_DIR="$CONDA_PREFIX/share/trimmomatic"
+ JARFILE="trimmomatic.jar"
+else
+ JARFILE="trimmomatic-0.36.jar"
+fi
+
+if [ -z "$TRIMMOMATIC_DIR" ] ; then
+ echo "TRIMMOMATIC_DIR variable not set, can't find jar file"
+ exit 1
+fi
+
+java -mx16G -jar $TRIMMOMATIC_DIR/$JARFILE $@ 2>&1 | tee trimmomatic.log
+status=$?
+echo "Exit status: $status"
+# Check for successful completion
+if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
+ echo "Trimmomatic did not finish successfully" >&2
+ exit 1
+fi
+exit $status
+##
+#
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic_REMOTE_16831.sh
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic_REMOTE_16925.sh
diff -r f6cb99d6afd3 -r 642a39a927c9 trimmomatic_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_macros.xml Mon Jan 23 07:46:47 2017 -0500
@@ -0,0 +1,8 @@
+
+
+ if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi
+ if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi
+